# HG changeset patch
# User galaxyp
# Date 1610719587 0
# Node ID bb0130ff73cef6d27cfbd835e9514c0a9a48673c
# Parent  7fdd9119cc4ffd64baa21ec9793250bd29ffd6df
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"

diff -r 7fdd9119cc4f -r bb0130ff73ce README.rst
--- a/README.rst	Thu Feb 20 05:51:38 2020 -0500
+++ b/README.rst	Fri Jan 15 14:06:27 2021 +0000
@@ -3,7 +3,7 @@
 
 - Home: <https://github.com/galaxyproteomics/tools-galaxyp/>
 - Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/peptideshaker>
-- Tool ID: `peptideshaker`, `search_gui`
+- Tools ID: `peptide_shaker`, `search_gui`, `ident_params`, `fasta_cli`
 
 
 Description
@@ -11,13 +11,23 @@
 
 Perform protein identification combining numerous search engines (using SearchGUI) followed by peptide and protein inference with PeptideShaker.
 
-Includes tool wrappers for SearchGUI and PeptideShaker. The SearchGUI tool takes any number of mgf files and performs searches on these.  It creates a large zip archive with all search results, the original database and spectra.  This can then be fed to the PeptideShaker tool which merges the results and performs peptide and protein inference.
+Includes tool wrappers for FastaCLI, IdentificationParametersCLI, SearchGUI and PeptideShaker.
+
+
+
+FastaCLI adds decoy sequences to any fasta file.
+
+The Identification Parameters tool allows to create a parameters (par) file which can be (re)used later to parameterize SearchGUI or PeptideShaker.
+
+The SearchGUI tool takes any number of mgf files and performs searches on these. It creates a large zip archive with all search results, the original database and spectra.
+
+This can then be fed to the PeptideShaker tool which merges the results and performs peptide and protein inference.
 
 
 General Requirements
 --------------------
 
-This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell:
+To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell:
 
     export _JAVA_OPTIONS='-Xmx1500M'
 
@@ -31,34 +41,23 @@
 -----------------
 
 Running MS Amanda on Linux requires that you have Mono installed. Mono 3.2.1 or newer is required.  If you install via the toolshed Mono should be installed automatically, however if this does not work you can install it manually.
-  
+
 On ubuntu Mono can be installed as follows
 
 	sudo apt-get install mono-runtime
 	sudo apt-get install libmono-system-core4.0-cil
 
-For more help on installing Mono please see http://www.mono-project.com/download. 
+For more help on installing Mono please see http://www.mono-project.com/download.
 
 Note
 ----
 
-- Requires Galaxy release v15.10 or later, which fixes the installation of package_peptideshaker_1_1 and provides a searchgui_archive datatype that includes a version
-
-- PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server.
+- Requires Galaxy release v16.01 or later.
 
 See:
 
-* <https://code.google.com/p/peptide-shaker/>
-* <https://code.google.com/p/searchgui/>
-
-
-Search GUI - Fixed and Variable Modifications
--------------------------------------------
-
- - Options for modifications are read from local data file: searchgui_mods.loc
-   This is copied from searchgui_mods.loc.sample on the first installation.  
-
-The modifications are from:  https://github.com/compomics/compomics-utilities/blob/master/src/main/java/com/compomics/util/experiment/identification/search_parameters_cli/IdentificationParametersInputBean.java
+* <http://compomics.github.io/projects/peptide-shaker.html/>
+* <http://compomics.github.io/projects/searchgui.html/>
 
 GalaxyP Community
 -----------------
@@ -101,3 +100,4 @@
 * Gerben Menschaert
 * Elvis Ndah
 * Minnesota Supercomputing Institute, Univeristy of Minnesota
+* Carlos Horro
diff -r 7fdd9119cc4f -r bb0130ff73ce admin_scripts/build_mods_loc.py
--- a/admin_scripts/build_mods_loc.py	Thu Feb 20 05:51:38 2020 -0500
+++ b/admin_scripts/build_mods_loc.py	Fri Jan 15 14:06:27 2021 +0000
@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
 import xml.etree.ElementTree as ET
-from os.path import exists
 
 with open("searchgui_mods.loc.sample", "w") as output:
     for mods_path in ["searchGUI_mods.xml", "searchGUI_usermods.xml"]:
diff -r 7fdd9119cc4f -r bb0130ff73ce admin_scripts/build_species.py
--- a/admin_scripts/build_species.py	Thu Feb 20 05:51:38 2020 -0500
+++ b/admin_scripts/build_species.py	Fri Jan 15 14:06:27 2021 +0000
@@ -2,9 +2,9 @@
 
 import sys
 
-for line in open( sys.argv[1] ):
+for line in open(sys.argv[1]):
     line = line.strip()
     if line and not line.startswith('>'):
         name, id = line.split('\t')
         line = '<option value="%s">%s</option>' % (name, name)
-    print line
+    print(line)
diff -r 7fdd9119cc4f -r bb0130ff73ce fasta_cli.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_cli.xml	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,75 @@
+<tool id="fasta_cli" name="FastaCLI" version="1.0.1">
+    <description>
+        Appends decoy sequences to FASTA files
+    </description>
+    <macros>
+        <import>macros_basic.xml</import>
+    </macros>
+    <requirements>
+	<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
+    </requirements>
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        #set $temp_stderr = "fasta_cli_stderr"
+        #set $output_db_name = $input_database.display_name.replace(".fasta", "") + $database_processing_options.decoy_file_tag.value + ".fasta"
+
+        mkdir output &&
+        cwd=`pwd` &&
+
+        echo 'DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}' &&
+        cp '${input_database}' '${input_database.display_name}' &&
+
+        ###########################################
+        ####       Creating decoy database     ####
+        ###########################################
+
+        echo 'Creating decoy database.' &&
+        searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="./bin/" -temp_folder `pwd` -in '${input_database.display_name}' -decoy -decoy_flag $database_processing_options.decoy_tag -suffix $database_processing_options.decoy_type -decoy_suffix $database_processing_options.decoy_file_tag 2>> $temp_stderr &&
+        mv '${output_db_name}' output &&
+        cat $temp_stderr 2>&1;
+]]>
+    </command>
+    <inputs>
+        <param format="fasta" name="input_database" type="data" label="Protein Database"
+            help="Select FASTA database from history"/>
+
+        <section name="database_processing_options" expanded="true" title="Database Processing Options">
+
+            <param name="decoy_tag" type="text" value="-REVERSED" label="The decoy flag">
+            </param>
+            <param name="decoy_type" type="select" label="Location of the decoy flag: prefix or suffix">
+                <option value="1">Prefix</option>
+                <option value="2" selected="True">Suffix</option>
+            </param>
+
+            <param name="decoy_file_tag" type="text" value="_concatenated_target_decoy" label="Target decoy suffix">
+            </param>
+
+        </section>
+    </inputs>
+    <outputs>
+        <data name="input_database_concatenated_target_decoy" format="fasta" label="${tool.name}: ${input_database.display_name} with decoys on ${on_string}">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta" directory="output" visible="true"  format="fasta" assign_primary_output="true" />
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_database" value="fastacli_searchgui_tinydb1.fasta" ftype="fasta"/>
+            <output name="input_database_concatenated_target_decoy" file="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" compare="sim_size" delta="1000" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Appends decoy sequences to FASTA files. Default format is adequated to be used by SearchGUI and PeptideShaker tools, ie:
+
+* Decoy flag: -REVERSED
+
+* Location: suffix
+
+* Target decoy suffix: _concatenated_target_decoy
+
+    </help>
+    <expand macro="citations" />
+</tool>
diff -r 7fdd9119cc4f -r bb0130ff73ce ident_params.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ident_params.xml	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,1904 @@
+<tool id="ident_params" name="Identification Parameters" version="1.5.1">
+    <description>
+        Sets the identification parameters to be used in SearchGUI and PeptideShaker apps
+    </description>
+    <macros>
+        <import>macros_basic.xml</import>
+        <import>macros_modifications.xml</import>
+    </macros>
+    <requirements>
+      	<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
+    </requirements>
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        #set $temp_stderr = "searchgui_stderr"
+        #set $bin_dir = "bin"
+
+        mkdir output;
+        cwd=`pwd`;
+        export HOME=\$cwd;
+
+
+        echo "" > $temp_stderr &&
+
+        echo 'running Identification Parameters CLI' &&
+        #####################################################
+        ## generate IdentificationParameters for SearchGUI ##
+        #####################################################
+        (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
+            --exec_dir="./bin/"
+            -out './IdentificationParametersOutput.par'
+
+            ## SPECTRUM MATCHING PARAMETERS
+
+            -frag_tol '${spectrum_matching_options.fragment_tol}'
+            -frag_ppm '${spectrum_matching_options.fragment_tol_units}'
+            -prec_tol '${spectrum_matching_options.precursor_ion_tol}'
+            -prec_ppm '${spectrum_matching_options.precursor_ion_tol_units}'
+
+            #if $spectrum_matching_options.digestion.cleavage == 'default':
+              -mc $spectrum_matching_options.digestion.missed_cleavages
+            #elif $spectrum_matching_options.digestion.cleavage == '0' and len($spectrum_matching_options.digestion.digests) > 0:
+              #set $enzymes = []
+              #set $missed_cleavages = []
+              #set $specificities = []
+              #for $i, $digest in enumerate($spectrum_matching_options.digestion.digests):
+                  #silent $enzymes.append(str($digest.enzyme))
+                  #silent $missed_cleavages.append(str($digest.missed_cleavages))
+                  #silent $specificities.append(str($digest.specificity))
+              #end for
+              -enzyme "#echo ','.join($enzymes)#"
+              -mc "#echo ','.join($missed_cleavages)#"
+              -specificity "#echo ','.join($specificities)#"
+            #else:
+               -digestion $spectrum_matching_options.digestion.cleavage
+            #end if
+
+
+            #set $fixed_mods_str = $spectrum_matching_options.fixed_modifications or ''
+            #set $variable_mods_str = $spectrum_matching_options.variable_modifications or ''
+            #if $fixed_mods_str
+                -fixed_mods "$fixed_mods_str"
+            #end if
+            #if $variable_mods_str
+                -variable_mods "$variable_mods_str"
+            #end if
+
+
+            -min_charge $spectrum_matching_options.min_charge
+            -max_charge $spectrum_matching_options.max_charge
+            -fi $spectrum_matching_options.forward_ion
+            -ri $spectrum_matching_options.reverse_ion
+            -min_isotope ${spectrum_matching_options.min_isotope}
+            -max_isotope ${spectrum_matching_options.max_isotope}
+            ## TODO: TO CHECK, these last two both are also present in the app in the import filters section.
+
+
+            ## -- SEARCH ENGINES SPECIFIC PARAMETERS --
+
+            ## XTANDEM ADVANCED SETTINGS
+
+            #if $searchengines_options.xtandem.xtandem_advanced == "yes"
+
+                ## Spectrum import
+                #if $searchengines_options.xtandem.xtandem_spectrum.xtandem_spectrum_selector == "yes"
+                    -xtandem_dynamic_range ${searchengines_options.xtandem.xtandem_spectrum.xtandem_dynamic_range}
+                    -xtandem_npeaks ${searchengines_options.xtandem.xtandem_spectrum.xtandem_npeaks}
+                    -xtandem_min_frag_mz ${searchengines_options.xtandem.xtandem_spectrum.xtandem_min_frag_mz}
+                    -xtandem_min_peaks ${searchengines_options.xtandem.xtandem_spectrum.xtandem_min_peaks}
+                    -xtandem_noise_suppr ${searchengines_options.xtandem.xtandem_spectrum.xtandem_noise_suppr}
+                    -xtandem_min_prec_mass ${searchengines_options.xtandem.xtandem_spectrum.xtandem_min_prec_mass}
+                    -xtandem_parent_isotope_correction ${searchengines_options.xtandem.xtandem_spectrum.xtandem_parent_isotope_correction}
+                #end if
+
+                ## Advanced search
+                #if $searchengines_options.xtandem.xtandem_asearch.xtandem_asearch_selector == "yes"
+                    -xtandem_quick_acetyl ${searchengines_options.xtandem.xtandem_asearch.xtandem_quick_acetyl}
+                    -xtandem_quick_pyro ${searchengines_options.xtandem.xtandem_asearch.xtandem_quick_pyro}
+                    -xtandem_stp_bias ${searchengines_options.xtandem.xtandem_asearch.xtandem_stp_bias}
+                    -xtandem_ptm_complexity ${searchengines_options.xtandem.xtandem_asearch.xtandem_ptm_complexity}
+                #end if
+
+                ## Output
+                #if $searchengines_options.xtandem.xtandem_output.xtandem_output_selector == "yes"
+                    -xtandem_output_results $searchengines_options.xtandem.xtandem_output.xtandem_output_results_conditional.xtandem_output_results_selector
+                    #if $searchengines_options.xtandem.xtandem_output.xtandem_output_results_conditional.xtandem_output_results_selector != "all"
+                      -xtandem_evalue ${searchengines_options.xtandem.xtandem_output.xtandem_output_results_conditional.xtandem_evalue}
+                    #end if
+                    -xtandem_output_proteins ${searchengines_options.xtandem.xtandem_output.xtandem_output_proteins}
+                    -xtandem_output_sequences ${searchengines_options.xtandem.xtandem_output.xtandem_output_sequences}
+                    -xtandem_output_spectra ${searchengines_options.xtandem.xtandem_output.xtandem_output_spectra}
+                    -xtandem_output_histograms ${searchengines_options.xtandem.xtandem_output.xtandem_output_histograms}
+                    ## TODO: Integration with Skyline not ready yet: -xtandem_skyline_path ${searchengines_options.xtandem.xtandem_output.xtandem_skyline_path}
+                #end if
+
+                ## Refinement
+                #if $searchengines_options.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
+                    -xtandem_refine 1
+                    -xtandem_refine_evalue ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_evalue}
+                    -xtandem_refine_unc ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_unc}
+                    -xtandem_refine_semi ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_semi}
+                    -xtandem_refine_pot ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_pot}
+                    -xtandem_refine_p_mut ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_p_mut}
+                    -xtandem_refine_snaps ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_snaps}
+                    -xtandem_refine_spec_synt ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_spec_synt}
+                #else
+                    -xtandem_refine 0
+                #end if
+            #else
+                -xtandem_output_spectra 1
+            #end if
+
+            ## MYRIMATCH ADVANCED SETTINGS
+
+            #if $searchengines_options.myrimatch.myrimatch_advanced == "yes"
+                -myrimatch_min_pep_length ${searchengines_options.myrimatch.myrimatch_min_pep_length}
+                -myrimatch_max_pep_length ${searchengines_options.myrimatch.myrimatch_max_pep_length}
+                -myrimatch_min_prec_mass ${searchengines_options.myrimatch.myrimatch_min_prec_mass}
+                -myrimatch_max_prec_mass ${searchengines_options.myrimatch.myrimatch_max_prec_mass}
+                -myrimatch_num_matches ${searchengines_options.myrimatch.myrimatch_num_matches}
+                -myrimatch_num_ptms ${searchengines_options.myrimatch.myrimatch_num_ptms}
+                -myrimatch_fragmentation ${searchengines_options.myrimatch.myrimatch_fragmentation}
+                -myrimatch_termini ${searchengines_options.myrimatch.myrimatch_termini}
+                -myrimatch_plus_three ${searchengines_options.myrimatch.myrimatch_plus_three}
+                -myrimatch_xcorr ${searchengines_options.myrimatch.myrimatch_xcorr}
+                -myrimatch_tic_cutoff ${searchengines_options.myrimatch.myrimatch_tic_cutoff}
+                -myrimatch_intensity_classes ${searchengines_options.myrimatch.myrimatch_intensity_classes}
+                -myrimatch_class_multiplier ${searchengines_options.myrimatch.myrimatch_class_multiplier}
+                -myrimatch_num_batches ${searchengines_options.myrimatch.myrimatch_num_batches}
+                -myrimatch_max_peak ${searchengines_options.myrimatch.myrimatch_max_peak}
+                -myrimatch_output ${searchengines_options.myrimatch.myrimatch_output}
+            #else
+                -myrimatch_output mzIdentML
+            #end if
+
+
+            ## MSGF+ ADVANCED SETTINGS
+
+            #if $searchengines_options.msgf.msgf_advanced == "yes"
+                -msgf_decoy ${searchengines_options.msgf.msgf_decoy}
+                -msgf_instrument ${searchengines_options.msgf.msgf_instrument}
+                -msgf_fragmentation ${searchengines_options.msgf.msgf_fragmentation}
+                -msgf_protocol ${searchengines_options.msgf.msgf_protocol}
+                -msgf_termini ${searchengines_options.msgf.msgf_termini}
+                -msgf_min_pep_length ${searchengines_options.msgf.msgf_min_pep_length}
+                -msgf_max_pep_length ${searchengines_options.msgf.msgf_max_pep_length}
+                -msgf_num_ptms ${searchengines_options.msgf.msgf_num_ptms}
+                -msgf_num_matches ${searchengines_options.msgf.msgf_num_matches}
+                -msgf_additional ${searchengines_options.msgf.msgf_additional}
+                #if $searchengines_options.msgf.msgf_tasks.msgf_tasks_custom == "yes"
+                -msgf_num_tasks ${searchengines_options.msgf.msgf_tasks.msgf_num_tasks}
+                #end if
+            #end if
+
+
+            ## MSAMANDA ADVANCED SETTINGS
+
+            #if $searchengines_options.ms_amanda.ms_amanda_advanced == "yes"
+                 -ms_amanda_decoy ${searchengines_options.ms_amanda.ms_amanda_decoy}
+                 -ms_amanda_instrument "${searchengines_options.ms_amanda.ms_amanda_instrument}"
+                 -ms_amanda_max_rank ${searchengines_options.ms_amanda.ms_amanda_max_rank}
+                 -ms_amanda_mono ${searchengines_options.ms_amanda.ms_amanda_mono}
+            #end if
+
+
+            ## ANDROMEDA ADVANCED SETTINGS
+
+            #* Not working in tests
+            #if $searchengines_options.andromeda.andromeda_advanced == "yes"
+                -andromeda_max_pep_mass ${searchengines_options.andromeda.andromeda_max_pep_mass}
+                -andromeda_max_comb ${searchengines_options.andromeda.andromeda_max_comb}
+                -andromeda_top_peaks ${searchengines_options.andromeda.andromeda_top_peaks}
+                -andromeda_top_peaks_window ${searchengines_options.andromeda.andromeda_top_peaks_window}
+                -andromeda_incl_water ${searchengines_options.andromeda.andromeda_incl_water}
+                -andromeda_incl_ammonia ${searchengines_options.andromeda.andromeda_incl_ammonia}
+                -andromeda_neutral_losses ${searchengines_options.andromeda.andromeda_neutral_losses}
+                -andromeda_fragment_all ${searchengines_options.andromeda.andromeda_fragment_all}
+                -andromeda_emp_correction ${searchengines_options.andromeda.andromeda_emp_correction}
+                -andromeda_higher_charge ${searchengines_options.andromeda.andromeda_higher_charge}
+                -andromeda_equal_il ${searchengines_options.andromeda.andromeda_equal_il}
+                -andromeda_frag_method ${searchengines_options.andromeda.andromeda_frag_method}
+                -andromeda_max_mods ${searchengines_options.andromeda.andromeda_max_mods}
+                -andromeda_min_pep_length ${searchengines_options.andromeda.andromeda_min_pep_length}
+                -andromeda_max_pep_length ${searchengines_options.andromeda.andromeda_max_pep_length}
+                -andromeda_max_psms ${searchengines_options.andromeda.andromeda_max_psms}
+                -andromeda_decoy_mode ${searchengines_options.andromeda.andromeda_decoy_mode}
+            #end if
+            *#
+
+
+            ## OMSSA ADVANCED SETTINGS
+
+            #if $searchengines_options.omssa.omssa_advanced == "yes"
+                ## Spectrum
+                #if $searchengines_options.omssa.omssa_spectrum.omssa_spectrum_selector == "yes"
+                    -omssa_low_intensity "${searchengines_options.omssa.omssa_spectrum.omssa_low_intensity}"
+                    -omssa_high_intensity ${searchengines_options.omssa.omssa_spectrum.omssa_high_intensity}
+                    -omssa_intensity_incr ${searchengines_options.omssa.omssa_spectrum.omssa_intensity_incr}
+                    -omssa_min_peaks ${searchengines_options.omssa.omssa_spectrum.omssa_min_peaks}
+                    -omssa_remove_prec ${searchengines_options.omssa.omssa_spectrum.omssa_remove_prec}
+                    -omssa_estimate_charge ${searchengines_options.omssa.omssa_spectrum.omssa_estimate_charge}
+                    -omssa_plus_one ${searchengines_options.omssa.omssa_spectrum.omssa_plus_one}
+                    -omssa_fraction ${searchengines_options.omssa.omssa_spectrum.omssa_fraction}
+                    -omssa_prec_per_spectrum ${searchengines_options.omssa.omssa_spectrum.omssa_prec_per_spectrum}
+                    -omssa_scale_prec ${searchengines_options.omssa.omssa_spectrum.omssa_scale_prec}
+                #end if
+
+                ## Spectrum
+                #if $searchengines_options.omssa.omssa_database.omssa_database_selector == "yes"
+                    -omssa_memory ${searchengines_options.omssa.omssa_database.omssa_memory}
+                    -omssa_methionine ${searchengines_options.omssa.omssa_database.omssa_methionine}
+                #end if
+
+                ## Database
+                #if $searchengines_options.omssa.omssa_search.omssa_search_selector == "yes"
+                    -omssa_neutron ${searchengines_options.omssa.omssa_search.omssa_neutron}
+                    -omssa_single_window_wd ${searchengines_options.omssa.omssa_search.omssa_single_window_wd}
+                    -omssa_double_window_wd ${searchengines_options.omssa.omssa_search.omssa_double_window_wd}
+                    -omssa_single_window_pk ${searchengines_options.omssa.omssa_search.omssa_single_window_pk}
+                    -omssa_double_window_pk ${searchengines_options.omssa.omssa_search.omssa_double_window_pk}
+                    -omssa_min_ann_int_pks ${searchengines_options.omssa.omssa_search.omssa_min_ann_int_pks}
+                    -omssa_min_annotated_peaks ${searchengines_options.omssa.omssa_search.omssa_min_annotated_peaks}
+                    -omssa_max_ladders ${searchengines_options.omssa.omssa_search.omssa_max_ladders}
+                    -omssa_max_frag_charge ${searchengines_options.omssa.omssa_search.omssa_max_frag_charge}
+                    -omssa_charge ${searchengines_options.omssa.omssa_search.omssa_charge}
+                    -omssa_forward ${searchengines_options.omssa.omssa_search.omssa_forward}
+                    -omssa_rewind ${searchengines_options.omssa.omssa_search.omssa_rewind}
+                    -omssa_max_frag_series ${searchengines_options.omssa.omssa_search.omssa_max_frag_series}
+                    -omssa_corr ${searchengines_options.omssa.omssa_search.omssa_corr}
+                    -omssa_consecutive_p ${searchengines_options.omssa.omssa_search.omssa_consecutive_p}
+                    -omssa_hitlist_charge ${searchengines_options.omssa.omssa_search.omssa_hitlist_charge}
+                #end if
+
+                ## Iterative Search
+                #if $searchengines_options.omssa.omssa_isearch.omssa_isearch_selector == "yes"
+                    -omssa_it_sequence_evalue ${searchengines_options.omssa.omssa_isearch.omssa_it_sequence_evalue}
+                    -omssa_it_spectrum_evalue ${searchengines_options.omssa.omssa_isearch.omssa_it_spectrum_evalue}
+                    -omssa_it_replace_evalue ${searchengines_options.omssa.omssa_isearch.omssa_it_replace_evalue}
+                #end if
+
+                ## Semi-enzymatic
+                #if $searchengines_options.omssa.omssa_senzymatic.omssa_senzymatic_selector == "yes"
+                    -omssa_min_pep_length ${searchengines_options.omssa.omssa_senzymatic.omssa_min_pep_length}
+                    -omssa_max_pep_length ${searchengines_options.omssa.omssa_senzymatic.omssa_max_pep_length}
+                #end if
+
+                ## Output
+                #if $searchengines_options.omssa.omssa_output_conditional.omssa_output_conditional_selector == "yes"
+                    -omssa_max_evalue ${searchengines_options.omssa.omssa_output_conditional.omssa_max_evalue}
+                    -omssa_hitlist_length ${searchengines_options.omssa.omssa_output_conditional.omssa_hitlist_length}
+                    -omssa_format ${searchengines_options.omssa.omssa_output_conditional.omssa_format}
+                #end if
+            #end if
+
+
+            ## COMET ADVANCED SETTINGS
+
+            #if $searchengines_options.comet.comet_advanced == "yes"
+
+                #if $searchengines_options.comet.comet_spectrum.comet_spectrum_selector == "yes"
+                    -comet_min_peaks ${searchengines_options.comet.comet_spectrum.comet_min_peaks}
+                    -comet_min_peak_int ${searchengines_options.comet.comet_spectrum.comet_min_peak_int}
+                    -comet_remove_prec ${searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec}
+                     #if $searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "1"
+                        -comet_remove_prec_tol ${searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
+                     #end if
+                     #if $searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "2"
+                        -comet_remove_prec_tol ${searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
+                     #end if
+                     #if $searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "3"
+                        -comet_remove_prec_tol ${searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
+                     #end if
+                    -comet_clear_mz_range_lower ${searchengines_options.comet.comet_spectrum.comet_clear_mz_range_lower}
+                    -comet_clear_mz_range_upper ${searchengines_options.comet.comet_spectrum.comet_clear_mz_range_upper}
+                #end if
+
+                #if $searchengines_options.comet.comet_search.comet_search_selector == "yes"
+                    -comet_enzyme_type ${searchengines_options.comet.comet_search.comet_enzyme_type}
+                    -comet_isotope_correction ${searchengines_options.comet.comet_search.comet_isotope_correction}
+                    -comet_min_prec_mass ${searchengines_options.comet.comet_search.comet_min_prec_mass}
+                    -comet_max_prec_mass ${searchengines_options.comet.comet_search.comet_max_prec_mass}
+                    -comet_max_frag_charge ${searchengines_options.comet.comet_search.comet_max_frag_charge}
+                    -comet_remove_meth ${searchengines_options.comet.comet_search.comet_remove_meth}
+                    -comet_batch_size ${searchengines_options.comet.comet_search.comet_batch_size}
+                    -comet_num_ptms ${searchengines_options.comet.comet_search.comet_num_ptms}
+                    -comet_req_ptms ${searchengines_options.comet.comet_search.comet_req_ptms}
+                #end if
+
+                #if $searchengines_options.comet.comet_fragment_ions.comet_fragment_ions_selector == "yes"
+                    -comet_theoretical_fragment_ions ${searchengines_options.comet.comet_fragment_ions.comet_theoretical_fragment_ions}
+                    -comet_frag_bin_offset ${searchengines_options.comet.comet_fragment_ions.comet_frag_bin_offset}
+                #end if
+
+                #if $searchengines_options.comet.comet_output.comet_output_selector == "yes"
+                    -comet_num_matches ${searchengines_options.comet.comet_output.comet_num_matches}
+                    -comet_output ${searchengines_options.comet.comet_output.comet_output_type}
+                #end if
+            #end if
+
+
+            ## TIDE ADVANCED SETTINGS
+
+            #if $searchengines_options.tide.tide_advanced == "yes"
+                ## Index parameters
+                #if $searchengines_options.tide.tide_index.tide_index_selector == "yes"
+                    -tide_min_pep_length ${searchengines_options.tide.tide_index.tide_min_pep_length}
+                    -tide_max_pep_length ${searchengines_options.tide.tide_index.tide_max_pep_length}
+                    -tide_min_prec_mass ${searchengines_options.tide.tide_index.tide_min_prec_mass}
+                    -tide_max_prec_mass ${searchengines_options.tide.tide_index.tide_max_prec_mass}
+                    -tide_monoisotopic ${searchengines_options.tide.tide_index.tide_monoisotopic}
+                    -tide_clip_n_term ${searchengines_options.tide.tide_index.tide_clip_n_term}
+                    #if str($searchengines_options.tide.tide_index.tide_num_ptms).strip() != '':
+                      -tide_num_ptms ${searchengines_options.tide.tide_index.tide_num_ptms}
+                    #end if
+                    -tide_num_ptms_per_type ${searchengines_options.tide.tide_index.tide_num_ptms_per_type}
+                    -tide_digestion_type ${searchengines_options.tide.tide_index.tide_digestion_type}
+                    -tide_print_peptides ${searchengines_options.tide.tide_index.tide_print_peptides}
+                    -tide_decoy_format ${searchengines_options.tide.tide_index.tide_decoy_format}
+                    -tide_keep_terminals ${searchengines_options.tide.tide_index.tide_keep_terminals}
+                    -tide_decoy_seed ${searchengines_options.tide.tide_index.tide_decoy_seed}
+                    -tide_remove_temp ${searchengines_options.tide.tide_index.tide_remove_temp}
+                #end if
+
+                ## Search parameters
+                #if $searchengines_options.tide.tide_search.tide_search_selector == "yes"
+                    -tide_compute_p ${searchengines_options.tide.tide_search.tide_compute_p}
+                    -tide_compute_sp ${searchengines_options.tide.tide_search.tide_compute_sp}
+                    -tide_min_spectrum_mz ${searchengines_options.tide.tide_search.tide_min_spectrum_mz}
+                    #if str($searchengines_options.tide.tide_search.tide_max_spectrum_mz).strip() != '':
+                      -tide_max_spectrum_mz ${searchengines_options.tide.tide_search.tide_max_spectrum_mz}
+                    #end if
+                    -tide_min_spectrum_peaks ${searchengines_options.tide.tide_search.tide_min_spectrum_peaks}
+                    -tide_spectrum_charges ${searchengines_options.tide.tide_search.tide_spectrum_charges}
+                    -tide_remove_prec ${searchengines_options.tide.tide_search.tide_remove_prec}
+                    -tide_remove_prec_tol ${searchengines_options.tide.tide_search.tide_remove_prec_tol}
+                    -tide_use_flanking ${searchengines_options.tide.tide_search.tide_use_flanking}
+                    -tide_use_neutral_losses ${searchengines_options.tide.tide_search.tide_use_neutral_losses}
+                    -tide_mz_bin_width ${searchengines_options.tide.tide_search.tide_mz_bin_width}
+                    -tide_mz_bin_offset ${searchengines_options.tide.tide_search.tide_mz_bin_offset}
+                    -tide_max_psms ${searchengines_options.tide.tide_search.tide_max_psms}
+
+                    #set $format_list = str($searchengines_options.tide.tide_search.tide_export).split(',')
+                    #set $formats_available = ["tide_export_text", "tide_export_sqt", "tide_export_pepxml", "tide_export_mzid", "tide_export_pin"]
+                    #for $format_available in $formats_available:
+                        #if $format_available in $format_list:
+                          -$format_available 1
+                        #else:
+                          -$format_available 0
+                        #end if
+                    #end for
+                #end if
+                    -tide_output_folder ${searchengines_options.tide.tide_output_folder}
+                    -tide_verbosity ${searchengines_options.tide.tide_verbosity}
+                    -tide_progress_indicator ${searchengines_options.tide.tide_progress_indicator}
+                    -tide_concat ${searchengines_options.tide.tide_concat}
+                    #if str($searchengines_options.tide.tide_store_spectra).strip() != '':
+                      -tide_store_spectra ${searchengines_options.tide.tide_store_spectra}
+                    #end if
+
+            #end if
+
+
+            ## DIRECTTAG ADVANCED SETTINGS
+
+            #if $searchengines_options.directtag.directtag_advanced == "yes"
+                -directag_tag_length ${searchengines_options.directtag.directag_tag_length}
+                -directag_max_var_mods ${searchengines_options.directtag.directag_max_var_mods}
+                -directag_charge_states ${searchengines_options.directtag.directag_charge_states}
+                -directag_duplicate_spectra ${searchengines_options.directtag.directag_duplicate_spectra}
+                -directag_isotope_tolerance ${searchengines_options.directtag.directag_isotope_tolerance}
+                -directag_deisotoping ${searchengines_options.directtag.directag_deisotoping}
+                -directag_intensity_classes ${searchengines_options.directtag.directag_intensity_classes}
+                #if str($searchengines_options.directtag.directag_output_suffix).strip() != '':
+                -directag_output_suffix ${searchengines_options.directtag.directag_output_suffix}
+                #end if
+                -directag_max_peak_count ${searchengines_options.directtag.directag_max_peak_count}
+                -directag_max_tag_count ${searchengines_options.directtag.directag_max_tag_count}
+                -directag_tic_cutoff ${searchengines_options.directtag.directag_tic_cutoff}
+                -directag_complement_tolerance ${searchengines_options.directtag.directag_complement_tolerance}
+                -directag_adjustment_step ${searchengines_options.directtag.directag_adjustment_step}
+                -directag_min_adjustment ${searchengines_options.directtag.directag_min_adjustment}
+                -directag_max_adjustment ${searchengines_options.directtag.directag_max_adjustment}
+                -directag_intensity_weight ${searchengines_options.directtag.directag_intensity_weight}
+                -directag_fidelity_weight ${searchengines_options.directtag.directag_fidelity_weight}
+                -directag_complement_weight ${searchengines_options.directtag.directag_complement_weight}
+                -directag_adjust_precursor ${searchengines_options.directtag.directag_adjust_precursor}
+                -directag_ms_charge_state ${searchengines_options.directtag.directag_ms_charge_state}
+            #end if
+
+            ## METAMORPHEUS ADVANCED SETTINGS
+
+            #if $searchengines_options.metamorpheus.metamorpheus_advanced == "yes"
+                ## Search options
+                #if $searchengines_options.metamorpheus.metamorpheus_search.metamorpheus_search_selector == "yes"
+                    -meta_morpheus_search_type ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_search_type}
+                    -meta_morpheus_num_partitions ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_num_partitions}
+                    -meta_morpheus_dissociation_type ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_dissociation_type}
+                    -meta_morpheus_max_mods_for_peptide ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_max_mods_for_peptide}
+                    -meta_morpheus_score_cutoff ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_score_cutoff}
+                    -meta_morpheus_use_delta_score ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_use_delta_score}
+                    -meta_morpheus_mass_diff_acceptor_type ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_mass_diff_acceptor_type}
+                    -meta_morpheus_min_pep_length ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_min_pep_length}
+                    -meta_morpheus_max_pep_length ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_max_pep_length}
+                #end if
+
+                ## Output options
+                #if $searchengines_options.metamorpheus.metamorpheus_output.metamorpheus_output_selector == "yes"
+                    -meta_morpheus_write_mzid ${searchengines_options.metamorpheus.metamorpheus_output.meta_morpheus_write_mzid}
+                    -meta_morpheus_write_pepxml ${searchengines_options.metamorpheus.metamorpheus_output.meta_morpheus_write_pepxml}
+                #end if
+
+                ## Deisotoping options
+                #if $searchengines_options.metamorpheus.metamorpheus_deisotoping.metamorpheus_deisotoping_selector == "yes"
+                    -meta_morpheus_use_provided_prec ${searchengines_options.metamorpheus.metamorpheus_deisotoping.meta_morpheus_use_provided_prec}
+                    -meta_morpheus_do_prec_deconv ${searchengines_options.metamorpheus.metamorpheus_deisotoping.meta_morpheus_do_prec_deconv}
+                    -meta_morpheus_deconv_int_ratio ${searchengines_options.metamorpheus.metamorpheus_deisotoping.meta_morpheus_deconv_int_ratio}
+                    -meta_morpheus_deconv_mass_tol ${searchengines_options.metamorpheus.metamorpheus_deisotoping.meta_morpheus_deconv_mass_tol}
+                    -meta_morpheus_deconv_mass_tol_type ${searchengines_options.metamorpheus.metamorpheus_deisotoping.meta_morpheus_deconv_mass_tol_type}
+                #end if
+
+                ## Protein grouping options
+                #if $searchengines_options.metamorpheus.metamorpheus_proteingrouping.metamorpheus_proteingrouping_selector == "yes"
+                    -meta_morpheus_mod_peptides_are_different ${searchengines_options.metamorpheus.metamorpheus_proteingrouping.meta_morpheus_mod_peptides_are_different}
+                    -meta_morpheus_no_one_hit_wonders ${searchengines_options.metamorpheus.metamorpheus_proteingrouping.meta_morpheus_no_one_hit_wonders}
+                #end if
+
+                ## Peak trimming options
+                #if $searchengines_options.metamorpheus.metamorpheus_peaktrimming.metamorpheus_peaktrimming_selector == "yes"
+                    -meta_morpheus_trim_ms1 ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_trim_ms1}
+                    -meta_morpheus_trim_msms ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_trim_msms}
+                    -meta_morpheus_num_peaks_per_window ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_num_peaks_per_window}
+                    -meta_morpheus_min_allowed_int_ratio_to_base_peak ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_min_allowed_int_ratio_to_base_peak}
+                    -meta_morpheus_window_with_thompson ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_window_with_thompson}
+                    -meta_morpheus_num_windows ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_num_windows}
+                    -meta_morpheus_norm_across_all_windows ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_norm_across_all_windows}
+                #end if
+
+                ## Silico digestion related options
+                #if $searchengines_options.metamorpheus.metamorpheus_silico.metamorpheus_silico_selector == "yes"
+                    -meta_morpheus_frag_term ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_frag_term}
+                    -meta_morpheus_max_frag_size ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_max_frag_size}
+                    -meta_morpheus_search_target ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_search_target}
+                    -meta_morpheus_decoy_type ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_decoy_type}
+                    -meta_morpheus_max_mod_isoforms ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_max_mod_isoforms}
+                    -meta_morpheus_min_variant_depth ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_min_variant_depth}
+                    -meta_morpheus_min_variant_depth ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_min_variant_depth}
+                #end if
+
+                ## G-PTM search related options
+                #if $searchengines_options.metamorpheus.metamorpheus_gptm.metamorpheus_gptm_selector == "yes"
+                    -meta_morpheus_gptm ${searchengines_options.metamorpheus.metamorpheus_gptm.meta_morpheus_gptm}
+
+                    ## Need to transform the list of gptm acronyms to real gptm values for SearchGUI
+                    #if str($searchengines_options.metamorpheus.metamorpheus_gptm.meta_morpheus_gptm_categories) != "None" and str($searchengines_options.metamorpheus.metamorpheus_gptm.meta_morpheus_gptm_categories) != ""
+                        #set $meta_morpheus_gptm_categories_list = set(str($searchengines_options.metamorpheus.metamorpheus_gptm.meta_morpheus_gptm_categories).split(','))
+                    #else
+                        #set $meta_morpheus_gptm_categories_list = set()
+                    #end if
+                    #set $meta_morpheus_categories_mapping = {'common_fixed_variable': 'Common Fixed and Variable', 'common_biological': 'Common Biological','common_artifact': 'Common Artifact', 'metal': 'Metal','less_common': 'Less Common','labeling': 'Labeling','subs_1n': 'Substitution (1 Nucleotide)','subs_2n': 'Substitution (2+ Nucleotides)','other': 'Other'}
+                    #set $meta_morpheus_gptm_real_categories_list = []
+                    #for $meta_morpheus_gptm_category_item in $meta_morpheus_gptm_categories_list:
+                        $meta_morpheus_gptm_real_categories_list.append("'"+$meta_morpheus_categories_mapping[$meta_morpheus_gptm_category_item]+"'")
+                    #end for
+
+                    #if len($meta_morpheus_gptm_real_categories_list) > 0
+                            -meta_morpheus_gptm_categories #echo ','.join($meta_morpheus_gptm_real_categories_list)#
+                    #end if
+
+                #end if
+
+            #end if
+
+            ## NOVOR ADVANCED SETTINGS
+
+            #if $searchengines_options.novor.novor_advanced == "yes"
+                -novor_fragmentation ${searchengines_options.novor.novor_fragmentation}
+                -novor_mass_analyzer ${searchengines_options.novor.novor_mass_analyzer}
+            #end if
+
+
+            ## PEPNOVO+ ADVANCED SETTINGS
+
+            #if $searchengines_options.pepnovo.pepnovo_advanced == "yes"
+                -pepnovo_hitlist_length ${searchengines_options.pepnovo.pepnovo_hitlist_length}
+                -pepnovo_estimate_charge ${searchengines_options.pepnovo.pepnovo_estimate_charge}
+                -pepnovo_correct_prec_mass ${searchengines_options.pepnovo.pepnovo_correct_prec_mass}
+                -pepnovo_discard_spectra ${searchengines_options.pepnovo.pepnovo_discard_spectra}
+                -pepnovo_generate_blast ${searchengines_options.pepnovo.pepnovo_generate_blast}
+            #end if
+
+
+            ## PNOVO+ ADVANCED SETTINGS
+
+            #if $searchengines_options.pnovo.pnovo_advanced == "yes"
+                -pnovo_num_peptides ${searchengines_options.pnovo.pnovo_num_peptides}
+                -pnovo_lower_prec ${searchengines_options.pnovo.pnovo_lower_prec}
+                -pnovo_upper_prec ${searchengines_options.pnovo.pnovo_upper_prec}
+                -pnovo_activation ${searchengines_options.pnovo.pnovo_activation}
+            #end if
+
+
+            ## -- ADVANCED PARAMETERS
+
+            ## SPECTRUM ANNOTATION
+            -annotation_level $advanced_options.spectrum_annotation_options.annotation_level
+            -annotation_mz_tolerance $advanced_options.spectrum_annotation_options.annotation_mz_tolerance
+            -annotation_high_resolution $advanced_options.spectrum_annotation_options.annotation_high_resolution
+            ## TODO: There are still many options from the GUI to be incorporated to the CLI
+
+
+            ## SEQUENCE MATCHING
+            -sequence_matching_type $advanced_options.sequence_matching_options.sequence_matching_type
+            -sequence_matching_x $advanced_options.sequence_matching_options.sequence_matching_x
+            -sequence_matching_enzymatic_tags $advanced_options.sequence_matching_options.sequence_matching_enzymatic_tags
+            -sequence_matching_max_ptms_per_tag $advanced_options.sequence_matching_options.sequence_matching_max_ptms_per_tag
+            -sequence_matching_min_amino_acid_score $advanced_options.sequence_matching_options.sequence_matching_min_amino_acid_score
+            -sequence_matching_min_tag_length $advanced_options.sequence_matching_options.sequence_matching_min_tag_length
+
+
+            ## IMPORT FILTERS
+
+            -import_peptide_length_min '${advanced_options.import_filters_options.min_peptide_length}'
+            -import_peptide_length_max '${advanced_options.import_filters_options.max_peptide_length}'
+            -import_precursor_mz '${advanced_options.import_filters_options.max_precursor_error}'
+            -import_precursor_mz_ppm '${advanced_options.import_filters_options.max_precursor_error_type}'
+            #if $advanced_options.import_filters_options.missed_cleavages_min
+              -import_missed_cleavages_min '${advanced_options.import_filters_options.missed_cleavages_min}'
+            #end if
+            #if $advanced_options.import_filters_options.missed_cleavages_max
+              -import_missed_cleavages_max '${advanced_options.import_filters_options.missed_cleavages_max}'
+            #end if
+            -exclude_unknown_ptms '${advanced_options.import_filters_options.exclude_unknown_ptms}'
+
+
+            ## PTM LOCALIZATION
+
+            -ptm_score '${advanced_options.ptm_localization_options.ptm_score.ptm_score_selector}'
+                #if $advanced_options.ptm_localization_options.ptm_score.ptm_score_selector == 1
+                    -score_neutral_losses '${advanced_options.ptm_localization_options.ptm_score.neutral_losses}'
+                    #if str($advanced_options.ptm_localization_options.ptm_score.ptm_threshold) != ''
+                        -ptm_threshold '${advanced_options.ptm_localization_options.ptm_score.ptm_threshold}'
+                    #end if
+                #end if
+            -ptm_alignment '${advanced_options.ptm_localization_options.ptm_alignment}'
+            -ptm_sequence_matching_type '${advanced_options.ptm_localization_options.ptm_sequence_matching_type}'
+
+
+            ## GENE ANNOTATION
+
+            $advanced_options.gene_annotation_options.use_gene_mapping
+            #if $advanced_options.gene_annotation_options.use_gene_mapping:
+                $advanced_options.gene_annotation_options.update_gene_mapping
+            #else:
+                -updateGeneMapping 0
+            #end if
+
+
+            ## PROTEIN INFERENCE
+
+            #if $advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_selector == "yes"
+                -simplify_groups 1
+                -simplify_evidence ${advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_evidence}
+                -simplify_confidence ${advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_confidence}
+                -simplify_confidence_threshold ${advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_confidence_threshold}
+                -simplify_enzymaticity ${advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_enzymaticity}
+                -simplify_variant ${advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_variant}
+            #else
+                -simplify_groups 0
+            #end if
+            -pi_modifications ${advanced_options.protein_inference_options.simplify_protein_pi_modifications}
+
+
+
+
+            ## VALIDATION LEVELS
+
+            -protein_fdr '${advanced_options.validation_levels_options.protein_fdr}'
+            -peptide_fdr '${advanced_options.validation_levels_options.peptide_fdr}'
+            -psm_fdr '${advanced_options.validation_levels_options.psm_fdr}'
+
+
+            ## FRACTION ANALYSIS
+
+            -protein_fraction_mw_confidence '${advanced_options.fraction_analysis_options.protein_fraction_mw_confidence}'
+
+
+
+            ## DATABASE PROCESSING OPTIONS
+
+            #if $advanced_options.database_processing_options.decoy_conditional.create_decoy_selector == "yes"
+                -fasta_target_decoy 1
+                -fasta_decoy_tag $advanced_options.database_processing_options.decoy_conditional.decoy_tag
+                -fasta_decoy_type $advanced_options.database_processing_options.decoy_conditional.decoy_type
+            #end if
+                -fasta_target_decoy 0
+                -fasta_decoy_file_tag $advanced_options.database_processing_options.decoy_file_tag
+
+        2> $temp_stderr) &&
+
+        cat $temp_stderr 2>&1;
+]]>
+    </command>
+    <inputs>
+
+
+        <!-- SPECTRUM MATCHING PARAMETERS -->
+
+        <section name="spectrum_matching_options" expanded="false" title="Spectrum Matching Options">
+
+            <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
+                help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
+                <expand macro="modifications"/>
+            </param>
+            <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true"
+                help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
+                <expand macro="modifications"/>
+            </param>
+
+            <conditional name="digestion">
+                <param name="cleavage" type="select" label="Digestion">
+                    <option value="0">Select Enzymes</option>
+                    <option value="1">Unspecific Cleavage</option>
+                    <option value="2">Whole Protein</option>
+                </param>
+                <when value="0">
+                    <repeat name="digests" min="1" title="Enzymes">
+                        <param name="enzyme" type="select" label="Enzyme"
+                            help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
+                            <option value="Trypsin">Trypsin</option>
+                            <option value="Trypsin (no P rule)">Trypsin (no P rule)</option>
+                            <option value="Arg-C">Arg-C</option>
+                            <option value="Arg-C (no P rule)">Arg-C</option>
+                            <option value="Arg-N">Arg-N</option>
+                            <option value="Glu-C">Glu-C</option>
+                            <option value="Lys-C">Lys-C</option>
+                            <option value="Lys-C (no P rule)">Lys-C (no P rule)</option>
+                            <option value="Lys-N">Lys-N</option>
+                            <option value="Asp-N">Asp-N</option>
+                            <option value="Asp-N (ambic)">Asp-N (ambic)</option>
+                            <option value="Chymotrypsin">Chymotrypsin</option>
+                            <option value="Chymotrypsin (no P rule)">Chymotrypsin (no P rule)</option>
+                            <option value="Pepsin A">Pepsin A</option>
+                            <option value="CNBr">CNBr</option>
+                            <option value="Thermolysin">Thermolysin</option>
+                            <option value="LysargiNase">LysargiNase</option>
+                        </param>
+                        <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
+                            help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
+
+                        <param name="specificity" type="select" label="Specificity">
+                            <option value="0" selected="true">Specific at both termini</option>
+                            <option value="1">Semi-Specific - one terminus</option>
+                            <option value="2">Specific at the N-terminus only</option>
+                            <option value="3">Specific at the C-terminus only</option>
+                        </param>
+
+                    </repeat>
+                </when>
+                <when value="1"/>
+                <when value="2"/>
+            </conditional>
+
+            <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
+                help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
+                <option value="1">Parts per million (ppm)</option>
+                <option value="0">Daltons</option>
+            </param>
+            <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance"
+                help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
+            <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units"
+                help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
+                <option value="1">Parts per million (ppm)</option>
+                <option value="0" selected="true">Daltons</option>
+            </param>
+            <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance"
+                help="Provide error value for fragment ions, based on instrument used"/>
+            <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
+            <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
+            <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
+                <option value="a">a</option>
+                <option value="b" selected="true">b</option>
+                <option value="c">c</option>
+            </param>
+            <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
+                <option value="x">x</option>
+                <option value="y" selected="true">y</option>
+                <option value="z">z</option>
+            </param>
+            <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />
+            <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />
+        </section>
+
+
+        <!-- - SEARCH ENGINES OPTIONS -->
+
+        <section name="searchengines_options" expanded="false" title="Search Engines Options">
+
+            <!-- X!TANDEM ADVANCED PARAMETERS -->
+            <conditional name="xtandem">
+                <param name="xtandem_advanced" type="select" label="X!Tandem Options">
+                    <option value="yes">Advanced</option>
+                    <option value="no" selected="True">Default</option>
+                </param>
+                <when value="no" />
+                <when value="yes">
+                    <!-- Spectrum Import -->
+                    <conditional name="xtandem_spectrum">
+                        <param name="xtandem_spectrum_selector" type="select" label="X!Tandem: Spectrum Import Related">
+                            <option value="yes" selected="True">Set Spectrum Import Parameters</option>
+                            <option value="no">Keep Default Spectrum Import Parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                          <param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra"
+                              label="X!Tandem: Dynamic Range" value="100" type="integer" />
+                          <param name="xtandem_npeaks" type="integer" value="50"
+                              label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/>
+                          <param name="xtandem_min_frag_mz" type="integer" value="200"
+                              label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/>
+                          <param name="xtandem_min_peaks" type="integer" value="5"
+                              label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
+                          <param name="xtandem_noise_suppr" type="boolean" checked="false" truevalue="1" falsevalue="0"
+                              label="X!Tandem: Noise Suppression" help="Use noise suppression"/>
+                          <param name="xtandem_min_prec_mass" type="integer" value="500"
+                              label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/>
+                          <param name="xtandem_parent_isotope_correction" type="boolean" checked="true" truevalue="1" falsevalue="0"
+                              label="X!Tandem: Parent monoisotopic mass isotope error" help="when activated, the parent ion mass tolerance is expanded by opening up multiple tolerance windows centered on the first and second 13C isotope peaks for a peptide. "/>
+                        </when>
+                    </conditional>
+                    <!-- Advanced search -->
+                    <conditional name="xtandem_asearch">
+                        <param name="xtandem_asearch_selector" type="select" label="X!Tandem: Advanced Search Related">
+                            <option value="yes">Set Advanced Search Parameters</option>
+                            <option value="no" selected="True">Keep Default Advanced Search Parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection"
+                                label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" />
+                            <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection"
+                                label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" />
+                            <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
+                                label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" />
+                            <param name="xtandem_ptm_complexity" type="float" value="6.0" help="maximum number of variable modification alternatives that will be tested for a particular peptide"
+                                 label="X!Tandem: PTM complexity" />
+                       </when>
+                   </conditional>
+                    <!-- Output -->
+                    <conditional name="xtandem_output">
+                        <param name="xtandem_output_selector" type="select" label="X!Tandem: Output Related">
+                            <option value="yes">Set Output Parameters</option>
+                            <option value="no" selected="True">Keep Default Output Parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <conditional name="xtandem_output_results_conditional">
+                                <param name="xtandem_output_results_selector" type="select" label="" help="Determines which results are written to the output file at the end of a modelling session">
+                                    <option value="all" selected="True">All</option>
+                                    <option value="valid" >Valid</option>
+                                    <option value="stochastic" >Stochastic</option>
+                                </param>
+                                <when value="all"/>
+                                <when value="valid">
+                                    <param name="xtandem_evalue" help="Highest value for recorded peptides"
+                                        label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" />
+                                </when>
+                                <when value="stochastic">
+                                    <param name="xtandem_evalue" help="Highest value for recorded peptides"
+                                        label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" />
+                                </when>
+                            </conditional>
+
+                            <param name="xtandem_output_proteins" help="Controls output of protein sequences"
+                                label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="true" />
+                            <param name="xtandem_output_sequences" help="Controls output of sequence information"
+                                label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
+                            <param name="xtandem_output_spectra" help="Controls output of spectrum information"
+                                label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" />
+                            <param name="xtandem_output_histograms" help="Controls output of statistical information about an spectrum-to-sequence assignment"
+                                label="X!Tandem: Output Histograms" type="boolean" truevalue="1" falsevalue="0" checked="false" />
+                            <!-- TODO: Integration with Skyline not ready yet
+                            <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="txt" help="Path to a spectrum data file for use by skyline." -->
+                        </when>
+                    </conditional>
+
+                    <!-- Refine -->
+                    <conditional name="xtandem_refine">
+                        <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
+                            <option value="no">Don't refine</option>
+                            <option value="yes" selected="True">Use refinement</option>
+                        </param>
+                        <when value="no"/>
+                        <when value="yes">
+                            <param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement"
+                                label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" />
+                            <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                                label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
+                            <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                                label="X!Tandem: semi-enzymatic cleavage, refinement" help="Search for semi-tryptic peptides during refinement"/>
+                            <param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                                label="X!Tandem: Use potential modifications for full refinement" help="Controls the use of refinement modifications in all refinement modules."/>
+                            <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                                label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
+                            <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                                label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
+                            <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                                label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
+                            <!-- TODO: Refinement modifications when implemented in the command line -->
+                        </when>
+                    </conditional>
+                </when>
+            </conditional>
+
+
+            <!-- MyriMatch ADVANCED PARAMETERS -->
+            <conditional name="myrimatch">
+                <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
+                    <option value="yes">Advanced</option>
+                    <option value="no" selected="True">Default</option>
+                </param>
+                <when value="no" />
+                <when value="yes">
+                    <param name="myrimatch_min_pep_length"  type="integer" value="6"
+                        label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" />
+                    <param name="myrimatch_max_pep_length"  type="integer" value="30"
+                        label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" />
+                    <param name="myrimatch_min_prec_mass"  type="float" value="0.0"
+                        label="MyriMatch: Minimum Precursor Mass" help="Minimum precursor mass of parent ion to be considered" />
+                    <param name="myrimatch_max_prec_mass"  type="float" value="5000.0"
+                        label="MyriMatch: Maximum Precursor Mass" help="Maximum precursor mass of parent ion to be considered" />
+                    <param name="myrimatch_num_matches"  type="integer" value="10"
+                        label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
+                    <param name="myrimatch_num_ptms"  type="integer" value="2"
+                        label="MyriMatch: Max Variable PTMs per Peptide" help="Set the number of PTMS allowed per peptide" />
+
+                    <!-- TODO : TO BE UPDATED WHEN CLI DOES. TO CONFIRM MANUAL OPTION FIRSTLY -->
+                    <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)">
+                        <option value="CID" selected="True">CID</option>
+                        <option value="HCD" >HCD</option>
+                        <option value="ETD" >ETD</option>
+                    </param>
+                    <param name="myrimatch_termini" label="MyriMatch: Enzymatic Terminals" type="select" help="Select the number of enzymatic terminals">
+                        <option value="0">non-tryptic</option>
+                        <option value="1">semi-tryptic</option>
+                        <option value="2" selected="True" >fully-tryptic</option>
+                    </param>
+                    <param name="myrimatch_plus_three"  type="boolean" truevalue="1" falsevalue="0" checked="true"
+                        label="MyriMatch: Use Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" />
+                    <param name="myrimatch_xcorr"  type="boolean" truevalue="1" falsevalue="0" checked="false"
+                        label="MyriMatch: Compute Xcorr" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" />
+                    <param name="myrimatch_tic_cutoff"  type="float" value="0.98"
+                        label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained (0.0 - 1.0)" />
+                    <param name="myrimatch_intensity_classes"  type="integer" value="3"
+                        label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" />
+                    <param name="myrimatch_class_multiplier"  type="integer" value="2"
+                        label="MyriMatch: Class Size Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" />
+                    <param name="myrimatch_num_batches"  type="integer" value="50"
+                        label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" />
+                    <param name="myrimatch_max_peak"  type="integer" value="100"
+                        label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
+                    <param name="myrimatch_output" type="select" label="MyriMatch: output format option">
+                        <option value="mzIdentML" selected="True" >mzIdentML</option>
+                        <option value="pepXML">pepXML</option>
+                    </param>
+                </when>
+            </conditional>
+
+            <!-- MS-GF+ ADVANCED PARAMETERS -->
+            <conditional name="msgf">
+                <param name="msgf_advanced" type="select" label="MSGF Options">
+                    <option value="yes">Advanced</option>
+                    <option value="no" selected="True">Default</option>
+                </param>
+                <when value="no" />
+                <when value="yes">
+                    <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                        label="MSGF: Search Decoy Database" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
+                    <param name="msgf_instrument" label="MSGF: MS/MS Detector" type="select" help="Identifier of the instrument to generate MS/MS spectra (used to determine the scoring model)">
+                        <option value="0" >Low-res LCQ/LTQ</option>
+                        <option value="1" >Orbitrap/FTICR</option>
+                        <option value="2" >TOF</option>
+                        <option value="3" selected="True">Q-Exactive</option>
+                    </param>
+                    <param name="msgf_fragmentation" label="MSGF: Fragmentation method" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
+                        <option value="0" >As written in the spectrum or CID if no info</option>
+                        <option value="1" >CID</option>
+                        <option value="2" >ETD</option>
+                        <option value="3" selected="True">HCD</option>
+                        <option value="4" >UVPD</option>
+                    </param>
+                    <param name="msgf_protocol" label="MSGF: Protocol" type="select" help="Protocol identifier. Protocols are used to enable scoring parameters for enriched and/or labeled samples">
+                        <option value="0" selected="True">Automatic</option>
+                        <option value="1" >Phosphorylation</option>
+                        <option value="2" >iTRAQ</option>
+                        <option value="3" >iTRAQPhospho</option>
+                        <option value="4" >TMT</option>
+                        <option value="5" >Standard</option>
+                    </param>
+                    <param name="msgf_termini" type="select" format="txt"
+                        label="MSGF: Enzymatic Terminals" help="Searches will take much longer if selecting a value other than 2">
+                        <option value="0">None required</option>
+                        <option value="1">At least one</option>
+                        <option value="2" selected="true">Both</option>
+                    </param>
+                    <param name="msgf_min_pep_length" type="integer" value="8"
+                        label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
+                    <param name="msgf_max_pep_length" type="integer" value="30"
+                        label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
+                    <param name="msgf_num_ptms" label="MSGF: Max Variable PTMs per Peptide" type="integer" value="2"/>
+                    <param name="msgf_num_matches" label="MSGF: Number of Spectrum Matches" type="integer" value="10" help="Number of peptide matches per spectrum to report" />
+                    <param name="msgf_additional" label="MS-GF+ additional Output" type="select" help="Additional features to export">
+                        <option value="0" selected="True">output basic scores only</option>
+                        <option value="1" >output additional features</option>
+                    </param>
+                    <conditional name="msgf_tasks">
+                        <param name="msgf_tasks_custom" type="select" label="Number of tasks to use on the threads">
+                            <option value="yes">Custom</option>
+                            <option value="no" selected="True">Default</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="msgf_num_tasks" type="integer" value="4"
+                                label="MSGF: Custom number of tasks to use on the threads"
+                                help="Manually set the number of tasks to create for the search. More tasks than threads will reduce the memory requirements of the search, but will be slower (how much depends on the inputs). Check the documentation carefully. "/>
+                        </when>
+                    </conditional>
+                </when>
+            </conditional>
+
+              <!-- MS-AMANDA ADVANCED PARAMETERS  -->
+            <conditional name="ms_amanda">
+                <param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
+                    <option value="yes">Advanced</option>
+                    <option value="no" selected="True">Default</option>
+                </param>
+                <when value="no" />
+                <when value="yes">
+                    <param name="ms_amanda_decoy"  type="boolean" truevalue="1" falsevalue="0" checked="false"
+                        label="MS Amanda: Generate Decoys" help="generate decoys" />
+                    <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="select"
+                      help="MS Amanda instrument id option. Available ion types are listed here.">
+
+                      <option value="b, y" selected="True">b, y</option>
+                      <option value="b, y, -H2O, -NH3" >b, y, -H2O, -NH3</option>
+                      <option value="a, b, y, -H2O, -NH3, Imm" >a, b, y, -H2O, -NH3, Imm</option>
+                      <option value="a, b, y, -H2O, -NH3" >a, b, y, -H2O, -NH3</option>
+                      <option value="a, b, y" >a, b, y</option>
+                      <option value="a, b, y, Imm" >a, b, y, Imm</option>
+                      <option value="a, b, y, z, -H2O, -NH3, Imm" >a, b, y, z, -H2O, -NH3, Imm</option>
+                      <option value="c, y, z+1, z+2" >c, y, z+1, z+2</option>
+                      <option value="b, c, y, z+1, z+2" >b, c, y, z+1, z+2</option>
+                      <option value="b, y, INT" >b, y, INT</option>
+                      <option value="b, y, INT, Imm" >b, y, INT, Imm</option>
+                      <option value="a, b, y, INT" >a, b, y, INT</option>
+                      <option value="a, b, y, INT, IMM" >a, b, y, INT, IMM</option>
+                      <option value="a, b, y, INT, IMM, -H2O" >a, b, y, INT, IMM, -H2O</option>
+                      <option value="a, b, y, INT, IMM, -H2O, -NH3" >a, b, y, INT, IMM, -H2O, -NH3</option>
+                      <option value="a, b, y, INT, IMM, -NH3" >a, b, y, INT, IMM, -NH3</option>
+
+                    </param>
+                    <param name="ms_amanda_max_rank" type="integer" value="10"
+                        label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" />
+                    <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                        label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" />
+                </when>
+            </conditional>
+
+            <!-- OMSSA ADVANCED PARAMETERS -->
+            <conditional name="omssa">
+                <param name="omssa_advanced" type="select" label="OMSSA Options">
+                    <option value="yes">Advanced</option>
+                    <option value="no" selected="True">Default</option>
+                </param>
+                <when value="no" />
+                <when value="yes">
+                    <!-- Spectrum -->
+                    <conditional name="omssa_spectrum">
+                        <param name="omssa_spectrum_selector" type="select" label="OMSSA: Spectrum Related">
+                            <option value="yes" selected="True">Set Spectrum Parameters</option>
+                            <option value="no">Keep Default Spectrum Parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="omssa_low_intensity" type="float" value="0.0"
+                                label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
+                            <param name="omssa_high_intensity" type="float" value="0.2"
+                                label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />
+                            <param name="omssa_intensity_incr" type="float" value="0.0005"
+                                label="OMSSA: Intensity Increment" help="Intensity increment" />
+                            <param name="omssa_min_peaks" type="integer" value="4"
+                                label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" />
+                            <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                                label="OMSSA: Remove precursors" help="Eliminate charge reduced precursors in spectra" />
+                            <param name="omssa_estimate_charge" type="select"
+                                label="OMSSA: Estimate charge" help="estimate precursor charge" >
+                                <option value="0" >Believe input file</option>
+                                <option value="1" selected="True">Use range</option>
+                            </param>
+                            <param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                                label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/>
+                            <param name="omssa_fraction" type="float" value="0.95"
+                                label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" />
+                            <param name="omssa_prec_per_spectrum" type="integer" value="1"
+                                label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" />
+                            <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                                label="OMSSA: Scale Precursor Mass" help="scale precursor mass" />
+                        </when>
+                    </conditional>
+                    <!-- Database -->
+                    <conditional name="omssa_database">
+                        <param name="omssa_database_selector" type="select" label="OMSSA: Database Related">
+                            <option value="yes" >Set Database Parameters</option>
+                            <option value="no" selected="True">Keep Default Database Parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                                label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
+                            <param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                             label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" />
+                        </when>
+                    </conditional>
+                    <!-- Search -->
+                    <conditional name="omssa_search">
+                        <param name="omssa_search_selector" type="select" label="OMSSA: Search Related">
+                            <option value="yes">Set Search Parameters</option>
+                            <option value="no" selected="True">Keep Default Search Parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <!-- TODO: TO BE IMPLEMENTED IN THE CLI, MINIMUM PRECURSOR CHARGE FOR MULTIPLY CHARGED FRAGMENTS -->
+                            <param name="omssa_neutron" type="float" value="1446.94"
+                                   label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
+                            <param name="omssa_single_window_wd" type="integer" value="27"
+                                label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" />
+                            <param name="omssa_double_window_wd" type="integer" value="14"
+                                label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" />
+                            <param name="omssa_single_window_pk" type="integer" value="2"
+                                label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" />
+                            <param name="omssa_double_window_pk" type="integer" value="2"
+                                label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" />
+                            <param name="omssa_min_ann_int_pks" type="integer" value="6"
+                                label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" />
+                            <param name="omssa_min_annotated_peaks" type="integer" value="2"
+                                label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" />
+                            <param name="omssa_max_ladders" type="integer" value="128"
+                                label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" />
+                            <param name="omssa_max_frag_charge" type="integer" value="2"
+                                label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" />
+                            <param name="omssa_charge" type="select"
+                                label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" >
+                                <option value="0" >Minus</option>
+                                <option value="1" selected="True">Plus</option>
+                            </param>
+                            <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                                label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" />
+                            <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                                label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" />
+                            <param name="omssa_max_frag_series" type="integer" value="100"
+                                label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" />
+                            <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                                label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" />
+                            <param name="omssa_consecutive_p" type="float" value="0.5"
+                                label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" />
+                            <param name="omssa_hitlist_charge" type="integer" value="30"
+                                label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" />
+                        </when>
+                    </conditional>
+                    <!-- Iterative Search -->
+                    <conditional name="omssa_isearch">
+                        <param name="omssa_isearch_selector" type="select" label="OMSSA: Iterative Search Related">
+                            <option value="yes" >Set Iterative Search Parameters</option>
+                            <option value="no" selected="True">Keep Default Iterative Search Parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="omssa_it_sequence_evalue" type="float" value="0.0"
+                                label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" />
+                            <param name="omssa_it_spectrum_evalue" type="float" value="0.01"
+                                label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" />
+                            <param name="omssa_it_replace_evalue" type="float" value="0.0"
+                                label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search (0.0 means all)" />
+                        </when>
+                    </conditional>
+
+                    <!-- Semi-enzymatic -->
+                    <conditional name="omssa_senzymatic">
+                        <param name="omssa_senzymatic_selector" type="select" label="OMSSA: Semi-enzymatic Related">
+                            <option value="yes" >Set Semi-enzymatic Parameters</option>
+                            <option value="no" selected="True">Keep Default Semi-enzymatic Parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="omssa_min_pep_length" type="integer" value="8"
+                                label="OMSSA: Minimum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" />
+                            <param name="omssa_max_pep_length" type="integer" value="30"
+                                label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" />
+                        </when>
+                    </conditional>
+
+                    <!-- Output -->
+                    <conditional name="omssa_output_conditional">
+                        <param name="omssa_output_conditional_selector" type="select" label="OMSSA: Output Related">
+                            <option value="yes">Set Output Parameters</option>
+                            <option value="no" selected="True">Keep Default Output Parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="omssa_max_evalue" type="float" value="100"
+                                label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" />
+                            <param name="omssa_hitlist_length" type="integer" value="10"
+                                label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" />
+                            <param name="omssa_format" label="OMSSA output format" type="select" >
+                                <option value="0" selected="True">OMX</option>
+                                <option value="1" >CSV</option>
+                                <option value="2" >pepXML</option>
+                            </param>
+                        </when>
+                    </conditional>
+
+                </when>
+            </conditional>
+
+
+            <!-- Comet ADVANCED PARAMETERS -->
+            <conditional name="comet">
+                <param name="comet_advanced" type="select" label="Comet Options">
+                    <option value="yes">Advanced</option>
+                    <option value="no" selected="True">Default</option>
+                </param>
+                <when value="no" />
+                <when value="yes">
+                    <!-- Spectrum Related parameters -->
+                    <conditional name="comet_spectrum">
+                        <param name="comet_spectrum_selector" type="select" label="Comet: Spectrum Related">
+                            <option value="yes"  selected="True">Set Spectrum Parameters</option>
+                            <option value="no">Keep Default Spectrum Parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="comet_min_peaks"  type="integer" value="10"
+                                label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" />
+                            <param name="comet_min_peak_int"  type="float" value="0.0"
+                                label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" />
+                            <conditional name="comet_prec">
+                                <param name="comet_remove_prec" label="Comet: Remove Precursor peaks" type="select" help="Select for precursor m/z signal removal">
+                                    <option value="0" selected="True" >no</option>
+                                    <option value="1">yes</option>
+                                    <option value="2">yes + charge reduced</option>
+                                    <option value="3">yes + phospate neutral</option>
+                                </param>
+                                <when value="0" />
+                                <when value="1">
+                                    <param name="comet_remove_prec_tol"  type="float" value="1.5"
+                                        label="Comet: Remove Precursor Tolerance" />
+                                </when>
+                                <when value="2">
+                                    <param name="comet_remove_prec_tol"  type="float" value="1.5"
+                                        label="Comet: Remove Precursor Tolerance" />
+                                </when>
+                                <when value="3">
+                                    <param name="comet_remove_prec_tol"  type="float" value="1.5"
+                                        label="Comet: Remove Precursor Tolerance" />
+                                </when>
+                            </conditional>
+                            <param name="comet_clear_mz_range_lower"  type="float" value="0.0"
+                                label="Comet: Minimum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, lower m/z range" />
+                            <param name="comet_clear_mz_range_upper"  type="float" value="0.0"
+                                label="Comet: Maximum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, upper m/z range" />
+                        </when>
+                    </conditional>
+                      <!-- Search Related parameters -->
+                    <conditional name="comet_search">
+                        <param name="comet_search_selector" type="select" label="Comet: Search Related">
+                            <option value="yes">Set Search Parameters</option>
+                            <option value="no" selected="True">Keep Default Search Parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="comet_enzyme_type" label="Comet: Enzyme Type" type="select" help="Specifies the number of enzyme termini a peptide must have">
+                                <option value="1">semi-specific</option>
+                                <option value="2" selected="True">full-enzyme</option>
+                                <option value="8">unspecific N-term</option>
+                                <option value="9">unspecific C-term</option>
+                            </param>
+                            <param name="comet_isotope_correction" label="Comet: Isotope Correction" type="select" help="Controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement">
+                                <option value="0">off</option>
+                                <option value="1" selected="True">0,+1</option>
+                                <option value="2">0,+1,+2</option>
+                                <option value="3">0,+1,+2,+3</option>
+                                <option value="4">-8,-4,0,+4,+8</option>
+                            </param>
+                            <param name="comet_min_prec_mass"  type="float" value="600.0"
+                                label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" />
+                            <param name="comet_max_prec_mass"  type="float" value="5000.0"
+                                label="Comet: Maximum Precursor Mass" help="The maximum precursor mass considered" />
+                            <param name="comet_max_frag_charge"  type="integer" value="3"
+                                label="Comet: Maximum Fragment Charge" help="Sets the maximum fragment charge (fill value between 1 and 5)" />
+                            <param name="comet_remove_meth"  type="boolean" truevalue="1" falsevalue="0" checked="false"
+                                label="Comet: Remove Methionine" help="Specifies whether the N-terminal methionine is cleaved prior to matching" />
+                            <param name="comet_batch_size"  type="integer" value="0"
+                                label="Comet: Batch Size" help="0 means load and search all spectra at once, otherwise spectra are loaded and searched in batches of the number specified" />
+                            <param name="comet_num_ptms"  type="integer" value="10"
+                                label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" />
+                            <param name="comet_req_ptms" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                                label="Comet: Require Variable PTMs" help="Require at least one variable PTM per peptide" />
+                        </when>
+                    </conditional>
+                    <!-- Fragment Ions Related parameters -->
+                    <conditional name="comet_fragment_ions">
+                        <param name="comet_fragment_ions_selector" type="select" label="Comet: Fragment Ions Related">
+                            <option value="yes">Set Fragment Ions Parameters</option>
+                            <option value="no" selected="True">Keep Default Fragment Ions Parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="comet_theoretical_fragment_ions" type="select"
+                                label="Comet: Correlation Score type" help="Specifies how theoretical fragment ion peaks are represented (on the sum in the bin alone or using flanking bins too)">
+                                <option value="0" selected="True">Summed intensities + flanking</option>
+                                <option value="1">Summed intensities</option>
+                            </param>
+                            <param name="comet_frag_bin_offset"  type="float" value="0.01"
+                                label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" />
+                        </when>
+                    </conditional>
+                    <!-- Output Related parameters -->
+                    <conditional name="comet_output">
+                        <param name="comet_output_selector" type="select" label="Comet: Output Related">
+                            <option value="yes">Set Output Parameters</option>
+                            <option value="no" selected="True">Keep Default Output Parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="comet_num_matches"  type="integer" value="10"
+                                label="Comet: Maximum Number of Matches" help="The maximum number of peptide matches per spectrum" />
+                            <param name="comet_output_type" type="select"
+                                label="Comet: Output type" help="Output type: PepXML, SQT, TXT or Percolator">
+                                <option value="PepXML" selected="True">PepXML</option>
+                                <option value="SQT">SQT</option>
+                                <option value="TXT">TXT</option>
+                                <option value="Percolator">Percolator</option>
+                            </param>
+                        </when>
+                    </conditional>
+                </when>
+            </conditional>
+
+            <!-- TIDE ADVANCED PARAMETERS -->
+            <conditional name="tide">
+                <param name="tide_advanced" type="select" label="TIDE Options">
+                    <option value="yes">Advanced</option>
+                    <option value="no" selected="True">Default</option>
+                </param>
+                <when value="no" />
+                <when value="yes">
+                    <!-- Index parameters -->
+                    <conditional name="tide_index">
+                        <param name="tide_index_selector" type="select" label="Tide: Index Related">
+                            <option value="yes" selected="True">Set Index Parameters</option>
+                            <option value="no" >Keep Default Index Parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="tide_min_pep_length" type="integer" value="6"
+                                label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/>
+                            <param name="tide_max_pep_length" type="integer" value="30"
+                                label="TIDE: Maximum Peptide Length" help="Set the maximum length of peptide to be considered"/>
+                            <param name="tide_min_prec_mass" type="float" value="200.0"
+                                label="TIDE: Minimum Precursor Mass" help="Set the minimum precursor mass to be considered"/>
+                            <param name="tide_max_prec_mass" type="float" value="7200.0"
+                                label="TIDE: Maximum Precursor Mass" help="Set the maximum precursor mass to be considered"/>
+                            <param name="tide_monoisotopic" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                                label="TIDE: Monoisotopic" help="If true, the precursor mass is monoisotopic"/>
+                            <param name="tide_clip_n_term" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                                label="TIDE: Clip Nterm Methionine" help="If true, the Nterm Methionine will be clipped"/>
+                            <param name="tide_num_ptms" type="integer" value="" optional="true"
+                                label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/>
+                            <param name="tide_num_ptms_per_type" type="integer" value="2"
+                                label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/>
+                            <param name="tide_digestion_type" label="TIDE: Enzyme/Digestion Type" type="select" help="Either both ends (full-digest) or at least one end (partial-digest) of a peptide must conform to enzyme specificity rules">
+                                <option value="full-digest" selected="True">full-digest</option>
+                                <option value="partial-digest" >partial-digest</option>
+                            </param>
+                            <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                                label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/>
+                            <param name="tide_decoy_format" label="TIDE: Decoy Format" type="select" help="Select the format for generating the decoy sequences">
+                                <option value="none" selected="True">none</option>
+                                <option value="shuffle" >shuffle</option>
+                                <option value="peptide-revers" >peptide-reverse</option>
+                                <option value="protein-reverse" >protein-reverse</option>
+                            </param>
+                            <param name="tide_keep_terminals" label="TIDE: Keep Terminals" type="select" help="Select to keep the terminal amino acids when creating decoys">
+                                <option value="N" >N</option>
+                                <option value="C" >C</option>
+                                <option value="NC" selected="True">NC</option>
+                                <option value="non" >none</option>
+                            </param>
+                            <param name="tide_decoy_seed" type="integer" value="1"
+                                label="TIDE: Decoy Seed" help="Set the decoy seed"/>
+                            <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                                label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done."/>
+                        </when>
+                    </conditional>
+
+                    <!-- Search parameters -->
+                    <conditional name="tide_search">
+                        <param name="tide_search_selector" type="select" label="Tide: Search Related">
+                            <option value="yes">Set Search Parameters</option>
+                            <option value="no" selected="True">Keep Default Search Parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                                label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/>
+                            <param name="tide_compute_sp" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                                label="TIDE: Compute SP" help="If true, the SP-score is calculated"/>
+                            <param name="tide_min_spectrum_mz" type="float" value="0.0"
+                                label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/>
+                            <param name="tide_max_spectrum_mz" type="float" value="" optional="true"
+                                label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/>
+                            <param name="tide_min_spectrum_peaks" type="integer" value="20"
+                                label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/>
+                            <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching">
+                                <option value="1" >1</option>
+                                <option value="2" >2</option>
+                                <option value="3" >3</option>
+                                <option value="all" selected="True">all</option>
+                            </param>
+                            <param name="tide_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                                label="TIDE: Remove Precursor Peak" help="If true, the peak that corresponds to the precursor mass is excluded"/>
+                            <param name="tide_remove_prec_tol" type="float" value="1.5"
+                                label="TIDE: Remove Precursor Tolerance" help="Choose the threshold for precursor mass searching (for precursor peak removal)"/>
+                            <param name="tide_use_flanking" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                                label="TIDE: Use Flanking" help="Includes two flanking peaks on either side of each b- and y-ion to compute the XCorr"/>
+                            <param name="tide_use_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                                label="TIDE: Neutral Losses" help="Includes fragment peaks with neutral losses to perform the matching"/>
+                            <param name="tide_mz_bin_width" type="float" value="0.02"
+                                label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/>
+                            <param name="tide_mz_bin_offset" type="float" value="0.0"
+                                label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/>
+                            <param name="tide_max_psms" type="integer" value="10"
+                                label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/>
+                            <param name="tide_export" label="TIDE: Output Format" type="select" multiple="true"
+                              display="checkboxes" help="Choose the output format">
+                                <option value="tide_export_text" selected="True">Text</option>
+                                <option value="tide_export_sqt" >SQT</option>
+                                <option value="tide_export_pepxml" >pepxml</option>
+                                <option value="tide_export_mzid" >MzIdentML</option>
+                                <option value="tide_export_pin" >Percolator input file</option>
+                            </param>
+                        </when>
+                    </conditional>
+
+                    <!-- other options -->
+                    <param name="tide_output_folder" type="text" value="crux-output"
+                        label="TIDE: Output Folder" help="Tide output folder (relative to the Tide working folder). Not to be changed if the .par file will be used by SearchGUI in Galaxy"/>
+                    <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress">
+                        <option value="0" >0</option>
+                        <option value="10" >10</option>
+                        <option value="20" >20</option>
+                        <option value="30" selected="True">30</option>
+                        <option value="40" >40</option>
+                        <option value="50" >50</option>
+                        <option value="60" >60</option>
+                    </param>
+                    <param name="tide_progress_indicator" type="integer" value="1000"
+                        label="TIDE: Progress Indicator" help="Choose the progress indicator frequency  (in number of fragmentation spectra processed)"/>
+                    <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                        label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/>
+                    <param name="tide_store_spectra" type="text" value=""
+                        label="TIDE: Store spectra" help="Tide file name in with to store the binary spectra. Not to be changed if the .par file will be used by SearchGUI in Galaxy"/>
+                </when>
+            </conditional>
+
+            <!-- Andromeda ADVANCED PARAMETERS -->
+            <!-- Windows only
+            <conditional name="andromeda">
+                <param name="andromeda_advanced" type="select" label="Andromeda Options">
+                    <option value="yes">Advanced</option>
+                    <option value="no" selected="True">Default</option>
+                </param>
+                <when value="no" />
+                <when value="yes">
+                    <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" />
+                    <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" />
+                    <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" />
+                    <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" />
+                    <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" />
+                    <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" />
+                    <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" />
+                    <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" />
+                    <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" />
+                    <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" />
+                    <param name="andromeda_equal_il" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda whether I and L should be considered indistinguishable, default is: false" />
+                    <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." >
+                       <option value="CID" selected="true">CID</option>
+                       <option value="HCD">HCD</option>
+                       <option value="EDT">EDT</option>
+                    </param>
+                    <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" />
+                    <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" />
+                    <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" />
+                    <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" />
+                    <param name="andromeda_decoy_mode" type="boolean" truevalue="decoy" falsevalue="none" checked="false" label="Andromeda decoy mode" />
+                </when>
+            </conditional>
+            -->
+
+            <!-- DIRECTAG ADVANDED PARAMETERS-->
+            <conditional name="directtag">
+                <param name="directtag_advanced" type="select" label="DirectTag Options">
+                    <option value="yes">Advanced</option>
+                    <option value="no" selected="True">Default</option>
+                </param>
+                <when value="no" />
+                <when value="yes">
+                    <param name="directag_tag_length" type="integer" value="4" label="DirecTag tag length"/>
+                    <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence"/>
+                    <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered"/>
+                    <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge"/>
+                    <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance"/>
+                    <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode">
+                        <option value="0" selected="true">no deisotoping</option>
+                        <option value="1">precursor only</option>
+                        <option value="2">precursor and candidate</option>
+                    </param>
+                    <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses."/>
+                    <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix"/>
+                    <param name="directag_max_peak_count" type="integer" value="100" label="DirecTag max peak count"/>
+                    <param name="directag_max_tag_count" type="integer" value="10" label="DirecTag maximum tag count"/>
+                    <param name="directag_tic_cutoff" type="integer" value="100" label="DirecTag TIC cutoff in percent">
+                        <validator type="in_range" min="0" max="100" />
+                    </param>
+                    <param name="directag_complement_tolerance" type="float" value="0.1" label="DirecTag complement mz tolerance"/>
+                    <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step"/>
+                    <param name="directag_min_adjustment" type="float" value="-0.5" label="DirecTag minimum precursor adjustment"/>
+                    <param name="directag_max_adjustment" type="float" value="1.5" label="DirecTag maximum precursor adjustment"/>
+                    <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight"/>
+                    <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight"/>
+                    <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight"/>
+                    <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor"/>
+                    <param name="directag_ms_charge_state" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag use charge state from M spectrum"/>
+                </when>
+            </conditional>
+
+
+            <!-- METAMORPHEUS ADVANDED PARAMETERS-->
+            <conditional name="metamorpheus">
+                <param name="metamorpheus_advanced" type="select" label="MetaMorpheus Options">
+                    <option value="yes">Advanced</option>
+                    <option value="no" selected="True">Default</option>
+                </param>
+                <when value="no" />
+                <when value="yes">
+                    <conditional name="metamorpheus_search">
+                        <param name="metamorpheus_search_selector" type="select" label="MetaMorpheus: Search related options">
+                            <option value="yes" selected="True">Set Search parameters</option>
+                            <option value="no">Keep Default Search parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="meta_morpheus_search_type" type="select" label="MetaMorpheus search type">
+                                <option value="Classic" selected="true">Classic</option>
+                                <option value="Modern">Modern</option>
+                                <option value="NonSpecific">NonSpecific</option>
+                            </param>
+                            <param name="meta_morpheus_num_partitions" type="integer" value="1" label="MetaMorpheus number of partitions when indexing"/>
+                            <param name="meta_morpheus_dissociation_type" type="select" label="MetaMorpheus dissociation type">
+                                <option value="HCD" selected="true">HCD</option>
+                                <option value="CID">CID</option>
+                                <option value="ECD">ECD</option>
+                                <option value="ETD">ETD</option>
+                            </param>
+                            <param name="meta_morpheus_max_mods_for_peptide" type="integer" value="2" label="MetaMorpheus maximum modifications per peptide"/>
+                            <param name="meta_morpheus_meth" type="select" label="MetaMorpheus initiator methionine behavior">
+                                <option value="Undefined" >Undefined</option>
+                                <option value="Retain">Retain</option>
+                                <option value="Cleave">Cleave</option>
+                                <option value="Variable" selected="true">Variable</option>
+                            </param>
+                            <param name="meta_morpheus_score_cutoff" type="float" value="5.0" label="MetaMorpheus score cutoff"/>
+                            <param name="meta_morpheus_use_delta_score" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus use delta score"/>
+                            <param name="meta_morpheus_mass_diff_acceptor_type" type="select" label="MetaMorpheus mass difference acceptor type">
+                                <option value="Exact">Exact</option>
+                                <option value="OneMM" selected="true">OneMM</option>
+                                <option value="TwoMM">TwoMM</option>
+                                <option value="ThreeMM" >ThreeMM</option>
+                                <option value="PlusOrMinusThreeMM">PlusOrMinusThreeMM</option>
+                                <option value="ModOpen">ModOpen</option>
+                                <option value="Open">Open</option>
+                            </param>
+                            <param name="meta_morpheus_min_pep_length" type="integer" value="8"
+                                label="MetaMorpheus minimum peptide length" help="Minimum length for a peptide to be considered"/>
+                            <param name="meta_morpheus_max_pep_length" type="integer" value="30"
+                                label="MetaMorpheus maximum peptide length" help="Maximum length for a peptide to be considered"/>
+                        </when>
+                    </conditional>
+
+                    <conditional name="metamorpheus_output">
+                        <param name="metamorpheus_output_selector" type="select" label="MetaMorpheus: Output related options">
+                            <option value="yes" >Set Output parameters</option>
+                            <option value="no" selected="True">Keep Default Output parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="meta_morpheus_write_mzid" type="boolean" truevalue="1" falsevalue="0" checked="true" label="MetaMorpheus write mzid"/>
+                            <param name="meta_morpheus_write_pepxml" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus write pepxml"/>
+                        </when>
+                    </conditional>
+
+                    <conditional name="metamorpheus_deisotoping">
+                        <param name="metamorpheus_deisotoping_selector" type="select" label="MetaMorpheus: Deisotoing related options">
+                            <option value="yes" >Set Deisotoping parameters</option>
+                            <option value="no" selected="True">Keep Default Deisotoping parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="meta_morpheus_use_provided_prec" type="boolean" truevalue="1" falsevalue="0" checked="true" label="MetaMorpheus use provided precursor info"/>
+                            <param name="meta_morpheus_do_prec_deconv" type="boolean" truevalue="1" falsevalue="0" checked="true" label="MetaMorpheus do precursor deconvolution"/>
+                            <param name="meta_morpheus_deconv_int_ratio" type="float" value="3.0" label="MetaMorpheus deconvolution intensity ratio"/>
+                            <param name="meta_morpheus_deconv_mass_tol" type="float" value="4.0" label="MetaMorpheus score cutoff"/>
+                            <param name="meta_morpheus_deconv_mass_tol_type" type="select" label="MetaMorpheus deoconvolution mass tolerance type">
+                                <option value="PPM" selected="true">PPM</option>
+                                <option value="Absolute">Absolute</option>
+                            </param>
+                        </when>
+                    </conditional>
+
+
+                    <conditional name="metamorpheus_proteingrouping">
+                        <param name="metamorpheus_proteingrouping_selector" type="select" label="MetaMorpheus: Protein grouping related options">
+                            <option value="yes" >Set Protein grouping parameters</option>
+                            <option value="no" selected="True">Keep Default Protein grouping parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="meta_morpheus_mod_peptides_are_different" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus modified peptides are different"/>
+                            <param name="meta_morpheus_no_one_hit_wonders" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus exclude one hit wonders"/>
+                        </when>
+                    </conditional>
+
+
+
+                    <conditional name="metamorpheus_peaktrimming">
+                        <param name="metamorpheus_peaktrimming_selector" type="select" label="MetaMorpheus: Peak trimming related options">
+                            <option value="yes" >Set Peak trimming parameters</option>
+                            <option value="no" selected="True">Keep Default Peak trimming parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                          <param name="meta_morpheus_trim_ms1" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus trim MS1 peaks"/>
+                          <param name="meta_morpheus_trim_msms" type="boolean" truevalue="1" falsevalue="0" checked="true" label="MetaMorpheus trim MSMS peaks"/>
+                          <param name="meta_morpheus_num_peaks_per_window" type="integer" value="200" label="MetaMorpheus number of peaks per window" />
+                          <param name="meta_morpheus_min_allowed_int_ratio_to_base_peak" type="float" value="0.01" label="MetaMorpheus minimum allowed intensity ratio to base peak"/>
+                          <param name="meta_morpheus_window_with_thompson" type="integer" optional="true" label="MetaMorpheus window width in Thompson" />
+                          <param name="meta_morpheus_num_windows" type="integer" optional="true" label="MetaMorpheus number of windows" />
+                          <param name="meta_morpheus_norm_across_all_windows" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus normalize peaks across all windows"/>
+                        </when>
+                    </conditional>
+
+                    <conditional name="metamorpheus_silico">
+                        <param name="metamorpheus_silico_selector" type="select" label="MetaMorpheus: Silico digestion related options">
+                            <option value="yes" >Set Silico digestion parameters</option>
+                            <option value="no" selected="True">Keep Default Silico digestion parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="meta_morpheus_frag_term" type="select" label="MetaMorpheus fragmentation terminus">
+                                <option value="Both" selected="true">Both</option>
+                                <option value="N">N</option>
+                                <option value="C">C</option>
+                            </param>
+                            <param name="meta_morpheus_max_frag_size" type="float" value="30000.0" label="MetaMorpheus maximum fragmentation size"/>
+                            <param name="meta_morpheus_search_target" type="boolean" truevalue="1" falsevalue="0" checked="true" label="MetaMorpheus search target sequences"/>
+                            <param name="meta_morpheus_decoy_type" type="select" label="MetaMorpheus decoy type">
+                                <option value="None" selected="true">None</option>
+                                <option value="Reverse">Reverse</option>
+                                <option value="Slide">Slide</option>
+                            </param>
+                            <param name="meta_morpheus_max_mod_isoforms" type="integer" value="1024" label="MetaMorpheus maximum modified isoforms" />
+                            <param name="meta_morpheus_min_variant_depth" type="integer" value="1" label="MetaMorpheus minimum variant depth" />
+                            <param name="meta_morpheus_max_hetrozygous_var" type="integer" value="4" label="MetaMorpheus maximum hetrozygous variants" />
+                        </when>
+                    </conditional>
+
+                    <conditional name="metamorpheus_gptm">
+                        <param name="metamorpheus_gptm_selector" type="select" label="MetaMorpheus: G-PTM search related options">
+                            <option value="yes" >Set G-PTM search parameters</option>
+                            <option value="no" selected="True">Keep Default G-PTM search parameters</option>
+                        </param>
+                        <when value="no" />
+                        <when value="yes">
+                            <param name="meta_morpheus_gptm" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus run G-PTM"/>
+                            <param name="meta_morpheus_gptm_categories" type="select"  display="checkboxes" multiple="True"
+                              label="MetaMorpheus G-PTM categories to include in the G-PTM search">
+                                <option value="common_fixed_variable" >Common Fixed and Variable</option>
+                                <option value="common_biological" selected="true">Common Biological</option>
+                                <option value="common_artifact" selected="true">Common Artifact</option>
+                                <option value="metal" selected="true">Metal</option>
+                                <option value="less_common">Less Common</option>
+                                <option value="labeling">Labeling</option>
+                                <option value="subs_1n">Substitution (1 Nucleotide)</option>
+                                <option value="subs_2n">Substitution (2+ Nucleotides)</option>
+                                <option value="other">Other</option>
+                            </param>
+                        </when>
+                    </conditional>
+
+
+                </when>
+            </conditional>
+
+
+            <!-- NOVOR ADVANDED PARAMETERS-->
+            <conditional name="novor">
+                <param name="novor_advanced" type="select" label="Novor Options">
+                    <option value="yes">Advanced</option>
+                    <option value="no" selected="True">Default</option>
+                </param>
+                <when value="no" />
+                <when value="yes">
+                    <param name="novor_fragmentation" type="select" label="Novor fragmentation method">
+                        <option value="HCD" selected="True">HCD</option>
+                        <option value="CID">CID</option>
+                    </param>
+                    <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra">
+                        <option value="Trap" >Trap</option>
+                        <option value="TOF" >TOF</option>
+                        <option value="FT" selected="True">FT</option>
+                    </param>
+                </when>
+            </conditional>
+
+            <!-- PEPNOVO+ ADVANDED PARAMETERS-->
+            <conditional name="pepnovo">
+                <param name="pepnovo_advanced" type="select" label="PepNovo+ Options">
+                    <option value="yes">Advanced</option>
+                    <option value="no" selected="True">Default</option>
+                </param>
+                <when value="no" />
+                <when value="yes">
+                    <param name="pepnovo_hitlist_length" type="integer" value="10" label="PepNovo+ number of de novo solutions [0-2000], default is '10'.">
+                      <validator type="in_range" min="0" max="2000" />
+                    </param>
+                    <param name="pepnovo_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="PepNovo+ estimate precursor charge option."/>
+                    <param name="pepnovo_correct_prec_mass" type="boolean" truevalue="1" falsevalue="0" checked="true" label="PepNovo+ correct precursor mass option."/>
+                    <param name="pepnovo_discard_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="PepNovo+ discard low quality spectra option."/>
+                    <param name="pepnovo_generate_blast" type="boolean" truevalue="1" falsevalue="0" checked="false" label="PepNovo+ generate a BLAST query."/>
+                </when>
+            </conditional>
+
+            <!-- PNOVO+ ADVANDED PARAMETERS-->
+            <conditional name="pnovo">
+                <param name="pnovo_advanced" type="select" label="pNovo+ Options">
+                    <option value="yes">Advanced</option>
+                    <option value="no" selected="True">Default</option>
+                </param>
+                <when value="no" />
+                <when value="yes">
+                    <param name="pnovo_num_peptides" type="integer" value="10" label="pNovo+ number of peptides per spectrum, default is '10'."/>
+                    <param name="pnovo_lower_prec" type="integer" value="300" label="pNovo+ minimum precursor mass, default is '300'."/>
+                    <param name="pnovo_upper_prec" type="integer" value="5000" label="pNovo+ maximum precursor mass, default is '5000'."/>
+                    <param name="pnovo_activation" type="select" label="pNovo+ activation type (HCD, CID or EDT)">
+                        <option value="HCD" selected="True">HCD</option>
+                        <option value="CID" >CID</option>
+                        <option value="EDT">EDT</option>
+                    </param>
+                </when>
+            </conditional>
+        </section>
+
+
+
+
+
+
+
+
+
+
+        <!-- ADVANCED PARAMETERS -->
+
+        <section name="advanced_options" expanded="false" title="Show/Hide advanced options">
+
+            <!-- SPECTRUM ANNOTATION -->
+
+            <section name="spectrum_annotation_options" expanded="false" title="Spectrum Annotation Options">
+                <param name="annotation_level" label="Percent of the possible annotations relative to the most intensive peak" help="The intensity percentile to consider for annotation, e.g. 0.75 means that the 25% most intense peaks will be annotated, default is 0.75." value="0.75" type="float">
+                    <validator type="in_range" min="0" max="1" />
+                </param>
+                <param name="annotation_mz_tolerance" label="Fragment ion annotation accuracy" help=" The m/z tolerance to annotate peaks, default is equal to the search settings MS2 tolerance." value="10" type="float" />
+                <param name="annotation_high_resolution" label="High resolution" help="The most accurate peak will be selected within the m/z tolerance if chosen" truevalue="1" falsevalue="0" checked="true" type="boolean"/>
+            </section>
+
+            <!-- SEQUENCE MATCHING -->
+
+            <section name="sequence_matching_options" expanded="false" title="Sequence Matching Options">
+                <param name="sequence_matching_type" label="The peptide to protein sequence matching type" type="select">
+                    <option value="0">Character Sequence</option>
+                    <option value="1">Amino Acids</option>
+                    <option value="2" selected="true">Indistinguishable Amino Acids</option>
+                </param>
+                <param name="sequence_matching_x" label="The maximal share of Xs in a sequence" help="0.25 means 25% of Xs" value="0.25" type="float">
+                    <validator type="in_range" min="0" max="1" />
+                </param>
+                <param name="sequence_matching_enzymatic_tags" label="Tags should only be mapped to enzymatic peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
+                <param name="sequence_matching_max_ptms_per_tag" label="The maximum number of PTMs per peptide when mapping tags" type="integer" value="3">
+                    <validator type="in_range" min="0" max="2147483647" />
+                </param>
+                <param name="sequence_matching_min_amino_acid_score" label="The minimum amino acid score when mapping tags" type="integer" value="30">
+                    <validator type="in_range" min="0" max="2147483647" />
+                </param>
+                <param name="sequence_matching_min_tag_length" label="The minimum tag length when mapping tags" type="integer" value="3">
+                    <validator type="in_range" min="0" max="2147483647" />
+                </param>
+
+            </section>
+
+
+            <!-- IMPORT FILTERS -->
+
+            <section name="import_filters_options" expanded="false" title="Import filters">
+                    <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="8" />
+                    <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" />
+                    <param name="max_precursor_error" type="float" label="Maximum Precursor Error" help="The higher precursor mass error allowed in order to filter out outliers" value="10" />
+                    <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select" >
+                        <option value="1">ppm</option>
+                        <option value="0">Daltons</option>
+                    </param>
+                    <param name="missed_cleavages_min" type="integer" label="Minimal number of missed cleavages to consider when importing identification files" help="Default is no filter" value="" optional="true"/>
+                    <param name="missed_cleavages_max" type="integer" label="Maximal number of missed cleavages to consider when importing identification files" help="Default is no filter" value="" optional="true"/>
+                    <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" help="If true, peptides presenting unrecognized PTMs will be excluded" type="boolean" truevalue="1" falsevalue="0" checked="true" />
+            </section>
+
+
+            <!-- PTM LOCALIZATION -->
+
+            <section name="ptm_localization_options" expanded="false" title="PTM Localizacion">
+                <conditional name="ptm_score">
+                    <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
+                        <option value="1" selected="True">PhosphoRS</option>
+                        <option value="2">None</option>
+                    </param>
+                    <when value="1">
+                        <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
+                        <param name="ptm_threshold" label="The threshold to use for the PTM scores" value="95.0" type="float"
+                            help="Automatic mode will be used if not set" />
+                    </when>
+                    <when value="2" />
+                </conditional>
+                <param name="ptm_sequence_matching_type" type="select" label="The modification to peptide sequence matching type." >
+                     <option value="0">Character Sequence</option>
+                     <option value="1" selected="true">Amino Acids</option>
+                     <option value="2">Indistinguishable Amino Acids</option>
+                </param>
+                <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
+            </section>
+
+
+            <!-- GENE ANNOTATION -->
+
+            <section name="gene_annotation_options" expanded="false" title="Gene Annotation">
+                <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false"
+                    label="gene mappings will be used and saved along with the project (UniProt databases only)"
+                    help="This should only be enabled for UniProt databaases" />
+                <param name="update_gene_mapping" type="boolean" truevalue="-updateGeneMapping 1" falsevalue="-updateGeneMapping 0" checked="false"
+                    label="Update gene mappings automatically from Ensembl (UniProt databases only)"
+                help="This should only be enabled for UniProt databaases" />
+            </section>
+
+
+            <!-- PROTEIN INFERENCE -->
+
+            <section name="protein_inference_options" expanded="false" title="Protein Inference">
+                <conditional name="simplify_protein_groups_conditional">
+                    <param name="simplify_protein_groups_selector" type="select" label="Simplify protein groups">
+                        <option value="yes" selected="True">Yes</option>
+                        <option value="no">No</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param name="simplify_protein_groups_evidence" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                            label="Based on Uniprot evidence level"/>
+                        <param name="simplify_protein_groups_confidence" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                            label="Based on the peptide confidence"/>
+                        <param name="simplify_protein_groups_confidence_threshold" value="0.05" type="float"
+                            label="Confidence below which a peptide is ignored"/>
+                        <param name="simplify_protein_groups_enzymaticity" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                            label="Based on Enzymaticity"/>
+                        <param name="simplify_protein_groups_variant" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                            label="Based on Variant Mapping"/>
+                    </when>
+                </conditional>
+                <param name="simplify_protein_pi_modifications" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                    label="Account for modifications when mapping peptides to proteins"/>
+            </section>
+
+            <!-- VALIDATION LEVELS -->
+
+            <section name="validation_levels_options" expanded="false" title="Validation Levels">
+                <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float">
+                    <validator type="in_range" min="0" max="100" />
+                </param>
+                <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float">
+                    <validator type="in_range" min="0" max="100" />
+                </param>
+                <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float">
+                    <validator type="in_range" min="0" max="100" />
+                </param>
+            </section>
+
+
+            <!-- FRACTION ANALYSIS -->
+
+            <section name="fraction_analysis_options" expanded="false" title="Fraction Analysis">
+                <param name="protein_fraction_mw_confidence" value="95.0" type="float"
+                  label="Minimum confidence required for a protein in the fraction MW plot (in percentage)"
+                    help="default 95%: '95.0'">
+                    <validator type="in_range" min="0" max="100" />
+                </param>
+            </section>
+
+
+            <!-- DATABASE PROCESSING OPTIONS -->
+
+            <section name="database_processing_options" expanded="false" title="Database Processing Options">
+                <conditional name="decoy_conditional">
+                    <param name="create_decoy_selector" type="select"
+                      label="Create a concatenated target/decoy database before running PeptideShaker"
+                      help="Selecting this option will help PeptideShaker calculate FDR values">
+                        <option value="yes" selected="True">Yes</option>
+                        <option value="no" >No</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param name="decoy_tag" type="text" value="-REVERSED" label="The decoy flag">
+                        </param>
+                        <param name="decoy_type" type="select" label="Location of the decoy flag: prefix or suffix">
+                            <option value="0">Prefix</option>
+                            <option value="1" selected="True">Suffix</option>
+                        </param>
+                    </when>
+                </conditional>
+                <param name="decoy_file_tag" type="text" value="_concatenated_target_decoy" label="Target decoy suffix.">
+                </param>
+            </section>
+
+        </section>
+
+    </inputs>
+    <outputs>
+        <data name="Identification_Parameters_File" format="json" from_work_dir="IdentificationParametersOutput.par" label="${tool.name}: PAR file" />
+    </outputs>
+    <tests>
+
+        <!-- Test that default parameters generates a standard par file -->
+        <test>
+            <param name="xtandem_advanced" value="yes"/>
+            <param name="xtandem_refine_selector" value="no"/>
+            <output name="Identification_Parameters_File" file="Identification_Parameters_default.par" ftype="json" compare="sim_size" delta="1000" />
+        </test>
+        <!-- Test specific parameters with modifications -->
+        <test>
+            <param name="precursor_ion_tol" value="100"/>
+            <param name="fixed_modifications" value="Carbamidomethylation of C"/>
+            <param name="variable_modifications" value="Oxidation of M"/>
+            <param name="min_charge" value="1"/>
+            <param name="max_charge" value="3"/>
+            <param name="xtandem_advanced" value="yes"/>
+            <param name="xtandem_refine_selector" value="yes"/>
+            <output name="Identification_Parameters_File" file="Identification_Parameters_specific.par" ftype="json" compare="sim_size" delta="1000" />
+        </test>
+
+    </tests>
+    <help>
+**What it does**
+
+Creates a parameters file (.par) which can be used independently by SearchGUI or PeptideShaker apps.
+
+A FASTA file with decoy sequences generated by FastaCLI is recommended if SearchGUI and PeptideShaker are going to use the output of this tool.
+
+    </help>
+    <expand macro="citations" />
+</tool>
diff -r 7fdd9119cc4f -r bb0130ff73ce macros.xml
--- a/macros.xml	Thu Feb 20 05:51:38 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,162 +0,0 @@
-<macros>
-    <import>macros_modifications.xml</import>
-    <xml name="stdio">
-        <stdio>
-            <exit_code range="1:" level="fatal" description="Job Failed" />
-	    <!--	    <regex match="java.lang.OutOfMemoryError" level="fatal_oom" description="Java memory Exception"/>
-	    <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/>
-	    <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/>
-	    <regex match="Native memory allocation (malloc) failed" level="fatal_oom" description="Java memory Exception"/>-->
-	    <regex match="java.*Exception" level="fatal" description="Java Exception"/>
-            <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
-	    <regex match="PeptideShaker ran out of memory" level="fatal" description="JVM Error"/>
-	    <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
-        </stdio>
-    </xml>
-
-    <token name="@GENERAL_PARAMETERS@">
-            -frag_tol '${precursor_options.fragment_tol}'
-            -frag_ppm '${precursor_options.fragment_tol_units}'
-            -prec_tol '${precursor_options.precursor_ion_tol}'
-            -prec_ppm '${precursor_options.precursor_ion_tol_units}'
-
-            -min_charge $precursor_options.min_charge
-            -max_charge $precursor_options.max_charge
-            -fi $precursor_options.forward_ion
-            -ri $precursor_options.reverse_ion
-            -min_isotope ${precursor_options.min_isotope}
-            -max_isotope ${precursor_options.max_isotope}
-            #if $protein_digest_options.digestion.cleavage == 'default':
-              ## -enzyme "Trysin"
-              -mc $protein_digest_options.digestion.missed_cleavages
-            #elif $protein_digest_options.digestion.cleavage == '0' and len($protein_digest_options.digestion.digests) > 0:
-              #set $enzymes = []
-              #set $missed_cleavages = []
-              ## #set $specificities = []
-              #for $i, $digest in enumerate($protein_digest_options.digestion.digests):
-                  #silent $enzymes.append(str($digest.enzyme))
-                  #silent $missed_cleavages.append(str($digest.missed_cleavages))
-                  ## #silent $specificities.append(str($digest.specificity))
-              #end for
-              -enzyme "#echo ','.join($enzymes)#"
-              -mc "#echo ','.join($missed_cleavages)#"
-              ## -specificity "#echo ','.join($specificities)#"
-            #else:
-               -digestion $protein_digest_options.digestion.cleavage
-            #end if
-
-            #set $fixed_mods_str = $protein_modification_options.fixed_modifications or ''
-            #set $variable_mods_str = $protein_modification_options.variable_modifications or ''
-            #if $fixed_mods_str
-                -fixed_mods "$fixed_mods_str"
-            #end if
-            #if $variable_mods_str
-                -variable_mods "$variable_mods_str"
-            #end if
-
-    </token>
-
-    <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
-    <token name="@SEARCHGUI_VERSION@">3.3.10</token>
-    <token name="@PEPTIDESHAKER_VERSION@">1.16.36</token>
-    <xml name="general_options">
-
-        <section name="protein_digest_options" expanded="false" title="Protein Digestion Options">
-            <conditional name="digestion">
-                <param name="cleavage" type="select" label="Digestion">
-                    <option value="0">Select Enzymes</option>
-                    <option value="1">Unspecific Cleavage</option>
-                    <option value="2">Whole Protein</option>
-                </param>
-                <when value="0">
-                    <repeat name="digests" min="1" title="Enzymes">
-                        <param name="enzyme" type="select" label="Enzyme"
-                            help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
-                            <option value="Trypsin">Trypsin</option>
-                            <option value="Trypsin (no P rule)">Trypsin (no P rule)</option>
-                            <option value="Arg-C">Arg-C</option>
-                            <option value="Arg-C (no P rule)">Arg-C</option>
-                            <option value="Arg-N">Arg-N</option>
-                            <option value="Glu-C">Glu-C</option>
-                            <option value="Lys-C">Lys-C</option>
-                            <option value="Lys-C (no P rule)">Lys-C (no P rule)</option>
-                            <option value="Lys-N">Lys-N</option>
-                            <option value="Asp-N">Asp-N</option>
-                            <option value="Asp-N (ambic)">Asp-N (ambic)</option>
-                            <option value="Chymotrypsin">Chymotrypsin</option>
-                            <option value="Chymotrypsin (no P rule)">Chymotrypsin (no P rule)</option>
-                            <option value="Pepsin A">Pepsin A</option>
-                            <option value="CNBr">CNBr</option>
-                            <option value="Thermolysin">Thermolysin</option>
-                            <option value="LysargiNase">LysargiNase</option>
-                        </param>
-                        <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
-                            help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
-                        <!--
-                        <param name="specificity" type="select" label="Specificity">
-                            <option value="0" selected="true">Specific at both termini</option>
-                            <option value="1">Semi-Specific - one terminus</option>
-                            <option value="2">Specific at the N-terminus only</option>
-                            <option value="3">Specific at the C-terminus only</option>
-                        </param>
-                        -->
-                    </repeat>
-                </when>
-                <when value="1"/>
-                <when value="2"/>
-            </conditional>
-        </section>
-
-        <section name="precursor_options" expanded="false" title="Precursor Options">
-            <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
-                help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
-                <option value="1">Parts per million (ppm)</option>
-                <option value="0">Daltons</option>
-            </param>
-            <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance"
-                help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
-            <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units"
-                help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
-                <option value="1">Parts per million (ppm)</option>
-                <option value="0" selected="true">Daltons</option>
-            </param>
-            <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance"
-                help="Provide error value for fragment ions, based on instrument used"/>
-            <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
-            <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
-            <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
-                <option value="a">a</option>
-                <option value="b" selected="true">b</option>
-                <option value="c">c</option>
-            </param>
-            <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
-                <option value="x">x</option>
-                <option value="y" selected="true">y</option>
-                <option value="z">z</option>
-            </param>
-            <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />
-            <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />
-        </section>
-
-        <section name="protein_modification_options" expanded="false" title="Protein Modification Options">
-            <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
-                help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
-                <expand macro="modifications"/>
-            </param>
-            <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true"
-                help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">                
-                <expand macro="modifications"/>
-            </param>
-        </section>
-
-    </xml>
-
-    <xml name="citations">
-        <citations>
-            <citation type="doi">10.1186/1471-2105-12-70</citation>
-            <citation type="doi">10.1002/pmic.201000595</citation>
-            <citation type="doi">doi:10.1038/nbt.3109</citation>
-        </citations>
-    </xml>
-
-</macros>
diff -r 7fdd9119cc4f -r bb0130ff73ce macros_basic.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros_basic.xml	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,24 @@
+<macros>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" description="Job Failed" />
+            <regex match="java.*Exception" level="fatal" description="Java Exception"/>
+            <regex match="Could not reserve enough space for * object heap" level="fatal" description="Out of memory"/>
+            <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
+            <regex match="PeptideShaker ran out of memory" level="fatal" description="JVM Error"/>
+            <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
+        </stdio>
+    </xml>
+    <token name="@SEARCHGUI_MAJOR_VERSION@">4</token>
+    <token name="@SEARCHGUI_VERSION@">4.0.7</token>
+    <token name="@SEARCHGUI_VERSION_SUFFIX@">0</token>
+    <token name="@PEPTIDESHAKER_VERSION@">2.0.5</token>
+    <token name="@PEPTIDESHAKER_VERSION_SUFFIX@">3</token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/1471-2105-12-70</citation>
+            <citation type="doi">10.1002/pmic.201000595</citation>
+            <citation type="doi">doi:10.1038/nbt.3109</citation>
+        </citations>
+    </xml>
+</macros>
diff -r 7fdd9119cc4f -r bb0130ff73ce peptide_shaker.xml
--- a/peptide_shaker.xml	Thu Feb 20 05:51:38 2020 -0500
+++ b/peptide_shaker.xml	Fri Jan 15 14:06:27 2021 +0000
@@ -1,12 +1,14 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@.3">
+<tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@+galaxy@PEPTIDESHAKER_VERSION_SUFFIX@">
     <description>
         Perform protein identification using various search engines based on results from SearchGUI
     </description>
     <macros>
-        <import>macros.xml</import>
+        <import>macros_basic.xml</import>
+        <import>macros_modifications.xml</import>
     </macros>
     <requirements>
         <requirement type="package" version="@PEPTIDESHAKER_VERSION@">peptide-shaker</requirement>
+        <requirement type="package">unzip</requirement>
     </requirements>
     <expand macro="stdio" />
 
@@ -17,7 +19,7 @@
         #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
         #set $temp_stderr = "peptideshaker_stderr"
         #set $bin_dir = "bin"
-
+        #set $exporting_followup_boolean = False
 
         mkdir output_reports &&
         cwd=`pwd` &&
@@ -26,67 +28,70 @@
         echo "" > $temp_stderr &&
 
         ln -s '$searchgui_input' searchgui_input.zip &&
-        jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&
-
 
-        peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI
-            --exec_dir="\$cwd/${bin_dir}"
-            -temp_folder \$cwd/PathSettingsCLI
-            -log \$cwd/peptideshaker.log &&
+        ## OPTIONAL MAIN PARAMETERS
+        ## If we have a specific Identification Parameters file to use, we will use it instead of the one provided in the search_gui file
+        #if $optional_main_parameters.input_optional_identification_parameters:
+            cp '${optional_main_parameters.input_optional_identification_parameters}' SEARCHGUI_IdentificationParameters.par &&
+        #else:
+            jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&
+        #end if
+        ## Optional Fasta file
+        #if $optional_main_parameters.input_fasta_file:
+            ## copy the input .fasta file to the working folder
+            cp '${optional_main_parameters.input_fasta_file}' './input_fasta_file.fasta' &&
+        #end if
+        ## Optional Spectrum files: if the user specified input spectra files, we use them
+        ## NOTE: != None DOES NOT SEEM TO WORK ANYMORE ON MODERN GALAXIES
+        #if str($optional_main_parameters.input_optional_spectrum_files) != 'None' and str($optional_main_parameters.input_optional_spectrum_files) != '':
+            mkdir peaklist_input_files &&
+            #for $peak_list_file in $optional_main_parameters.input_optional_spectrum_files:
+                #if $peak_list_file.is_of_type("mgf"):
+                    #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mgf", "") + ".mgf"
+                #else if $peak_list_file.is_of_type("mzml"):
+                    #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mzml", "") + ".mzml"
+                #end if
+                ln -s -f '${peak_list_file}' 'peaklist_input_files/${input_name}' &&
+            #end for
+        #end if
 
-        #if str($exporting_options.output_reports) != "None"
+        #if str($exporting_options.output_reports) != "None" and str($exporting_options.output_reports) != ""
             #set $output_reports_list = set(str($exporting_options.output_reports).split(','))
         #else
             #set $output_reports_list = set()
-        #end if
+	      #end if
 
         ######################
         ## PeptideShakerCLI ##
         ######################
         (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI
-            --exec_dir="\$cwd/${bin_dir}"
             -gui 0
             -temp_folder \$cwd/PeptideShakerCLI
-            -experiment '$exp_str'
-            -sample '$samp_str'
-            -replicate 1
+            -log \$cwd/resources
+            -reference '$exp_str'
             -identification_files \$cwd/searchgui_input.zip
             -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
-            -out \$cwd/peptideshaker_output.cpsx
-            #if $exporting_options.zip_conditional.zip_output_boolean == 'zip':
-                -zip \$cwd/peptideshaker_output.zip
-            #end if
-            -threads "\${GALAXY_SLOTS:-12}"
-
-        ##Optional processing parameters:
-        #if $processing_options.processing_options_selector == "yes"
-            -protein_fdr "${processing_options.protein_fdr}"
-            -peptide_fdr "${processing_options.peptide_fdr}"
-            -psm_fdr "${processing_options.psm_fdr}"
-            -ptm_score "${processing_options.ptm_score.ptm_score_selector}"
-            #if $processing_options.ptm_score.ptm_score_selector == 1
-                -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
-                #if str($processing_options.ptm_score.ptm_threshold) != ''
-                    -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
-                #end if
-            #end if
-            -ptm_alignment "${processing_options.ptm_alignment}"
-            -ptm_sequence_matching_type "${processing_options.ptm_sequence_matching_type}"
-            -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
+        #if $optional_main_parameters.input_fasta_file:
+            -fasta_file './input_fasta_file.fasta'
+        #end if
+        #if str($optional_main_parameters.input_optional_spectrum_files) != 'None' and str($optional_main_parameters.input_optional_spectrum_files) != '':
+            -spectrum_files  \$cwd/peaklist_input_files
         #end if
 
-        ##Optional filtering parameters:
-        #if $filtering_options.filtering_options_selector == "yes":
-            -import_peptide_length_min "${filtering_options.min_peptide_length}"
-            -import_peptide_length_max "${filtering_options.max_peptide_length}"
-            -import_precurosor_mz "${filtering_options.max_precursor_error}"
-            -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}"
-            ##-max_xtandem_e "${filtering_options.max_xtandem_e}"
-            ##-max_omssa_e "${filtering_options.max_omssa_e}"
-            ##-max_mascot_e "${filtering_options.max_mascot_e}"
-            -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
+        #if $exporting_options.zip_conditional.zip_output_boolean == 'zip':
+            -zip \$cwd/peptideshaker_output.zip
+            -out \$cwd/peptideshaker_output.psdb
+            #if $exporting_options.zip_conditional.export_mgf_when_zip:
+                -output_mgf 1
+    	    #end if
+        #else:
+            #if $exporting_options.zip_conditional.export_psdb:
+                -out \$cwd/peptideshaker_output.psdb
+            #end if
         #end if
 
+            -threads "\${GALAXY_SLOTS:-12}"
+
         ##################################
         ## mzidCLI options ##
         ##################################
@@ -94,19 +99,19 @@
         #if $exporting_options.mzidentml_conditional.mzidentml_creation == 1:
             -output_file \$cwd/output.mzid
             -include_sequences ${exporting_options.mzidentml_conditional.include_sequences}
-            #if $contact_options.contact_options_selector == "yes":
-                -contact_first_name "$contact_options.contact_first_name"
-                -contact_last_name "$contact_options.contact_last_name"
-                -contact_email "$contact_options.contact_email"
-                -contact_address "$contact_options.contact_address"
-                #if str($contact_options.contact_url).strip() != '':
-                    -contact_url = "$contact_options.contact_url"
+            #if $exporting_options.mzidentml_conditional.contact_options.contact_options_selector == "yes":
+                -contact_first_name "$exporting_options.mzidentml_conditional.contact_options.contact_first_name"
+                -contact_last_name "$exporting_options.mzidentml_conditional.contact_options.contact_last_name"
+                -contact_email "$exporting_options.mzidentml_conditional.contact_options.contact_email"
+                -contact_address "$exporting_options.mzidentml_conditional.contact_options.contact_address"
+                #if str($exporting_options.mzidentml_conditional.contact_options.contact_url).strip() != '':
+                    -contact_url = "$exporting_options.mzidentml_conditional.contact_options.contact_url"
                 #end if
-                -organization_name "$contact_options.organization_name"
-                -organization_email "$contact_options.organization_email"
-                -organization_address "$contact_options.organization_address"
-                #if str($contact_options.organization_url).strip() != '':
-                    -organization_url = "$contact_options.organization_url"
+                -organization_name "$exporting_options.mzidentml_conditional.contact_options.organization_name"
+                -organization_email "$exporting_options.mzidentml_conditional.contact_options.organization_email"
+                -organization_address "$exporting_options.mzidentml_conditional.contact_options.organization_address"
+                #if str($exporting_options.mzidentml_conditional.contact_options.organization_url).strip() != '':
+                    -organization_url = "$exporting_options.mzidentml_conditional.contact_options.organization_url"
                 #end if
             #else:
                 -contact_first_name "Proteomics"
@@ -119,23 +124,84 @@
             #end if
         #end if
 
-        ##################################
-        ## PeptideShaker Report options ##
-        ##################################
+        ####################################################################
+        ##    PeptideShaker Identification Features Reports options       ##
+        ####################################################################
         ## Generate Reports if the user has selected one of the 11 additional reports
         #if len($output_reports_list) > 0
                 -out_reports \$cwd/output_reports
                 -reports #echo ','.join($output_reports_list)#
         #end if
 
+        ####################################################
+        ##    PeptideShaker Follow-Up Analysis options    ##
+        ####################################################
+        ## TODO: When done in the app, export graph databases, TPP export, recalibrate espectra
+
+        #if $exporting_options.followup_conditional.followup_conditional_selector == "yes"
+            #if $exporting_options.followup_conditional.followup_export_spectra != "off"
+                #set $exporting_followup_boolean = True
+                -spectrum_folder \$cwd/output_reports -psm_type $exporting_options.followup_conditional.followup_export_spectra
+            #end if
+            #if $exporting_options.followup_conditional.followup_export_accession_numbers != "off"
+                #set $exporting_followup_boolean = True
+                -accessions_file \$cwd/output_reports/proteins_accession_numbers.txt -accessions_type $exporting_options.followup_conditional.followup_export_accession_numbers
+            #end if
+            #if $exporting_options.followup_conditional.followup_export_sequences != "off"
+                #set $exporting_followup_boolean = True
+                -sequences_file \$cwd/output_reports/proteins_sequences.fasta -sequences_type $exporting_options.followup_conditional.followup_export_sequences
+            #end if
+            #if $exporting_options.followup_conditional.followup_export_proteoforms != "off"
+                #set $exporting_followup_boolean = True
+                -proteoforms_file \$cwd/output_reports/proteins_proteoforms.txt
+            #end if
+            #if $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_selector != "off"
+                #set $exporting_followup_boolean = True
+                -progenesis_file \$cwd/output_reports/progenesis.txt -progenesis_type $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_selector
+                #if $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_selector == "3"
+                  #set $progenesis_ptms = $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_ptms or ''
+                  #if $progenesis_ptms
+                    -progenesis_ptms "$progenesis_ptms"
+                  #end if
+                #end if
+            #end if
+            #if $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_selector != "off"
+                #set $exporting_followup_boolean = True
+                -inclusion_list_file \$cwd/output_reports/inclusion_list.txt -inclusion_list_format $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_selector
+                #set $peptide_filters = $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_peptide_filters or ''
+                #if $peptide_filters
+                  -inclusion_list_peptide_filters "$peptide_filters"
+                #end if
+                #set $protein_filters = $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_protein_filters or ''
+                #if $protein_filters
+                  -inclusion_list_protein_filters "$protein_filters"
+                #end if
+                #if $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_rt_window
+                  -inclusion_list_rt_window $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_rt_window
+                #end if
+            #end if
+        #end if
+
         2>> $temp_stderr)
 
         ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them
-        #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip:
-            && unzip \$cwd/peptideshaker_output.zip 'reports/*' -d \$cwd/output_reports
+        #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip and (len(output_reports_list)>0 or $exporting_followup_boolean):
+            ## This unzipping command creates a reports folder into the current folder!
+            && unzip \$cwd/peptideshaker_output.zip "reports/*" -d \$cwd
+            && mv reports/* output_reports
+            && rm -r reports
         #end if
 
-        #if len($output_reports_list)>0:
+        ## If the user chose to export mgf file/s out of the zip file
+        #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_mgf_when_zip:
+          && mkdir output_mgf
+          && mkdir output_cui
+          && mv \$cwd/*.mgf output_mgf
+          && mv \$cwd/*.cui output_cui
+	      #end if
+
+        ## Renaming identification features reports to findable names and moving them to the root folder
+	      #if len(output_reports_list)>0:
             #if '0' in $output_reports_list:
                 && find \$cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
             #end if
@@ -174,6 +240,25 @@
             #end if
         #end if
 
+        ## Moving followup analysis to the root folder (it is necessary if zip option was not chosen, or it was chosen but also exporting out of the zip)
+        #if $exporting_options.followup_conditional.followup_conditional_selector == "yes" and ($exporting_options.zip_conditional.zip_output_boolean != 'zip' or ($exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip)):
+            ## Spectrum analysis are already expected to be into the output_reports folder itself
+            #if $exporting_options.followup_conditional.followup_export_accession_numbers != "off"
+                && mv \$cwd/output_reports/proteins_accession_numbers.txt \$cwd/proteins_accession_numbers.txt
+            #end if
+            #if $exporting_options.followup_conditional.followup_export_sequences != "off"
+                && mv \$cwd/output_reports/proteins_sequences.fasta \$cwd/proteins_sequences.fasta
+            #end if
+            #if $exporting_options.followup_conditional.followup_export_proteoforms != "off"
+                && mv \$cwd/output_reports/proteins_proteoforms.txt \$cwd/proteins_proteoforms.txt
+            #end if
+            #if $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_selector != "off"
+                && mv \$cwd/output_reports/progenesis.txt \$cwd/progenesis.txt
+            #end if
+            #if $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_selector != "off"
+                && mv \$cwd/output_reports/inclusion_list.txt \$cwd/inclusion_list.txt
+            #end if
+        #end if
         && cat $temp_stderr 2>&1;
 ]]>
     </command>
@@ -184,120 +269,202 @@
                 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
             </options>
         </param>
-        <conditional name="processing_options">
-            <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options">
-                <option value="no" selected="True">Default Processing Options</option>
-                <option value="yes">Advanced Processing Options</option>
-            </param>
-            <when value="no" />
-            <when value="yes">
-                <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
-                <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
-                <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
-                <param name="protein_fraction_mw_confidence" value="95.0" type="float" label="Minimum confidence required for a protein in the fraction MW plot"
-                    help="default 95%: '95.0'" />
-                <conditional name="ptm_score">
-                    <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
-                        <option value="0">A-score</option>
-                        <option value="1" selected="True">PhosphoRS</option>
-                        <option value="2">None</option>
-                    </param>
-                    <when value="0" />
-                    <when value="1">
-                        <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
-                        <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float"
-                            help="Automatic mode will be used if not set" />
-                    </when>
-                    <when value="2" />
-                </conditional>
-                <param name="ptm_sequence_matching_type" type="select" label="The PTM to peptide sequence matching type">
-                     <option value="0">Character Sequence</option>
-                     <option value="1" selected="true">Amino Acids</option>
-                     <option value="2">Indistinguishable Amino Acids</option>
-                </param>
-                <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
-                <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
-            </when>
-        </conditional>
-        <conditional name="filtering_options">
-            <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options"
-                help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s">
-                <option value="no" selected="True">Default Filtering Options</option>
-                <option value="yes">Advanced Filtering Options</option>
-            </param>
-            <when value="no" />
-            <when value="yes">
-                <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="6" />
-                <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" />
-                <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10"
-                    help="Next option specifies units (Da or ppm)" />
-                <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
-                    <option value="1">ppm</option>
-                    <option value="0">Daltons</option>
-                </param>
-                <!--param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /-->
-                <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /-->
-                <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /-->
-                <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
-            </when>
-        </conditional>
-        <conditional name="contact_options">
-            <param name="contact_options_selector" type="select" label="Specify Contact Information for mzIdendML"
-                help="Create a Galaxy workflow to save these values">
-                <option value="no" selected="True">GalaxyP Project contact (Not suitable for PRIDE submission)</option>
-                <option value="yes">Specify Contact Information</option>
-            </param>
-            <when value="no" />
-            <when value="yes">
-                <param name="contact_first_name" type="text" value="" label="Contact first name.">
-                    <validator type="regex" message="">\S+.*</validator>
-                </param>
-                <param name="contact_last_name" type="text" value="" label="Contact last name.">
-                    <validator type="regex" message="">\S+.*</validator>
-                </param>
-                <param name="contact_email" type="text" value="" label="Contact e-mail.">
-                    <validator type="regex" message="">\S+@\S+</validator>
-                </param>
-                <param name="contact_address" type="text" value="" label="Contact address.">
-                    <validator type="regex" message="">\S+.*</validator>
-                </param>
-                <param name="contact_url" type="text" value="" optional="true" label="Contact URL.">
-                </param>
-                <param name="organization_name" type="text" value="" label="Organization name.">
-                    <validator type="regex" message="">\S+.*</validator>
-                </param>
-                <param name="organization_email" type="text" value="" label="Organization e-mail.">
-                    <validator type="regex" message="">\S+@\S+</validator>
-                </param>
-                <param name="organization_address" type="text" value="" label="Organization address.">
-                    <validator type="regex" message="">\S+.*</validator>
-                </param>
-                <param name="organization_url" type="text" value="" optional="true" label="Organization URL.">
-                </param>
-            </when>
-        </conditional>
+
+        <section name="optional_main_parameters" expanded="false" title="Optional main parameters">
+              <param format="json" name="input_optional_identification_parameters" type="data" label="Identification parameters" optional="true" help="This optional parameter file will be used instead of the default one"/>
+              <param format="fasta" name="input_fasta_file" type="data" label="Fasta file" optional="true" help="This optional fasta file will be used instead of the one included in the SearchGUI file (if it exists). If the SearchGUI file does not include the fasta file, this parameter is must be considered as mandatory."/>
+              <param format="mgf,mzml" name="input_optional_spectrum_files" type="data" label="Spectrum files" optional="true" multiple="true" help="Optional spectrum files will be used together with spectra included in the SearchGUI output"/>
+        </section>
+
+        <section name="exporting_options" expanded="true" title="Exporting options" help="All different outputs PeptideShaker may produce">
 
-        <section name="exporting_options" expanded="true" title="Exporting options">
+            <conditional name="zip_conditional">
+                <param name="zip_output_boolean" type="boolean" truevalue="zip" falsevalue="separate" checked="false" label="Compress results into a single zip file" />
+                <when value="separate">
+                    <param name="export_psdb" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Exports PeptideShakers‘ .psdb file" />
+                </when>
+                <when value="zip">
+                    <param name="export_reports_when_zip" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Also export reports out of the zip" />
+                    <param name="export_mgf_when_zip" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Also export mgf file/s out of the zip" help=".cui index files are exported as a different collection too" />
+                </when>
+            </conditional>
 
             <conditional name="mzidentml_conditional">
                 <param name="mzidentml_creation" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Creates a mzIdentML file" />
                 <when value="1">
               	     <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in the mzIdentML file" />
+
+                     <conditional name="contact_options">
+                         <param name="contact_options_selector" type="select" label="Contact Information"
+                             help="Create a Galaxy workflow to save these values">
+                             <option value="no" selected="True">GalaxyP Project contact (Not suitable for PRIDE submission)</option>
+                             <option value="yes">Specify Contact Information</option>
+                         </param>
+                         <when value="no" />
+                         <when value="yes">
+                             <param name="contact_first_name" type="text" value="" label="Contact first name.">
+                                 <validator type="regex" message="">\S+.*</validator>
+                             </param>
+                             <param name="contact_last_name" type="text" value="" label="Contact last name.">
+                                 <validator type="regex" message="">\S+.*</validator>
+                             </param>
+                             <param name="contact_email" type="text" value="" label="Contact e-mail.">
+                                 <validator type="regex" message="">\S+@\S+</validator>
+                             </param>
+                             <param name="contact_address" type="text" value="" label="Contact address.">
+                                 <validator type="regex" message="">\S+.*</validator>
+                             </param>
+                             <param name="contact_url" type="text" value="" optional="true" label="Contact URL.">
+                             </param>
+                             <param name="organization_name" type="text" value="" label="Organization name.">
+                                 <validator type="regex" message="">\S+.*</validator>
+                             </param>
+                             <param name="organization_email" type="text" value="" label="Organization e-mail.">
+                                 <validator type="regex" message="">\S+@\S+</validator>
+                             </param>
+                             <param name="organization_address" type="text" value="" label="Organization address.">
+                                 <validator type="regex" message="">\S+.*</validator>
+                             </param>
+                             <param name="organization_url" type="text" value="" optional="true" label="Organization URL.">
+                             </param>
+                         </when>
+                     </conditional>
+
                 </when>
                 <when value="0" />
             </conditional>
 
-            <conditional name="zip_conditional">
-                <param name="zip_output_boolean" type="boolean" truevalue="zip" falsevalue="separate" checked="false" label="Compress results into a single zip file" />
-                <when value="separate">
-                    <param name="export_cps" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Exports the CPS file" />
-                </when>
-                <when value="zip">
-                    <param name="export_reports_when_zip" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Also export reports out of the zip" />
+            <!-- FOLLOW-UP REPORTS  -->
+            <conditional name="followup_conditional">
+                <param name="followup_conditional_selector" type="select" label="Follow-up analysis export options">
+                    <option value="yes">Export follow-up analysis</option>
+                    <option value="no" selected="True">Do not export</option>
+                </param>
+                <when value="no" />
+                <when value="yes">
+                    <param name="followup_export_spectra" label="Spectra: Export spectrum files as MGF" type="select" help="Commonly: spectra of Non-Validated PSMs">
+                        <option value="0" >Spectra of Non-Validated PSMs</option>
+                        <option value="1" >Spectra of Non-Validated Peptides</option>
+                        <option value="2" >Spectra of Non-Validated Proteins</option>
+                        <option value="3" >Spectra of Validated PSMs</option>
+                        <option value="4" >Spectra of Validated PSMs of Validated Peptides</option>
+                        <option value="5" >Spectra of validated PSMs of Validated Peptides of Validated Proteins</option>
+                        <option value="off" selected="True">Do not export</option>
+                    </param>
+                    <param name="followup_export_accession_numbers" label="Proteins: Export accession numbers as TXT" type="select" help="Commonly: Main Accession of Validated Protein Groups">
+                        <option value="0" >Main Accession of Validated Protein Groups</option>
+                        <option value="1" >All Accessions of Validated Protein Groups</option>
+                        <option value="2" >Non-Validated Accessions</option>
+                        <option value="off" selected="True">Do not export</option>
+                    </param>
+                    <param name="followup_export_sequences" label="Proteins: Export protein details/sequences in fasta format" type="select" help="Commonly: Main Accession of Validated Protein Groups">
+                        <option value="0" >Main Accession of Validated Protein Groups</option>
+                        <option value="1" >All Accessions of Validated Protein Groups</option>
+                        <option value="2" >Non-Validated Accessions</option>
+                        <option value="off" selected="True">Do not export</option>
+                    </param>
+                    <param name="followup_export_proteoforms" label="Proteins: Export proteoforms as TXT" type="select">
+                        <option value="on">Export</option>
+                        <option value="off" selected="True">Do not export</option>
+                    </param>
+                    <conditional name="followup_export_progenesis_conditional">
+                        <param name="followup_export_progenesis_selector" label="Label free quantification: Exports identification results in Progenesis LC-MS compatible format as TXT" type="select" help="Commonly: Validated PSMs of Validated Peptides of Validated Proteins">
+                            <option value="0">Validated PSMs of Validated Peptides of Validated Proteins</option>
+                            <option value="1">Validated PSMs of Validated Peptides</option>
+                            <option value="2">Validated PSMs</option>
+                            <option value="3">Confidently localized PTMs of Validated PSMs of Validated Peptides of Validated Proteins</option>
+                            <option value="off" selected="True">Do not export</option>
+                        </param>
+                        <when value="0"/>
+                        <when value="1"/>
+                        <when value="2"/>
+                        <when value="3">
+                            <param name="followup_export_progenesis_ptms" type="select" label="Targeted PTMs" multiple="true"
+                                help="">
+                                <expand macro="modifications"/>
+                            </param>
+                        </when>
+                        <when value="off"/>
+                    </conditional>
+                    <conditional name="followup_export_inclusion_list_conditional">
+                        <param name="followup_export_inclusion_list_selector" label="Inclusion/Exclusion list: Exports a file for an inclusion list of validated hits" type="select" help="Commonly: Thermo">
+                            <option value="0" >Thermo</option>
+                            <option value="1" >ABI</option>
+                            <option value="2" >Bruker</option>
+                            <option value="3" >MassLynx</option>
+                            <option value="off" selected="True">Do not export</option>
+                        </param>
+                        <when value="0">
+                            <param name="followup_export_inclusion_list_peptide_filters" type="select" label="Peptide Filters" multiple="true" optional="true" display="checkboxes"
+                                help="">
+                                <option value="0">Miscleaved Peptides</option>
+                                <option value="1">Reactive Peptides</option>
+                                <option value="2">Degenerated Peptides</option>
+                            </param>
+                            <param name="followup_export_inclusion_list_protein_filters" type="select" label="Protein Filters" multiple="true" optional="true" display="checkboxes"
+                                help="">
+                                <option value="1">Related Proteins</option>
+                                <option value="2">Related and Unrelated Proteins</option>
+                                <option value="3">Unrelated Proteins</option>
+                            </param>
+                            <param name="followup_export_inclusion_list_rt_window" type="integer" value="20" label="Retention time window for the inclusion list export (in seconds)"
+                                help=""/>
+                        </when>
+                        <when value="1">
+                            <param name="followup_export_inclusion_list_peptide_filters" type="select" label="Peptide Filters" multiple="true" optional="true" display="checkboxes"
+                                help="">
+                                <option value="0">Miscleaved Peptides</option>
+                                <option value="1">Reactive Peptides</option>
+                                <option value="2">Degenerated Peptides</option>
+                            </param>
+                            <param name="followup_export_inclusion_list_protein_filters" type="select" label="Protein Filters" multiple="true" optional="true" display="checkboxes"
+                                help="">
+                                <option value="1">Related Proteins</option>
+                                <option value="2">Related and Unrelated Proteins</option>
+                                <option value="3">Unrelated Proteins</option>
+                            </param>
+                            <param name="followup_export_inclusion_list_rt_window" type="integer" value="20" label="Retention time window for the inclusion list export (in seconds)"
+                                help=""/>
+                        </when>
+                        <when value="2">
+                            <param name="followup_export_inclusion_list_peptide_filters" type="select" label="Peptide Filters" multiple="true" optional="true" display="checkboxes"
+                                help="">
+                                <option value="0">Miscleaved Peptides</option>
+                                <option value="1">Reactive Peptides</option>
+                                <option value="2">Degenerated Peptides</option>
+                            </param>
+                            <param name="followup_export_inclusion_list_protein_filters" type="select" label="Protein Filters" multiple="true" optional="true" display="checkboxes"
+                                help="">
+                                <option value="1">Related Proteins</option>
+                                <option value="2">Related and Unrelated Proteins</option>
+                                <option value="3">Unrelated Proteins</option>
+                            </param>
+                            <param name="followup_export_inclusion_list_rt_window" type="integer" value="20" label="Retention time window for the inclusion list export (in seconds)"
+                                help=""/>
+                        </when>
+                        <when value="3">
+                            <param name="followup_export_inclusion_list_peptide_filters" type="select" label="Peptide Filters" multiple="true" optional="true" display="checkboxes"
+                                help="">
+                                <option value="0">Miscleaved Peptides</option>
+                                <option value="1">Reactive Peptides</option>
+                                <option value="2">Degenerated Peptides</option>
+                            </param>
+                            <param name="followup_export_inclusion_list_protein_filters" type="select" label="Protein Filters" multiple="true" optional="true" display="checkboxes"
+                                help="">
+                                <option value="1">Related Proteins</option>
+                                <option value="2">Related and Unrelated Proteins</option>
+                                <option value="3">Unrelated Proteins</option>
+                            </param>
+                            <param name="followup_export_inclusion_list_rt_window" type="integer" value="20" label="Retention time window for the inclusion list export (in seconds)"
+                                help=""/>
+                        </when>
+                        <when value="off"/>
+                    </conditional>
                 </when>
             </conditional>
 
-            <param name="output_reports" type="select" display="checkboxes" multiple="True" optional="true" label="Reports to be generated">
+            <!-- IDENTIFICATION FEATURES REPORTS  -->
+            <param name="output_reports" type="select" display="checkboxes" multiple="True" optional="true" label="Identification features reports to be generated">
                 <option value="3">PSM Report</option>
                 <option value="4">PSM Report with non-validated matches</option>
                 <option value="2">PSM Phosphorylation Report</option>
@@ -316,99 +483,189 @@
 
     </inputs>
     <outputs>
-        <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
-            <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['mzidentml_conditional']['mzidentml_creation'] is True</filter>
-        </data>
-        <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file">
-            <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['zip_conditional']['export_cps'] is True</filter>
-        </data>
         <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
             <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True</filter>
         </data>
-	<!--
-        <data format="tabular" name="reports">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="output_reports" visible="true" assign_primary_output="true" />
+        <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
+            <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['mzidentml_conditional']['mzidentml_creation'] is True</filter>
+        </data>
+        <data format="peptideshaker_archive" name="output_psdb" from_work_dir="peptideshaker_output.psdb" label="${tool.name} on ${on_string}: PSDB file">
+            <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['zip_conditional']['export_psdb'] is True</filter>
         </data>
-        -->
-	      <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
-            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '0' in exporting_options['output_reports']</filter>
+        <collection name="output_mgf" type="list" label="${tool.name} on ${on_string}: Mgf" >
+            <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_mgf_when_zip'] is True</filter>
+            <discover_datasets pattern="__name_and_ext__" directory="output_mgf" ext="mgf"/>
+        </collection>
+        <collection name="output_cui" type="list" label="${tool.name} on ${on_string}: Cui" >
+            <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_mgf_when_zip'] is True</filter>
+            <discover_datasets pattern="__name_and_ext__" directory="output_cui" ext="cui"/>
+        </collection>
+
+        <!-- Follow-up analysis -->
+        <collection name="output_spectra" type="list" label="${tool.name} on ${on_string}: Spectra" >
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_spectra'] != 'off' </filter>
+            <discover_datasets pattern="__name_and_ext__" directory="output_reports" ext="mgf"/>
+        </collection>
+        <data format="txt" name="output_proteins_accessions" from_work_dir="proteins_accession_numbers.txt" label="${tool.name} on ${on_string}: Proteins Accession Numbers">
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_accession_numbers'] != 'off' </filter>
+        </data>
+        <data format="fasta" name="output_proteins_sequences" from_work_dir="proteins_sequences.fasta" label="${tool.name} on ${on_string}: Proteins Sequences">
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_sequences'] != 'off' </filter>
+        </data>
+        <data format="txt" name="output_proteoforms" from_work_dir="proteins_proteoforms.txt" label="${tool.name} on ${on_string}: Proteins Proteoforms">
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_proteoforms'] != 'off' </filter>
+        </data>
+        <data format="txt" name="output_progenesis" from_work_dir="progenesis.txt" label="${tool.name} on ${on_string}: Progenesis">
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_progenesis_conditional']['followup_export_progenesis_selector'] != 'off' </filter>
+        </data>
+        <data format="txt" name="output_inclusion_list" from_work_dir="inclusion_list.txt" label="${tool.name} on ${on_string}: Inclusion/Exclusion List">
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_inclusion_list_conditional']['followup_export_inclusion_list_selector'] != 'off' </filter>
+        </data>
+
+        <!-- Identification Features outputs -->
+	      <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Certificate of Analysis">
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '0' in exporting_options['output_reports']</filter>
         </data>
         <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
-            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '1' in exporting_options['output_reports']</filter>
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '1' in exporting_options['output_reports']</filter>
         </data>
         <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
-            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '2' in exporting_options['output_reports']</filter>
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '2' in exporting_options['output_reports']</filter>
         </data>
         <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
-            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '3' in exporting_options['output_reports']</filter>
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '3' in exporting_options['output_reports']</filter>
         </data>
         <data format="tabular" name="output_psm_nonvalidated" from_work_dir="psm_nonvalidated.txt" label="${tool.name} on ${on_string}: PSM Report with non-validated matches">
-            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '4' in exporting_options['output_reports']</filter>
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '4' in exporting_options['output_reports']</filter>
         </data>
         <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
-            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '11' in exporting_options['output_reports']</filter>
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '11' in exporting_options['output_reports']</filter>
         </data>
         <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
-            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '5' in exporting_options['output_reports']</filter>
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '5' in exporting_options['output_reports']</filter>
         </data>
         <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
-            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '6' in exporting_options['output_reports']</filter>
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '6' in exporting_options['output_reports']</filter>
         </data>
         <data format="tabular" name="output_peptides_nonvalidated" from_work_dir="peptides_nonvalidated.txt" label="${tool.name} on ${on_string}: Peptide Report with non-validated matches">
-            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '7' in exporting_options['output_reports']</filter>
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '7' in exporting_options['output_reports']</filter>
         </data>
         <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
-            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '8' in exporting_options['output_reports']</filter>
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '8' in exporting_options['output_reports']</filter>
         </data>
         <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
-            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '9' in exporting_options['output_reports']</filter>
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '9' in exporting_options['output_reports']</filter>
         </data>
-        <data format="tabular" name="output_proteins_nonvalidated" from_work_dir="proteins_nonvalidated.txt" label="${tool.name} on ${on_string}: Protein Repor with non-validated matches">
-            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '10' in exporting_options['output_reports']</filter>
+        <data format="tabular" name="output_proteins_nonvalidated" from_work_dir="proteins_nonvalidated.txt" label="${tool.name} on ${on_string}: Protein Report with non-validated matches">
+            <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '10' in exporting_options['output_reports']</filter>
         </data>
     </outputs>
+
     <tests>
-        <test expect_num_outputs="1">
-            <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
-            <param name="processing_options_selector" value="no"/>
-            <param name="filtering_options_selector" value="no"/>
-            <param name="mzidentml_creation" value="0"/>
-            <param name="zip_output_boolean" value="zip"/>
-            <param name="export_cps" value="1"/>
-            <output name="output_zip" file="peptide_shaker_modifications_result1.zip" ftype="zip" compare="sim_size" delta="3000" />
-        </test>
-        <test expect_num_outputs="12">
-            <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
-            <param name="processing_options_selector" value="no"/>
-            <param name="filtering_options_selector" value="yes"/>
-            <param name="min_peptide_length" value="1"/>
-            <param name="mzidentml_creation" value="0"/>
-            <param name="zip_output_boolean" value="separate"/>
-            <param name="output_reports" value="0,1,2,3,4,5,6,7,8,9,10,11"/>
-            <output name="output_certificate" file="peptide_shaker_modifications_result1.output_certificate" ftype="txt" lines_diff="8"/>
-            <output name="output_hierarchical" file="peptide_shaker_modifications_result1.output_hierarchical" ftype="tabular"/>
-            <output name="output_extended_psm" file="peptide_shaker_modifications_result1.output_extended_psm" ftype="tabular"/>
-            <output name="output_psm" file="peptide_shaker_modifications_result1.output_psm" ftype="tabular"/>
-            <output name="output_psm_phosphorylation" file="peptide_shaker_modifications_result1.output_psm_phosphorylation" ftype="tabular"/>
-            <output name="output_psm_nonvalidated" file="peptide_shaker_modifications_result1.output_psm_nonvalidated" ftype="tabular"/>
-            <output name="output_peptides" file="peptide_shaker_modifications_result1.output_peptides" ftype="tabular"/>
-            <output name="output_peptides_phosphorylation" file="peptide_shaker_modifications_result1.output_peptides_phosphorylation" ftype="tabular"/>
-            <output name="output_peptides_nonvalidated" file="peptide_shaker_modifications_result1.output_peptides_nonvalidated" ftype="tabular"/>
-            <output name="output_proteins" file="peptide_shaker_modifications_result1.output_proteins" ftype="tabular"/>
-            <output name="output_proteins_phosphorylation" file="peptide_shaker_modifications_result1.output_proteins_phosphorylation" ftype="tabular"/>
-            <output name="output_proteins_nonvalidated" file="peptide_shaker_modifications_result1.output_proteins_nonvalidated" ftype="tabular"/>
-        </test>
-        <test expect_num_outputs="2">
-            <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
-            <param name="processing_options_selector" value="no"/>
-            <param name="filtering_options_selector" value="no"/>
-            <param name="mzidentml_creation" value="0"/>
-            <param name="zip_output_boolean" value="separate"/>
-            <param name="export_cps" value="1"/>
-            <param name="output_reports" value="3"/>
-            <output name="output_cps" file="peptide_shaker_modifications_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/>
-	          <output name="output_psm" file="peptide_shaker_modifications_result1.output_psm" ftype="tabular"/>
-        </test>
+      <!-- Basic test: default identification parameters, searchgui_tinydb1.fasta, 4 search engines xx-->
+      <test expect_num_outputs="1">
+          <param name="searchgui_input" value="searchgui_tiny_result_default_4engines.zip" ftype="searchgui_archive"/>
+          <param name="mzidentml_creation" value="0"/>
+          <param name="export_psdb" value="1"/>
+          <output name="output_psdb" ftype="peptideshaker_archive">
+              <assert_contents>
+                  <has_size value="122880" delta="3000"/>
+              </assert_contents>
+          </output>
+      </test>
+
+      <!-- Modifications test: default identification parameters with modifications, searchgui_tinydb1.fasta, 4 search engines -->
+      <test expect_num_outputs="1">
+          <param name="searchgui_input" value="searchgui_tiny_result_default_4engines_modifications.zip" ftype="searchgui_archive"/>
+          <param name="mzidentml_creation" value="0"/>
+          <param name="export_psdb" value="1"/>
+          <output name="output_zip" ftype="peptideshaker_archive">
+              <assert_contents>
+                  <has_size value="126976" delta="3000"/>
+              </assert_contents>
+          </output>
+      </test>
+
+      <!-- Reports tests: default identification parameters, small spectra, some search engines (XTandem,MSGF+, OMSSA), all identification reports -->
+      <test expect_num_outputs="12">
+          <param name="searchgui_input" value="searchgui_smallsearch_default_somesearchengines_modifications.zip" ftype="searchgui_archive"/>
+          <param name="mzidentml_creation" value="0"/>
+          <param name="zip_output_boolean" value="separate"/>
+          <param name="export_psdb" value="0"/>
+          <param name="output_reports" value="0,1,2,3,4,5,6,7,8,9,10,11"/>
+          <output name="output_certificate" file="peptideshaker_reports_output_certificate.txt" ftype="txt" lines_diff="8"/>
+          <output name="output_hierarchical" file="peptideshaker_reports_output_hierarchical.tabular" ftype="tabular"/>
+          <output name="output_extended_psm" file="peptideshaker_reports_output_extendedpsm.tabular" ftype="tabular"/>
+          <output name="output_psm" file="peptideshaker_reports_output_psm.tabular" ftype="tabular"/>
+          <output name="output_psm_phosphorylation" file="peptideshaker_reports_output_psmphosphorylation.tabular" ftype="tabular"/>
+          <output name="output_psm_nonvalidated" file="peptideshaker_reports_output_psmnonvalidated.tabular" ftype="tabular"/>
+          <output name="output_peptides" file="peptideshaker_reports_output_peptides.tabular" ftype="tabular"/>
+          <output name="output_peptides_phosphorylation" file="peptideshaker_reports_output_peptidesphosphorylation.tabular" ftype="tabular"/>
+          <output name="output_peptides_nonvalidated" file="peptideshaker_reports_output_peptidesnonvalidated.tabular" ftype="tabular"/>
+          <output name="output_proteins" file="peptideshaker_reports_output_proteins.tabular" ftype="tabular"/>
+          <output name="output_proteins_phosphorylation" file="peptideshaker_reports_output_proteinsphosphorylation.tabular" ftype="tabular"/>
+          <output name="output_proteins_nonvalidated" file="peptideshaker_reports_output_proteinsnonvalidated.tabular" ftype="tabular"/>
+      </test>
+
+      <!-- followup analysis tests: default identification parameters, small spectra, some search engines (XTandem,MSGF+, OMSSA), all followup analysis -->
+      <test expect_num_outputs="5">
+          <param name="searchgui_input" value="searchgui_smallsearch_default_somesearchengines_modifications.zip" ftype="searchgui_archive"/>
+          <param name="mzidentml_creation" value="0"/>
+          <param name="zip_output_boolean" value="separate"/>
+          <param name="export_psdb" value="0"/>
+          <param name="followup_conditional_selector" value="yes"/>
+          <param name="followup_export_spectra" value="0"/>
+          <param name="followup_export_accession_numbers" value="0"/>
+          <param name="followup_export_sequences" value="0"/>
+          <param name="followup_export_proteoforms" value="on"/>
+          <param name="followup_export_progenesis_selector" value="0"/>
+          <output_collection name="output_spectra" type="list">
+              <element name="searchgui_smallspectra_non_validated_PSMs" ftype="mgf">
+                  <assert_contents>
+                      <has_line_matching expression="236.0470428 11.674492836"/>
+                      <has_line_matching expression="520.9862671 4666.4399414063"/>
+                      <has_line_matching expression="267.4349976 50.7710571289"/>
+                      <has_line_matching expression="665.7418213 3.8165459633"/>
+                      <has_line_matching expression="672.2329102 146.2656707764"/>
+                      <has_line_matching expression="634.7792969 2367.6374511719"/>
+                  </assert_contents>
+              </element>
+          </output_collection>
+          <output name="output_proteins_accessions" ftype="txt">
+              <assert_contents>
+                  <has_line_matching expression="cds.comp41779_c0_seq1"/>
+                  <has_line_matching expression="cds.comp41890_c0_seq1"/>
+                  <has_line_matching expression="cds.comp41890_c0_seq1_REVERSED"/>
+                  <has_line_matching expression="cds.comp8310_c0_seq2"/>
+              </assert_contents>
+          </output>
+          <output name="output_proteins_sequences" ftype="fasta">
+              <assert_contents>
+                  <has_line_matching expression=">generic|cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-6"/>
+                  <has_line_matching expression="METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT"/>
+                  <has_line_matching expression="generic|cds.comp41890_c0_seq1_REVERSED|m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20-REVERSED"/>
+                  <has_line_matching expression="LNYTTELNYTAKEDGRTNLLVTNVKAGVGLRSKNHWVLDGSNPDGMGNAWVKAFGGPKLVLNEIEYESIDINDSNQMIKWGSLDVTHSNSTNELLIFSGDRDTESIAVPGKNNKRYTSHEQLEGKVLAPTPSQY"/>
+              </assert_contents>
+          </output>
+          <output name="output_proteoforms" ftype="txt">
+              <assert_contents>
+                  <has_line_matching expression="cds.comp8310_c0_seq2"/>
+                  <has_line_matching expression="cds.comp41890_c0_seq1_REVERSED"/>
+                  <has_line_matching expression="cds.comp41779_c0_seq1"/>
+                  <has_line_matching expression="cds.comp41779_c0_seq2"/>
+                  <has_line_matching expression="cds.comp41779_c0_seq3"/>
+              </assert_contents>
+          </output>
+          <output name="output_progenesis" ftype="txt">
+              <assert_contents>
+                  <has_text_matching expression="NLVAEESMNMLKNK\t:::::::::::::::\t100.0\tcds.comp8310_c0_seq2\tm.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16\tsmall.17.17."/>
+                  <has_text_matching expression="LDRLISATSISPEHKIDFLFK\t::::::::::::::::::::::\t100.0\tcds.comp41779_c0_seq1\tm.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67\tsmall.3.3."/>
+                  <has_n_columns n="8" />
+              </assert_contents>
+          </output>
+
+      </test>
+
     </tests>
     <help>
 **What it does**
@@ -419,144 +676,386 @@
 
 ----
 
-Reports
+Outputs
 =======
 
+*zip*
+------
+
+When choosing zip option, all other outputs are compressed and included into the zip file and, by default, no other file is shown in the Galaxy history. This last behaviour may be changed in order to have all other outputs also available in the history.
+
+*psdb*
+------
+
+psdb is the native format used by PeptideShaker. It contains all the information required by PeptideShaker to run.
+
+*mzIdentML*
+-----------
+
+PeptideShaker can load results from virtually any identification algorithm in the mzIdentML format as long as the minimal peptide to spectrum match information is present in the file.
+
+The following is required:
+
+• Spectrum file format has to be mgf.
+• Each PSM has a score or e-value as a PSM score CV term.
+
+
+*Follow-up analysis*
+--------------------
+
+Spectra
+'''''''
+
+Exports the spectra according to the category of the PSMs:
+
+• Spectra of Non-Validated PSMs
+• Spectra of Non-Validated Peptides
+• Spectra of Non-Validated Proteins
+• Spectra of Validated PSMs
+• Spectra of Validated PSMs of Validated Peptides
+• Spectra of validated PSMs of Validated Peptides of Validated Proteins.
+
+Exported results are in mgf format.
+
+Proteins: Accession numbers
+'''''''''''''''''''''''''''
+
+Export the protein accessions according to the category of the proteins:
+
+• Main Accession of Validated Protein Groups
+• All Accessions of Validated Protein Groups
+• Non-Validated Accessions
+
+Exported protein accessions are text format as TXT.
+
+
+Proteins: Sequences
+'''''''''''''''''''
+
+Exports the protein details according to a category of proteins:
+
+• Main Accession of Validated Protein Groups
+• All Accessions of Validated Protein Groups
+• Non-Validated Accessions.
+
+Exported protein details are in fasta format.
+
+
+Proteins: Proteoforms
+'''''''''''''''''''''
+
+Exports all possible proteoforms of the validated proteins.
+
+Exported results are in text format as TXT.
+Results file can be easily imported and used by PathwayMatcher_ tool.
+
+.. _PathwayMatcher: https://toolshed.g2.bx.psu.edu/repository?repository_id=6d75f02b86acc421
+
+
+Label free quantification
+'''''''''''''''''''''''''
+
+Exports the spectra from different categories of PSMs according to the export type:
+
+• Validated PSMs of Validated Peptides of Validated Proteins
+• Validated PSMs of Validated Peptides
+• Validated PSMs
+• Confidently localized PTMs of Validated PSMs of Validated Peptides of Validated Proteins
+
+Exported identification results are in Progenesis LC-MS compatible format as TXT.
+
+
+Inclusion/Exclusion list
+''''''''''''''''''''''''
+
+Exports an inclusion list of validated hits.
+
+Inclusion list may be filtered according to peptide types:
+
+• Miscleaved Peptides
+• Reactive Peptides
+• Degenerated Peptides.
+
+and also according to protein inferences:
+
+• Related Proteins
+• Related and Unrelated Proteins
+• Unrelated Proteins.
+
+Finally, a retention time window may be established as a final filter.
+
+Exported results can be in Thermo, ABI, Bruker or MassLynx formats.
+
+
+
+*Identification Features Reports*
+---------------------------------
 
 PSM Report
-----------
+''''''''''
+=============================  ========================================
+  Column                        Description
+=============================  ========================================
+ Protein(s)                     Protein(s) to which the peptide can be attached
+ Sequence                       Sequence of the peptide
+ AAs Before                     The amino acids before the sequence
+ AAs After                      The amino acids after the sequence
+ Position                       Position of the peptide in the protein sequence(s).
+ Modified Sequence              The amino acids sequence annotated with variable modifications.
+ Variable Modifications         The variable modifications
+ Fixed Modifications            The fixed modifications.
+ Spectrum File                  The spectrum file.
+ Spectrum Title                 The title of the spectrum.
+ Spectrum Scan Number           The spectrum scan number.
+ RT                             Retention time
+ m/z                            Measured m/z
+ Measured Charge                The charge as given in the spectrum file.
+ Identification Charge          The charge as inferred by the search engine.
+ Theoretical Mass               The theoretical mass of the peptide.
+ Isotope Number                 The isotope number targetted by the instrument.
+ Precursor m/z Error [ppm]      The precursor m/z matching error.
+ Localization Confidence        The confidence in variable PTM localization.
+ probabilistic PTM score        The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
+ D-score                        D-score for variable PTM localization
+ Confidence                     Confidence in percent associated to the retained PSM.
+ Validation                     Indicates the validation level of the protein group.
+=============================  ========================================
 
-* Protein(s):                Protein(s) to which the peptide can be attached
-* Sequence:                  Sequence of the peptide
-* Variable Modifications:   The variable modifications
-* D-score:	                D-score for variable PTM localization
-* probabilistic PTM score:	The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
-* Localization Confidence:	The confidence in variable PTM localization.
-* Fixed Modifications:	    The fixed modifications.
-* Spectrum File:	The spectrum file.
-* Spectrum Title:	The title of the spectrum.
-* Spectrum Scan Number:	The spectrum scan number.
-* RT:	Retention time
-* m/z:	Measured m/z
-* Measured Charge:	The charge as given in the spectrum file.
-* Identification Charge:	The charge as inferred by the search engine.
-* Theoretical Mass:	The theoretical mass of the peptide.
-* Isotope Number:	The isotope number targetted by the instrument.
-* Precursor m/z Error:	The precursor m/z matching error.
-* Score:	Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
-* Confidence:	Confidence in percent associated to the retained PSM.
-* Decoy:	Indicates whether the peptide is a decoy (1: yes, 0: no).
-* Validation: Indicates the validation level of the protein group.
+
+PSM Report with non-validated matches
+'''''''''''''''''''''''''''''''''''''
+
+Same columns as the original PSM report but also includes non-validated matches.
 
 
-Protein Report
---------------
+PSM Phosphorylation Report
+''''''''''''''''''''''''''
+=============================  =========================================================
+  Column                        Description
+=============================  =========================================================
+Protein(s)                     Protein(s) to which the peptide can be attached
+Sequence                       Sequence of the peptide
+Variable Modifications         The variable modifications
+Fixed Modifications            The fixed modifications.
+Spectrum File                  The spectrum file.
+Spectrum Title                 The title of the spectrum.
+Spectrum Scan Number           The spectrum scan number.
+RT                             Retention time
+m/z                            Measured m/z
+Measured Charge                The charge as given in the spectrum file.
+Identification Charge          The charge as inferred by the search engine.
+Theoretical Mass               The theoretical mass of the peptide.
+Isotope Number                 The isotope number targetted by the instrument.
+Precursor m/z Error [ppm]      The precursor m/z matching error.
+Localization Confidence        The confidence in variable PTM localization.
+probabilistic PTM score        The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
+D-score                        D-score for variable PTM localization
+Confident Phosphosites	       List of the sites where a phosphorylation was confidently localized.
+#Confident Phosphosites        Number of confidently localized phosphorylations.
+Ambiguous Phosphosites	       List of the sites where a phosphorylation was ambiguously localized.
+#Ambiguous Phosphosites	       Number of ambiguously localized phosphorylations.
+Confidence [%]                 Confidence in percent associated to the retained PSM.
+Validation                     Indicates the validation level of the protein group.
+=============================  =========================================================
 
-* Main Accession:	Main accession of the protein group.
-* Description:	Description of the protein designed by the main accession.
-* Gene Name:	The gene names of the Ensembl gene ID associated to the main accession.
-* Chromosome:	The chromosome of the Ensembl gene ID associated to the main accession.
-* PI:	Protein Inference status of the protein group.
-* Secondary Accessions:	Other accessions in the protein group (alphabetical order).
-* Protein Group:	The complete protein group (alphabetical order).
-* #Peptides:	Total number of peptides.
-* #Validated Peptides:	Number of validated peptides.
-* #Unique:	Total number of peptides unique to this protein group.
-* #PSMs:	Number of PSMs
-* #Validated PSMs:	Number of validated PSMs
-* Coverage (%):	Sequence coverage in percent of the protein designed by the main accession.
-* Possible Coverage (%):	Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
-* MW (kDa):	Molecular Weight.
-* Spectrum Counting NSAF: 	Normalized Spectrum Abundance Factor (NSAF)
-* Spectrum Counting emPAI:	exponentially modified Protein Abundance Index (emPAI)
-* Confident Modification Sites: Number of Confident Modification Sites	List of the sites where a variable modification was confidently localized.
-* Other Modification Sites: Number of other Modification Sites	List of the non*confident sites where a variable modification was localized.
-* Score:	Score of the protein group.
-* Confidence:	Confidence in percent associated to the protein group.
-* Decoy:	Indicates whether the protein group is a decoy (1: yes, 0: no).
-* Validation:	Indicates the validation level of the protein group.
+
+Extended PSM Report
+'''''''''''''''''''
+
+Same as the ordinary PSM report but adds a ``Decoy`` column and lacks the ``Confidence`` column.
+
+=============================  =========================================================
+  Extra column                  Description
+=============================  =========================================================
+  Decoy	                        Indicates whether the peptide is a decoy (1: yes, 0: no).
+
+=============================  =========================================================
+
 
 
 Peptide Report
---------------
+''''''''''''''
+
+==========================================  =====================================================
+  Column                                     Description
+==========================================  =====================================================
+Protein(s):		                               Protein(s) to which this peptide can be attached.
+Protein Group(s)                             List of identified protein groups this peptide can map to with associated validation level.
+#Validated Protein Group(s)	                 Indicates the number of protein groups this peptide maps to.
+Unique Group	                               Indicates whether the peptide maps to a unique protein group.
+Sequence	                                   Sequence of the peptide.
+Modified Sequence	                           The peptide sequence annotated with variable modifications.
+Position	                                   Position of the peptide in the protein sequence(s).
+AAs Before	                                 The amino acids before the sequence.
+AAs After                                    The amino acids after the sequence.
+Variable Modifications	                     The variable modifications.
+Fixed Modifications	                         The fixed modifications.
+Localization Confidence                      The confidence in PTMs localization.
+#Validated PSMs	                             Number of validated PSMs.
+#PSMs	                                       Number of PSMs.
+Confidence [%]	                             Confidence in percent associated to the peptide.
+Validation	                                 Indicates the validation level of the peptide.
+==========================================  =====================================================
+
+
+Peptide Report with non-validated matches
+'''''''''''''''''''''''''''''''''''''''''
+
+Same columns as the original Peptide report but also includes non-validated matches.
+
+
+Peptide Phosphorylation Report
+''''''''''''''''''''''''''''''
+
+==========================================  =====================================================
+  Column                                     Description
+==========================================  =====================================================
+Protein(s):		                               Protein(s) to which this peptide can be attached.
+Protein Group(s)                             List of identified protein groups this peptide can map to with associated validation level.
+#Validated Protein Group(s)	                 Indicates the number of protein groups this peptide maps to.
+Unique Group	                               Indicates whether the peptide maps to a unique protein group.
+Sequence	                                   Sequence of the peptide.
+Modified Sequence	                           The peptide sequence annotated with variable modifications.
+AAs Before	                                 The amino acids before the sequence.
+AAs After                                    The amino acids after the sequence.
+Variable Modifications	                     The variable modifications.
+Fixed Modifications	                         The fixed modifications.
+Localization Confidence                      The confidence in PTMs localization.
+Confident Phosphosites	                     List of the sites where a phosphorylation was confidently localized.
+#Confident Phosphosites	                     Number of confidently localized phosphorylations.
+Ambiguous Phosphosites	                     List of the sites where a phosphorylation was ambiguously localized.
+#Ambiguous Phosphosites	                     Number of ambiguously localized phosphorylations.
+#Validated PSMs	                             Number of validated PSMs.
+#PSMs	                                       Number of PSMs.
+Confidence [%]	                             Confidence in percent associated to the peptide.
+Validation	                                 Indicates the validation level of the peptide.
+==========================================  =====================================================
 
 
-* Protein(s):	Protein(s) to which this peptide can be attached.
-* AAs Before:	The amino-acids before the sequence.
-* Sequence:	Sequence of the peptide.
-* AAs After:	The amino-acids after the sequence.
-* Modified Sequence:	The peptide sequence annotated with variable modifications.
-* Variable Modifications:	The variable modifications.
-* Localization Confidence:	The confidence in PTMs localization.
-* Fixed Modifications:	The fixed modifications.
-* #Validated PSMs:	Number of validated PSMs.
-* #PSMs:	Number of PSMs.
-* Score:	Score of the peptide.
-* Confidence:	Confidence in percent associated to the peptide.
-* Decoy:	Indicates whether the peptide is a decoy (1: yes, 0: no).
-* Validation:	Indicates the validation level of the protein group.
+Protein Report
+''''''''''''''
+
+==========================================  =====================================================
+  Column                                     Description
+==========================================  =====================================================
+Main Accession	                             Main accession of the protein group.
+Description	                                 Description of the protein designed by the main accession.
+Gene Name                                    The gene names of the Ensembl gene ID associated to the main accession.
+Chromosome	                                 The chromosome of the Ensembl gene ID associated to the main accession.
+MW (kDa)                                     Molecular Weight.
+Possible Coverage (%)                        Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
+Coverage (%)	                               Sequence coverage in percent of the protein designed by the main accession.
+Spectrum Counting                            The selected spectrum counting metric.
+Confidently Localized Modification Sites	   List of the sites where a variable modification was confidently localized.
+# Confidently Localized Modification Sites	 Number of sites where a variable modification was confidently localized.
+Ambiguously Localized Modification Sites	   List of the sites where ambiguously localized variable modification could possibly be located.
+#Ambiguously Localized Modification Sites	   Number of ambiguously localized modifications.
+Protein Inference	                           Protein Inference status of the protein group.
+Secondary Accessions                         Other accessions in the protein group (alphabetical order).
+Protein Group                                The complete protein group (alphabetical order).
+#Validated Peptides                          Number of validated peptides.
+#Peptides                                    Total number of peptides.
+#Unique                                      Total number of peptides unique to this protein group.
+#Validated Unique	                           Total number of peptides unique to this protein group.
+#Validated PSMs                              Number of validated PSMs.
+#PSMs                                        Number of PSMs.
+Confidence [%]	                             Confidence in percent associated to the protein group.
+Validation                                   Indicates the validation level of the protein group.
+==========================================  =====================================================
+
+
+Protein Report with non-validated matches
+'''''''''''''''''''''''''''''''''''''''''
+
+Same columns as the original Protein report but also includes non-validated matches.
+
+
+Protein Phosphorylation Report
+''''''''''''''''''''''''''''''
+
+==========================================  =====================================================
+  Column                                     Description
+==========================================  =====================================================
+Main Accession	                             Main accession of the protein group.
+Description	                                 Description of the protein designed by the main accession.
+Gene Name                                    The gene names of the Ensembl gene ID associated to the main accession.
+Chromosome	                                 The chromosome of the Ensembl gene ID associated to the main accession.
+MW (kDa)                                     Molecular Weight.
+Possible Coverage (%)                        Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
+Coverage (%)	                               Sequence coverage in percent of the protein designed by the main accession.
+Spectrum Counting NSAF	                     Raw Normalized Spectrum Abundance Factor (NSAF).
+Confident Phosphosites	                     List of the sites where a phosphorylation was confidently localized.
+#Confident Phosphosites	                     Number of sites where a phosphorylation was confidently localized.
+Ambiguous Phosphosites	                     List of the sites where a phosphorylation was ambiguously localized.
+#Ambiguous Phosphosites	                     Number of sites where a phosphorylation was ambiguously localized.
+Protein Inference	                           Protein Inference status of the protein group.
+Secondary Accessions                         Other accessions in the protein group (alphabetical order).
+Protein Group                                The complete protein group (alphabetical order).
+#Validated Peptides                          Number of validated peptides.
+#Peptides                                    Total number of peptides.
+#Unique                                      Total number of peptides unique to this protein group.
+#Validated Unique	                           Total number of peptides unique to this protein group.
+#Validated PSMs                              Number of validated PSMs.
+#PSMs                                        Number of PSMs.
+Confidence [%]	                             Confidence in percent associated to the protein group.
+Validation                                   Indicates the validation level of the protein group.
+==========================================  =====================================================
+
+
+Certificate of Analysis
+'''''''''''''''''''''''
+
+Presents a summary of the most important statistics of the search, grouped by:
+
+* Project Details:
+    ‣ PeptideShaker Version, Date, Experiment, Sample, Replicate Number, Identification Algorithms.
+* Database Search Parameters:
+    ‣ Precursor Tolerance Unit, Precursor Ion m/z Tolerance, Fragment Ion Tolerance Unit, Fragment Ion m/z Tolerance, Cleavage, Enzyme, Missed Cleavages, Specificity, Database, Forward Ion, Rewind Ion, Fixed Modifications, Variable Modifications, Refinement Variable Modifications, Refinement Fixed Modifications.
+* Input Filters:
+    ‣ Minimal Peptide Length, Maximal Peptide Length, Precursor m/z Tolerance, Precursor m/z Tolerance Unit, Unrecognized Modifications Discarded.
+* Validation Summary:
+    • Proteins:
+        ‣ #Validated, Total Possible TP, FDR Limit [%], FNR Limit [%], Confidence Limit, PEP Limit [%], Confidence Accuracy [%].
+    • Peptides:
+        ‣ #Validated, Total Possible TP, FDR Limit [%], FNR Limit [%], Confidence Limit [%], PEP Limit [%], Confidence Accuracy [%].
+    • PSMs:
+        ‣ #Validated PSM, Total Possible TP, FDR Limit [%]: PSMs, Confidence Limit [%], PEP Limit [%], Confidence Accuracy [%].
+* PTM Scoring Settings:
+    ‣ Probabilistic Score, Accounting for Neutral Losses, Threshold.
+* Spectrum Counting Parameters:
+    ‣ Method, Validated Matches Only
+* Annotation Settings:
+    ‣ Intensity Limit, Automatic Annotation, Selected Ions, Neutral Losses, Neutral Losses Sequence Dependence, Fragment Ion m/z Tolerance.
 
 
 Hierachical Report
-------------------
+''''''''''''''''''
 
-* Main Accession:	Main accession of the protein group.
-* Description:	Description of the protein designed by the main accession.
-* PI:	Protein Inference status of the protein group.
-* Secondary Accessions:	Other accessions in the protein group (alphabetical order).
-* Protein Group:	The complete protein group (alphabetical order).
-* #Peptides:	Total number of peptides.
-* #Validated Peptides:	Number of validated peptides.
-* #Unique:	Total number of peptides unique to this protein group.
-* #PSMs:	Number of PSMs
-* #Validated PSMs:	Number of validated PSMs
-* Coverage (%):	Sequence coverage in percent of the protein designed by the main accession.
-* Possible Coverage (%):	Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
-* MW (kDa):	Molecular Weight.
-* Spectrum Counting NSAF: 	Normalized Spectrum Abundance Factor (NSAF)
-* Spectrum Counting emPAI:	exponentially modified Protein Abundance Index (emPAI)
-* Confident Modification Sites: # Confident Modification Sites	List of the sites where a variable modification was confidently localized.
-* Other Modification Sites: # Other Modification Sites	List of the non-confident sites where a variable modification was localized.
-* Score:	Score of the protein group.
-* Confidence:	Confidence in percent associated to the protein group.
-* Decoy:	Indicates whether the protein group is a decoy (1: yes, 0: no).
-* Validation:	Indicates the validation level of the protein group.
-* Protein(s):	Protein(s) to which this peptide can be attached.
-* AAs Before:	The amino-acids before the sequence.
-* Sequence:	Sequence of the peptide.
-* AAs After:	The amino-acids after the sequence.
-* Variable Modifications:	The variable modifications.
-* Localization Confidence:	The confidence in PTMs localization.
-* Fixed Modifications:	The fixed modifications.
-* #Validated PSMs:	Number of validated PSMs.
-* #PSMs:	Number of PSMs.
-* Score:	Score of the peptide.
-* Confidence:	Confidence in percent associated to the peptide.
-* Decoy:	Indicates whether the peptide is a decoy (1: yes, 0: no).
-* Validation:	Indicates the validation level of the protein group.
-* Protein(s):	Protein(s) to which the peptide can be attached.
-* Sequence:	Sequence of the peptide.
-* Modified Sequence:	The peptide sequence annotated with variable modifications.
-* Variable Modifications:	The variable modifications.
-* D-score:	D-score for variable PTM localization.
-* probabilistic PTM score:	The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
-* Localization Confidence:	The confidence in variable PTM localization.
-* Fixed Modifications:	The fixed modifications.
-* Spectrum File:	The spectrum file.
-* Spectrum Title:	The title of the spectrum.
-* Spectrum Scan Number:	The spectrum scan number.
-* RT:	Retention time
-* m/z:	Measured m/z
-* Measured Charge:	The charge as given in the spectrum file.
-* Identification Charge:	The charge as inferred by the search engine.
-* Theoretical Mass:	The theoretical mass of the peptide.
-* Isotope Number:	The isotope number targetted by the instrument.
-* Precursor m/z Error:	The precursor m/z matching error.
-* Score:	Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
-* Confidence:	Confidence in percent associated to the retained PSM.
-* Decoy:	Indicates whether the peptide is a decoy (1: yes, 0: no).
-* Validation:	Indicates the validation level of the protein group.
-
+==========================================  =====================================================
+  Column                                     Description
+==========================================  =====================================================
+Main Accession                               Main accession of the protein group.
+Description	                                 Description of the protein designed by the main accession.
+MW (kDa)                                     Molecular Weight.
+Possible Coverage (%)                        Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
+Coverage (%)                                 Sequence coverage in percent of the protein designed by the main accession.
+Spectrum Counting NSAF                       Normalized Spectrum Abundance Factor (NSAF)
+Confidently Localized Modification Sites	   List of the sites where a variable modification was confidently localized.
+# Confidently Localized Modification Sites	 Number of sites where a variable modification was confidently localized.
+Ambiguously Localized Modification Sites	   List of the sites where ambiguously localized variable modification could possibly be located.
+#Ambiguously Localized Modification Sites	   Number of ambiguously localized modifications.
+Protein Inference	                           Protein Inference status of the protein group.
+Secondary Accessions                         Other accessions in the protein group (alphabetical order).
+Protein Group                                The complete protein group (alphabetical order).
+#Validated Peptides                          Number of validated peptides.
+#Peptides                                    Total number of peptides.
+#Unique                                      Total number of peptides unique to this protein group.
+#Validated PSMs                              Number of validated PSMs
+#PSMs                                        Number of PSMs
+Confidence                                   Confidence in percent associated to the protein group.
+Decoy                                        Indicates whether the protein group is a decoy (1: yes, 0: no).
+Validation                                   Indicates the validation level of the protein group.
+==========================================  =====================================================
 
 ------
 
diff -r 7fdd9119cc4f -r bb0130ff73ce searchgui.xml
--- a/searchgui.xml	Thu Feb 20 05:51:38 2020 -0500
+++ b/searchgui.xml	Fri Jan 15 14:06:27 2021 +0000
@@ -1,9 +1,9 @@
-<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1">
+<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@+galaxy@SEARCHGUI_VERSION_SUFFIX@">
     <description>
         Perform protein identification using various search engines and prepare results for input to Peptide Shaker
     </description>
     <macros>
-        <import>macros.xml</import>
+        <import>macros_basic.xml</import>
     </macros>
     <requirements>
         <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
@@ -13,6 +13,8 @@
     <command use_shared_home="false">
 <![CDATA[
         #from datetime import datetime
+        #import json
+        #import os
         #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
         #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
         #set $temp_stderr = "searchgui_stderr"
@@ -27,313 +29,29 @@
 
         ## echo the search engines to run (single quotes important because X!Tandem)
         echo '$search_engines_options.engines';
-        echo 'DB: ${input_database.element_identifier} sequences: ${input_database.metadata.sequences}';
+        echo 'DB: ${input_fasta_file.element_identifier} sequences: ${input_fasta_file.metadata.sequences}';
 
         ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
         echo 'searchgui.version=@SEARCHGUI_VERSION@' >> searchgui.properties;
 
-        #for $mgf in $peak_lists:
-            #set $input_name = $mgf.element_identifier.split('/')[-1].replace(".mgf", "") + ".mgf"
-            ln -s -f '${mgf}' '${input_name}';
-            #set $encoded_id = $__app__.security.encode_id($mgf.id)
-            echo 'Spectrums:${mgf.element_identifier}(API:${encoded_id})';
-        #end for
-        ##ln -s "${input_database}" input_database.fasta;
-        cp "${input_database}" input_database.fasta;
-
-        ###########################################
-        ####       Set paths                   ####
-        ###########################################
-        echo 'Setting paths' &&
-        searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI
-            --exec_dir="\$cwd/${bin_dir}"
-            -temp_folder \$cwd
-            -log \$cwd/searchgui.log  2>> $temp_stderr &&
-
-        ###########################################
-        ####       Creating decoy database     ####
-        ###########################################
-        #if $protein_database_options.create_decoy:
-            echo 'Creating decoy database.' &&
-            searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI
-                --exec_dir="\$cwd/${bin_dir}"
-                -in input_database.fasta
-                -decoy  2>> $temp_stderr &&
-            rm input_database.fasta &&
-            cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
-            ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
-        #end if
-
-        #####################################################
-        ## generate IdentificationParameters for SearchGUI ##
-        #####################################################
-        echo 'setting identification parameters' &&
-        (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI
-            --exec_dir="\$cwd/${bin_dir}"
-            -out SEARCHGUI_IdentificationParameters.par
-
-            @GENERAL_PARAMETERS@
-
-            -db input_database.fasta
-            $protein_database_options.use_gene_mapping
-            #if $protein_database_options.use_gene_mapping:
-                $protein_database_options.update_gene_mapping
-            #else:
-                -updateGeneMapping 0
+        #for $peak_list_file in $peak_lists_files:
+            #set $input_name = ""
+            #if $peak_list_file.is_of_type("mgf"):
+                #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mgf", "") + ".mgf"
+            #else if $peak_list_file.is_of_type("mzml"):
+                #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mzml", "") + ".mzml"
             #end if
-
-            #if $advanced_options.xtandem.xtandem_advanced == "yes"
-
-                -xtandem_npeaks ${advanced_options.xtandem.xtandem_npeaks}
-                -xtandem_min_peaks ${advanced_options.xtandem.xtandem_min_peaks}
-                -xtandem_min_frag_mz ${advanced_options.xtandem.xtandem_min_frag_mz}
-                -xtandem_min_prec_mass ${advanced_options.xtandem.xtandem_min_prec_mass}
-                -xtandem_noise_suppr ${advanced_options.xtandem.xtandem_noise_suppr}
-                -xtandem_dynamic_range ${advanced_options.xtandem.xtandem_dynamic_range}
-                -xtandem_quick_acetyl ${advanced_options.xtandem.xtandem_quick_acetyl}
-                -xtandem_quick_pyro ${advanced_options.xtandem.xtandem_quick_pyro}
-                -xtandem_stp_bias ${advanced_options.xtandem.xtandem_stp_bias}
-                -xtandem_evalue ${advanced_options.xtandem.xtandem_evalue}
-                -xtandem_output_proteins ${advanced_options.xtandem.xtandem_output_proteins}
-                -xtandem_output_sequences ${advanced_options.xtandem.xtandem_output_sequences}
-                -xtandem_output_spectra ${advanced_options.xtandem.xtandem_output_spectra}
-                ## -xtandem_skyline_path ${advanced_options.xtandem.xtandem_skyline_path}
-
-                #if $advanced_options.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
-                    -xtandem_refine 1
-                    -xtandem_refine_unc ${advanced_options.xtandem.xtandem_refine.xtandem_refine_unc}
-                    -xtandem_refine_semi ${advanced_options.xtandem.xtandem_refine.xtandem_refine_semi}
-                    -xtandem_refine_p_mut ${advanced_options.xtandem.xtandem_refine.xtandem_refine_p_mut}
-                    -xtandem_refine_snaps ${advanced_options.xtandem.xtandem_refine.xtandem_refine_snaps}
-                    -xtandem_refine_spec_synt ${advanced_options.xtandem.xtandem_refine.xtandem_refine_spec_synt}
-                    -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_pot}
-                    -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_evalue}
-
-                #end if
-            #else
-                -xtandem_output_spectra 1
-            #end if
-
-            #if $advanced_options.omssa.omssa_advanced == "yes"
-                -omssa_hitlist_length ${advanced_options.omssa.hitlist_length}
-                -omssa_remove_prec ${advanced_options.omssa.remove_precursor}
-                -omssa_scale_prec ${advanced_options.omssa.scale_precursor}
-                -omssa_estimate_charge ${advanced_options.omssa.estimate_charge}
-                -omssa_memory ${advanced_options.omssa.omssa_memory}
-                -omssa_neutron ${advanced_options.omssa.omssa_neutron}
-                -omssa_low_intensity "${advanced_options.omssa.omssa_low_intensity}"
-                -omssa_high_intensity ${advanced_options.omssa.omssa_high_intensity}
-                -omssa_intensity_incr ${advanced_options.omssa.omssa_intensity_incr}
-                -omssa_single_window_wd ${advanced_options.omssa.omssa_single_window_wd}
-                -omssa_double_window_wd ${advanced_options.omssa.omssa_double_window_wd}
-                -omssa_single_window_pk ${advanced_options.omssa.omssa_single_window_pk}
-                -omssa_double_window_pk ${advanced_options.omssa.omssa_double_window_pk}
-                -omssa_min_ann_int_pks ${advanced_options.omssa.omssa_min_ann_int_pks}
-                -omssa_min_annotated_peaks ${advanced_options.omssa.omssa_min_annotated_peaks}
-                -omssa_min_peaks ${advanced_options.omssa.omssa_min_peaks}
-                -omssa_methionine ${advanced_options.omssa.omssa_methionine}
-                -omssa_max_ladders ${advanced_options.omssa.omssa_max_ladders}
-                -omssa_max_frag_charge ${advanced_options.omssa.omssa_max_frag_charge}
-                -omssa_fraction ${advanced_options.omssa.omssa_fraction}
-                -omssa_plus_one ${advanced_options.omssa.omssa_plus_one}
-                -omssa_charge ${advanced_options.omssa.omssa_charge}
-                -omssa_prec_per_spectrum ${advanced_options.omssa.omssa_prec_per_spectrum}
-                -omssa_forward ${advanced_options.omssa.omssa_forward}
-                -omssa_rewind ${advanced_options.omssa.omssa_rewind}
-                -omssa_max_frag_series ${advanced_options.omssa.omssa_max_frag_series}
-                -omssa_corr ${advanced_options.omssa.omssa_corr}
-                -omssa_consecutive_p ${advanced_options.omssa.omssa_consecutive_p}
-                -omssa_it_sequence_evalue ${advanced_options.omssa.omssa_it_sequence_evalue}
-                -omssa_it_spectrum_evalue ${advanced_options.omssa.omssa_it_spectrum_evalue}
-                -omssa_it_replace_evalue ${advanced_options.omssa.omssa_it_replace_evalue}
-                -omssa_max_evalue ${advanced_options.omssa.omssa_max_evalue}
-                -omssa_hitlist_charge ${advanced_options.omssa.omssa_hitlist_charge}
-                -omssa_min_pep_length ${advanced_options.omssa.omssa_min_pep_length}
-                -omssa_max_pep_length ${advanced_options.omssa.omssa_max_pep_length}
-                -omssa_format ${advanced_options.omssa.omssa_format}
-            #end if
-
-            #if $advanced_options.msgf.msgf_advanced == "yes"
-                -msgf_decoy ${advanced_options.msgf.msgf_decoy}
-                -msgf_min_pep_length ${advanced_options.msgf.msgf_min_pep_length}
-                -msgf_max_pep_length ${advanced_options.msgf.msgf_max_pep_length}
-                -msgf_termini ${advanced_options.msgf.msgf_termini}
-                -msgf_num_ptms ${advanced_options.msgf.msgf_num_ptms}
-                -msgf_instrument ${advanced_options.msgf.msgf_instrument}
-                -msgf_fragmentation ${advanced_options.msgf.msgf_fragmentation}
-                -msgf_protocol ${advanced_options.msgf.msgf_protocol}
-                -msgf_num_matches ${advanced_options.msgf.msgf_num_matches}
-                -msgf_additional ${advanced_options.msgf.msgf_additional}
-            #end if
-
-            #if $advanced_options.ms_amanda.ms_amanda_advanced == "yes"
-                 -ms_amanda_decoy ${advanced_options.ms_amanda.ms_amanda_decoy}
-                 -ms_amanda_instrument "${advanced_options.ms_amanda.ms_amanda_instrument}"
-                 -ms_amanda_max_rank ${advanced_options.ms_amanda.ms_amanda_max_rank}
-                 -ms_amanda_mono ${advanced_options.ms_amanda.ms_amanda_mono}
-            #end if
+            ln -s -f '${peak_list_file}' '${input_name}';
+            #set $encoded_id = $__app__.security.encode_id($peak_list_file.id)
+            echo 'Spectrums:${peak_list_file.element_identifier}(API:${encoded_id})';
+        #end for
 
-            #if $advanced_options.myrimatch.myrimatch_advanced == "yes"
-                -myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length}
-                -myrimatch_max_pep_length ${advanced_options.myrimatch.myrimatch_max_pep_length}
-                -myrimatch_min_prec_mass ${advanced_options.myrimatch.myrimatch_min_prec_mass}
-                -myrimatch_max_prec_mass ${advanced_options.myrimatch.myrimatch_max_prec_mass}
-                -myrimatch_num_matches ${advanced_options.myrimatch.myrimatch_num_matches}
-                -myrimatch_num_ptms ${advanced_options.myrimatch.myrimatch_num_ptms}
-                -myrimatch_fragmentation ${advanced_options.myrimatch.myrimatch_fragmentation}
-                -myrimatch_termini ${advanced_options.myrimatch.myrimatch_termini}
-                -myrimatch_plus_three ${advanced_options.myrimatch.myrimatch_plus_three}
-                -myrimatch_xcorr ${advanced_options.myrimatch.myrimatch_xcorr}
-                -myrimatch_tic_cutoff ${advanced_options.myrimatch.myrimatch_tic_cutoff}
-                -myrimatch_intensity_classes ${advanced_options.myrimatch.myrimatch_intensity_classes}
-                -myrimatch_class_multiplier ${advanced_options.myrimatch.myrimatch_class_multiplier}
-                -myrimatch_num_batches ${advanced_options.myrimatch.myrimatch_num_batches}
-                -myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak}
-            #end if
-
-
-            #* Not working in tests
-            #if $advanced_options.andromeda.andromeda_advanced == "yes"
-                -andromeda_max_pep_mass ${advanced_options.andromeda.andromeda_max_pep_mass}
-                -andromeda_max_comb ${advanced_options.andromeda.andromeda_max_comb}
-                -andromeda_top_peaks ${advanced_options.andromeda.andromeda_top_peaks}
-                -andromeda_top_peaks_window ${advanced_options.andromeda.andromeda_top_peaks_window}
-                -andromeda_incl_water ${advanced_options.andromeda.andromeda_incl_water}
-                -andromeda_incl_ammonia ${advanced_options.andromeda.andromeda_incl_ammonia}
-                -andromeda_neutral_losses ${advanced_options.andromeda.andromeda_neutral_losses}
-                -andromeda_fragment_all ${advanced_options.andromeda.andromeda_fragment_all}
-                -andromeda_emp_correction ${advanced_options.andromeda.andromeda_emp_correction}
-                -andromeda_higher_charge ${advanced_options.andromeda.andromeda_higher_charge}
-                -andromeda_equal_il ${advanced_options.andromeda.andromeda_equal_il}
-                -andromeda_frag_method ${advanced_options.andromeda.andromeda_frag_method}
-                -andromeda_max_mods ${advanced_options.andromeda.andromeda_max_mods}
-                -andromeda_min_pep_length ${advanced_options.andromeda.andromeda_min_pep_length}
-                -andromeda_max_pep_length ${advanced_options.andromeda.andromeda_max_pep_length}
-                -andromeda_max_psms ${advanced_options.andromeda.andromeda_max_psms}
-                -andromeda_decoy_mode ${advanced_options.andromeda.andromeda_decoy_mode}
-            #end if
-            *#
-
-            #if $advanced_options.tide.tide_advanced == "yes"
-                #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '':
-                  -tide_num_ptms ${advanced_options.tide.tide_max_spectrum_mz}
-                #end if
-                -tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type}
-                -tide_min_pep_length ${advanced_options.tide.tide_min_pep_length}
-                -tide_max_pep_length ${advanced_options.tide.tide_max_pep_length}
-                -tide_min_prec_mass ${advanced_options.tide.tide_min_prec_mass}
-                -tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass}
-                -tide_decoy_format ${advanced_options.tide.tide_decoy_format}
-                -tide_keep_terminals ${advanced_options.tide.tide_keep_terminals}
-                -tide_print_peptides ${advanced_options.tide.tide_print_peptides}
-                -tide_verbosity ${advanced_options.tide.tide_verbosity}
-                -tide_monoisotopic ${advanced_options.tide.tide_monoisotopic}
-                -tide_clip_n_term ${advanced_options.tide.tide_clip_n_term}
-                -tide_digestion_type ${advanced_options.tide.tide_digestion_type}
-                -tide_compute_sp ${advanced_options.tide.tide_compute_sp}
-                -tide_max_psms ${advanced_options.tide.tide_max_psms}
-                -tide_compute_p ${advanced_options.tide.tide_compute_p}
-                -tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz}
-                #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '':
-                  -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz}
-                #end if
-                -tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks}
-                -tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges}
-                -tide_remove_prec ${advanced_options.tide.tide_remove_prec}
-                -tide_remove_prec_tol ${advanced_options.tide.tide_remove_prec_tol}
-                -tide_progress_indicator ${advanced_options.tide.tide_progress_indicator}
-                -tide_use_flanking ${advanced_options.tide.tide_use_flanking}
-                -tide_use_neutral_losses ${advanced_options.tide.tide_use_neutral_losses}
-                -tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width}
-                -tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset}
-                -tide_concat ${advanced_options.tide.tide_concat}
+        ## copy the input .par file to the working folder
+        cp '${input_parameters_file}' './SEARCHGUI_IdentificationParameters.par';
 
-                #set $formats = ["tide_export_text", "tide_export_sqt", "tide_export_pepxml", "tide_export_mzid", "tide_export_pin"]
-                #for $format in $formats:
-                    #if str($advanced_options.tide.tide_export).strip() == $format:
-                      -$format 1
-                    #else:
-                      -$format 0
-                    #end if
-
-                #end for
-
-                -tide_remove_temp ${advanced_options.tide.tide_remove_temp}
-
-            #end if
-
-
-            #if $advanced_options.comet.comet_advanced == "yes"
-
-                #if $advanced_options.comet.comet_spectrum.comet_spectrum_selector == "yes"
-                    -comet_min_peaks ${advanced_options.comet.comet_spectrum.comet_min_peaks}
-                    -comet_min_peak_int ${advanced_options.comet.comet_spectrum.comet_min_peak_int}
-
-                    -comet_remove_prec ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec}
-
-
-                     #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "1"
-                        -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
-                     #end if
-
-                     #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "2"
-                        -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
-                     #end if
-
-                    -comet_clear_mz_range_lower ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_lower}
-                    -comet_clear_mz_range_upper ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_upper}
-                #end if
+        ## copy the input .fasta file to the working folder
+        cp '${input_fasta_file}' './input_fasta_file.fasta';
 
-                #if $advanced_options.comet.comet_search.comet_search_selector == "yes"
-                    -comet_enzyme_type ${advanced_options.comet.comet_search.comet_enzyme_type}
-                    -comet_isotope_correction ${advanced_options.comet.comet_search.comet_isotope_correction}
-                    -comet_min_prec_mass ${advanced_options.comet.comet_search.comet_min_prec_mass}
-                    -comet_max_prec_mass ${advanced_options.comet.comet_search.comet_max_prec_mass}
-                    -comet_num_matches ${advanced_options.comet.comet_search.comet_num_matches}
-                    -comet_max_frag_charge ${advanced_options.comet.comet_search.comet_max_frag_charge}
-                    -comet_remove_meth ${advanced_options.comet.comet_search.comet_remove_meth}
-                    -comet_batch_size ${advanced_options.comet.comet_search.comet_batch_size}
-                    -comet_num_ptms ${advanced_options.comet.comet_search.comet_num_ptms}
-                #end if
-
-                #if $advanced_options.comet.comet_fragment_ions.comet_fragment_ions_selector == "yes"
-                    -comet_frag_bin_offset ${advanced_options.comet.comet_fragment_ions.comet_frag_bin_offset}
-                    -comet_theoretical_fragment_ions ${advanced_options.comet.comet_fragment_ions.comet_theoretical_fragment_ions}
-                #end if
-            #end if
-
-            #if $advanced_options.directtag.directtag_advanced == "yes"
-                -directag_tic_cutoff ${advanced_options.directtag.directag_tic_cutoff}
-                -directag_max_peak_count ${advanced_options.directtag.directag_max_peak_count}
-                -directag_intensity_classes ${advanced_options.directtag.directag_intensity_classes}
-                -directag_adjust_precursor ${advanced_options.directtag.directag_adjust_precursor}
-                -directag_min_adjustment ${advanced_options.directtag.directag_min_adjustment}
-                -directag_max_adjustment ${advanced_options.directtag.directag_max_adjustment}
-                -directag_adjustment_step ${advanced_options.directtag.directag_adjustment_step}
-                -directag_charge_states ${advanced_options.directtag.directag_charge_states}
-                #if str($advanced_options.directtag.directag_output_suffix).strip() != '':
-                -directag_output_suffix ${advanced_options.directtag.directag_output_suffix}
-                #end if
-                -directag_ms_charge_state ${advanced_options.directtag.directag_ms_charge_state}
-                -directag_duplicate_spectra ${advanced_options.directtag.directag_duplicate_spectra}
-                -directag_deisotoping ${advanced_options.directtag.directag_deisotoping}
-                -directag_isotope_tolerance ${advanced_options.directtag.directag_isotope_tolerance}
-                -directag_complement_tolerance ${advanced_options.directtag.directag_complement_tolerance}
-                -directag_tag_length ${advanced_options.directtag.directag_tag_length}
-                -directag_max_var_mods ${advanced_options.directtag.directag_max_var_mods}
-                -directag_max_tag_count ${advanced_options.directtag.directag_max_tag_count}
-                -directag_intensity_weight ${advanced_options.directtag.directag_intensity_weight}
-                -directag_fidelity_weight ${advanced_options.directtag.directag_fidelity_weight}
-                -directag_complement_weight ${advanced_options.directtag.directag_complement_weight}
-            #end if
-
-            #if $advanced_options.novor.novor_advanced == "yes"
-                -novor_fragmentation ${advanced_options.novor.novor_fragmentation}
-                -novor_mass_analyzer ${advanced_options.novor.novor_mass_analyzer}
-            #end if
-
-        2> $temp_stderr)
-        &&
 
         ################
         ## Search CLI ##
@@ -342,24 +60,20 @@
         (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
             --exec_dir="\$cwd/${bin_dir}"
             -spectrum_files \$cwd
+            -fasta_file "\$cwd/input_fasta_file.fasta"
             -output_folder \$cwd/output
-            -id_params SEARCHGUI_IdentificationParameters.par
+            -id_params ./SEARCHGUI_IdentificationParameters.par
 
             -threads "\${GALAXY_SLOTS:-12}"
 
-            #if $advanced_options.searchgui_advanced.searchgui_advanced_selector == 'advanced'
-                -correct_titles "${advanced_options.searchgui_advanced.correct_titles}"
-                $advanced_options.searchgui_advanced.missing_titles
-                -mgf_splitting "${advanced_options.searchgui_advanced.mgf_splitting}"
-                -mgf_spectrum_count "${advanced_options.searchgui_advanced.mgf_spectrum_count}"
+            #if $searchgui_advanced.searchgui_advanced_selector == 'advanced'
+                -correct_titles "${searchgui_advanced.correct_titles}"
+                $searchgui_advanced.missing_titles
+                -mgf_splitting "${searchgui_advanced.mgf_splitting}"
+                -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}"
+                -output_gzip "${searchgui_advanced.output_gzip}"
             #end if
 
-            ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
-            ## the tree is generated afterwards in PeptideShaker
-            ## -protein_index 0
-
-            ##-makeblastdb_folder \$BLAST_ROOT_DIR
-
             #set $engines_list = str($search_engines_options.engines).split(',')
             #if 'X!Tandem' in $engines_list:
                 -xtandem 1
@@ -409,6 +123,12 @@
                 -andromeda 0
             #end if
 
+            #if 'MetaMorpheus' in $engines_list:
+                -meta_morpheus 1
+            #else
+                -meta_morpheus 0
+            #end if
+
             #if 'Novor' in $engines_list:
                 -novor 1
             #else
@@ -441,35 +161,26 @@
 ]]>
     </command>
     <inputs>
+        <param format="json" name="input_parameters_file" type="data" label="Identification Parameters file"/>
 
-        <param format="fasta" name="input_database" type="data" label="Protein Database"
-            help="Select FASTA database from history"/>
-        <section name="protein_database_options" expanded="false" title="Protein Database Options">
-            <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true"
-                label="Create a concatenated target/decoy database before running PeptideShaker"
-                help="Selecting this option will help PeptideShaker calculate FDR values" />
-            <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false"
-                label="gene mappings will be used and saved along with the project (UniProt databases only)"
-                help="This should only be enabled for UniProt databaases" />
-            <param name="update_gene_mapping" type="boolean" truevalue="-updateGeneMapping 1" falsevalue="-updateGeneMapping 0" checked="false"
-                label="Update gene mappings automatically from Ensembl (UniProt databases only)"
-            help="This should only be enabled for UniProt databaases" />
-        </section>
-        <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
-            help="Select appropriate MGF dataset(s) from history" />
+        <param format="fasta" name="input_fasta_file" type="data" label="Fasta file"/>
+
+        <param name="peak_lists_files" format="mgf,mzml" type="data" multiple="true" label="Input Peak Lists"
+            help="Select appropriate MGF/MZML dataset(s) from history" />
 
         <!-- Search Engine Selection -->
         <section name="search_engines_options" expanded="true" title="Search Engine Options">
             <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
-                <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
+                <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA may not work into isolated environments like containers.</help>
                 <option value="X!Tandem" selected="True">X!Tandem</option>
-
                 <option value="MSGF" selected="True">MS-GF+</option>
-                <option value="OMSSA" selected="True">OMSSA</option>
+                <option value="OMSSA">OMSSA</option>
                 <option value="Comet">Comet</option>
                 <option value="Tide">Tide</option>
                 <option value="MyriMatch">MyriMatch</option>
                 <option value="MS_Amanda">MS_Amanda</option>
+                <!-- TODO: MetaMorpheus Waiting for support for dotnet in bioconda package -->
+                <!-- <option value="MetaMorpheus">MetaMorpheus</option> -->
                 <!-- Windows only
                 <option value="Andromeda">Andromeda</option>
                 -->
@@ -483,679 +194,130 @@
             </param>
         </section>
 
-
-        <!-- General Parameters -->
-        <expand macro="general_options"/>
-
-
-        <section name="advanced_options" expanded="false" title="Andvanced Options">
-            <!-- Optional Advanced SearchGUI Parameters -->
-            <conditional name="searchgui_advanced">
-                <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
-                    <option value="basic" selected="True">Default</option>
-                    <option value="advanced">Advanced</option>
-                </param>
-                <when value="basic" />
-                <when value="advanced">
+        <conditional name="searchgui_advanced">
+            <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
+                <option value="basic" selected="True">Default</option>
+                <option value="advanced">Advanced</option>
+            </param>
+            <when value="basic" />
+            <when value="advanced">
                 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
                     help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
                     <option value="0">no correction</option>
                     <option value="1" selected="True">rename spectra</option>
                     <option value="2">delete spectra</option>
                 </param>
-
                 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
                     label="Add missing spectrum titles" help="(-missing_titles)"/>
-
                 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
                     help="Choose a smaller value if you are running on a machine with limited memory"/>
-
                 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
                     help="Choose a smaller value if you are running on a machine with limited memory"/>
-                </when>
-            </conditional>
-
-            <!-- X!TANDEM ADVANCED PARAMETERS -->
-            <conditional name="xtandem">
-                <param name="xtandem_advanced" type="select" label="X!Tandem Options">
-                    <option value="yes">Advanced</option>
-                    <option value="no" selected="True">Default</option>
-                </param>
-                <when value="no" />
-                <when value="yes">
-                    <param name="xtandem_npeaks" type="integer" value="50"
-                        label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/>
-                    <param name="xtandem_min_peaks" type="integer" value="15"
-                        label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
-                    <param name="xtandem_min_frag_mz" type="integer" value="200"
-                        label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/>
-                    <param name="xtandem_min_prec_mass" type="integer" value="200"
-                        label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/>
-                    <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0"
-                        label="X!Tandem: Noise Suppression" help="Use noise suppression"/>
-                    <param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra"
-                        label="X!Tandem: Dynamic Range" value="100" type="integer" />
-                    <param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection"
-                        label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" />
-                    <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection"
-                        label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" />
-                    <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
-                        label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" />
-                    <param name="xtandem_evalue" help="Highest value for recorded peptides"
-                        label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" />
-                    <param name="xtandem_output_proteins" help="Controls output of protein sequences"
-                        label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" />
-                    <param name="xtandem_output_sequences" help="Controls output of sequence information"
-                        label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
-                    <param name="xtandem_output_spectra" help="Controls output of spectrum information"
-                        label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" />
-                    <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="txt" help="Path to a spectrum data file for use by skyline." -->
-
-                    <conditional name="xtandem_refine"><!-- -xtandem_refine -->
-                        <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
-                            <option value="no" selected="True">Don't refine</option>
-                            <option value="yes" >Use refinement</option>
-                        </param>
-                        <when value="no"/>
-                        <when value="yes">
-                            <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" checked="true"
-                                label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
-                            <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false"
-                                label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/>
-                            <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" checked="false"
-                                label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
-                            <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true"
-                                label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
-                            <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" checked="true"
-                                label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
-                            <param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false"
-                                label="X!Tandem: Use potential modifications, refinement" help="Controls the use of refinement modifications in all refinement modules."/>
-                            <param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement"
-                                label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" />
-                        </when>
-                    </conditional>
-                </when>
-            </conditional>
-
-            <!-- OMSSA ADVANCED PARAMETERS -->
-            <conditional name="omssa">
-                <param name="omssa_advanced" type="select" label="OMSSA Options">
-                    <option value="yes">Advanced</option>
-                    <option value="no" selected="True">Default</option>
-                </param>
-                <when value="no" />
-                <when value="yes">
-                    <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
-                    <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
-                    <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
-                    <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
-
-                    <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
-                        label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
-                    <param name="omssa_neutron" type="float" value="1446.94"
-                           label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
-                    <param name="omssa_low_intensity" type="float" value="0.0"
-                        label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
-                    <param name="omssa_high_intensity" type="float" value="0.2"
-                        label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />
-                       <param name="omssa_intensity_incr" type="float" value="0.0005"
-                           label="OMSSA: Intensity Increment" help="Intensity increment" />
-                    <param name="omssa_single_window_wd" type="integer" value="27"
-                        label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" />
-                    <param name="omssa_double_window_wd" type="integer" value="14"
-                        label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" />
-                    <param name="omssa_single_window_pk" type="integer" value="2"
-                        label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" />
-                    <param name="omssa_double_window_pk" type="integer" value="2"
-                        label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" />
-                    <param name="omssa_min_ann_int_pks" type="integer" value="6"
-                        label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" />
-                    <param name="omssa_min_annotated_peaks" type="integer" value="2"
-                        label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" />
-                       <param name="omssa_min_peaks" type="integer" value="4"
-                           label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" />
-                    <param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true"
-                        label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" />
-                    <param name="omssa_max_ladders" type="integer" value="128"
-                        label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" />
-                    <param name="omssa_max_frag_charge" type="integer" value="2"
-                        label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" />
-                    <param name="omssa_fraction" type="float" value="0.95"
-                        label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" />
-                    <param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true"
-                        label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/>
-                    <param name="omssa_charge" type="select"
-                        label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" >
-                        <option value="0" >Minus</option>
-                        <option value="1" selected="True">Plus</option>
-                    </param>
-                    <param name="omssa_prec_per_spectrum" type="integer" value="1"
-                        label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" />
-                    <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true"
-                        label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" />
-                    <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true"
-                        label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" />
-                    <param name="omssa_max_frag_series" type="integer" value="100"
-                        label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" />
-                    <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true"
-                        label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" />
-                    <param name="omssa_consecutive_p" type="float" value="0.5"
-                        label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" />
-                    <param name="omssa_it_sequence_evalue" type="float" value="0.0"
-                        label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" />
-                    <param name="omssa_it_spectrum_evalue" type="float" value="0.01"
-                        label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" />
-                    <param name="omssa_it_replace_evalue" type="float" value="0.01"
-                        label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)" />
-                    <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
-                        label="OMSSA: Remove Precursor" help="Remove precursors" />
-                    <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
-                        label="OMSSA: Scale Precursor Mass" help="scale precursor mass" />
-                    <param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true"
-                        label="OMSSA: Remove Precursor" help="Remove precursors" />
-                    <param name="omssa_max_evalue" type="float" value="100"
-                        label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" />
-                    <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
-                        label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" />
-                    <param name="omssa_it_replace_evalue" type="float" value="100"
-                        label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" />
-                    <param name="omssa_hitlist_length" type="integer" value="0"
-                        label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" />
-                    <param name="omssa_hitlist_charge" type="integer" value="30"
-                        label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" />
-                    <param name="omssa_min_pep_length" type="integer" value="4"
-                        label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" />
-                    <param name="omssa_max_pep_length" type="integer" value="40"
-                        label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" />
-                    <param name="omssa_format" label="OMSSA output format" type="select" >
-                        <option value="0" selected="True">OMX</option>
-                        <option value="1" >CSV</option>
-                    </param>
-                </when>
-            </conditional>
-
-            <!-- MS-GF+ ADVANCED PARAMETERS -->
-            <conditional name="msgf">
-                <param name="msgf_advanced" type="select" label="MSGF Options">
-                    <option value="yes">Advanced</option>
-                    <option value="no" selected="True">Default</option>
-                </param>
-                <when value="no" />
-                <when value="yes">
-                    <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
-                        label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
-                    <param name="msgf_min_pep_length" type="integer" value="6"
-                        label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
-                    <param name="msgf_max_pep_length" type="integer" value="30"
-                        label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
-                    <param name="msgf_termini" type="select" format="txt"
-                        label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
-                        <option value="0">0 (ie non-specific cleavage)</option>
-                        <option value="1">1 (ie semi-tryptic cleavage)</option>
-                        <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
-                    </param>
-                    <param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/>
-
-                    <param name="msgf_instrument" label="MSGF: Instrument type" type="select" help="Identifier of the instrument to generate MS/MS spectra (used to determine the scoring model)">
-                        <option value="0" selected="True">Low-res LCQ/LTQ</option>
-                        <option value="1" >High-res LTQ</option>
-                        <option value="2" >TOF</option>
-                        <option value="3" >Q-Exactive</option>
-                    </param>
-                    <param name="msgf_fragmentation" label="MSGF: Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
-                        <option value="0" selected="True">As written in the spectrum or CID if no info</option>
-                        <option value="1" >CID</option>
-                        <option value="2" >ETD</option>
-                        <option value="3" >HCD</option>
-                    </param>
-                    <param name="msgf_protocol" label="MSGF: Protocol type" type="select" help="Protocol identifier. Protocols are used to enable scoring parameters for enriched and/or labeled samples">
-                        <option value="0" selected="True">Automatic</option>
-                        <option value="1" >Phosphorylation</option>
-                        <option value="2" >iTRAQ</option>
-                        <option value="3" >iTRAQPhospho</option>
-                        <option value="4" >TMT</option>
-                        <option value="5" >Standard</option>
-                    </param>
-                    <param name="msgf_num_matches" label="MSGF: Maximum Number of Spectrum Matches" type="integer" value="1" help="Number of peptide matches per spectrum to report" />
-                    <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export">
-                        <option value="0" selected="True">output basic scores only</option>
-                        <option value="1" >output additional features</option>
-                    </param>
-                </when>
-            </conditional>
-
-              <!-- MS-AMANDA ADVANCED PARAMETERS  -->
-            <conditional name="ms_amanda">
-                <param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
-                    <option value="yes">Advanced</option>
-                    <option value="no" selected="True">Default</option>
-                </param>
-                <when value="no" />
-                <when value="yes">
-                    <param name="ms_amanda_decoy"  type="boolean" truevalue="1" falsevalue="0" checked="false"
-                        label="MS Amanda: Generate Decoys" help="generate decoys" />
-                    <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="select"
-                      help="MS Amanda instrument id option. Available ion types are listed here.">
-
-                      <option value="b, y" selected="True">b, y</option>
-                      <option value="b, y, -H2O, -NH3" >b, y, -H2O, -NH3</option>
-                      <option value="a, b, y, -H2O, -NH3, Imm" >a, b, y, -H2O, -NH3, Imm</option>
-                      <option value="a, b, y, -H2O, -NH3" >a, b, y, -H2O, -NH3</option>
-                      <option value="a, b, y" >a, b, y</option>
-                      <option value="a, b, y, Imm" >a, b, y, Imm</option>
-                      <option value="a, b, y, z, -H2O, -NH3, Imm" >a, b, y, z, -H2O, -NH3, Imm</option>
-                      <option value="c, y, z+1, z+2" >c, y, z+1, z+2</option>
-                      <option value="b, c, y, z+1, z+2" >b, c, y, z+1, z+2</option>
-                      <option value="b, y, INT" >b, y, INT</option>
-                      <option value="b, y, INT, Imm" >b, y, INT, Imm</option>
-                      <option value="a, b, y, INT" >a, b, y, INT</option>
-                      <option value="a, b, y, INT, IMM" >a, b, y, INT, IMM</option>
-                      <option value="a, b, y, INT, IMM, -H2O" >a, b, y, INT, IMM, -H2O</option>
-                      <option value="a, b, y, INT, IMM, -H2O, -NH3" >a, b, y, INT, IMM, -H2O, -NH3</option>
-                      <option value="a, b, y, INT, IMM, -NH3" >a, b, y, INT, IMM, -NH3</option>
-
-                    </param>
-                    <param name="ms_amanda_max_rank" type="integer" value="10"
-                        label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" />
-                    <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true"
-                        label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" />
-                </when>
-            </conditional>
-
+                <param name="output_gzip" type="boolean" checked="true" truevalue="1" falsevalue="0"
+                    label="Gzip result files"/>
+            </when>
+        </conditional>
 
-            <!-- TIDE ADVANCED PARAMETERS -->
-            <conditional name="tide">
-                <param name="tide_advanced" type="select" label="TIDE Options">
-                    <option value="yes">Advanced</option>
-                    <option value="no" selected="True">Default</option>
-                </param>
-                <when value="no" />
-                <when value="yes">
-                    <param name="tide_num_ptms" type="integer" value="" optional="true"
-                        label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/>
-                    <param name="tide_num_ptms_per_type" type="integer" value="2"
-                        label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/>
-                    <param name="tide_min_pep_length" type="integer" value="6"
-                        label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/>
-                    <param name="tide_max_pep_length" type="integer" value="30"
-                        label="TIDE: Maximum Peptide Length" help="Set the maximum length of peptide to be considered"/>
-                    <param name="tide_min_prec_mass" type="float" value="200.0"
-                        label="TIDE: Minimum Precursor Mass" help="Set the minimum precursor mass to be considered"/>
-                    <param name="tide_max_prec_mass" type="float" value="7200.0"
-                        label="TIDE: Maximum Precursor Mass" help="Set the maximum precursor mass to be considered"/>
-                    <param name="tide_decoy_format" label="TIDE: Decoy Format" type="select" help="Select the format for generating the decoy sequences">
-                        <option value="none" selected="True">none</option>
-                        <option value="shuffle" >shuffle</option>
-                        <option value="peptide-revers" >peptide-reverse</option>
-                        <option value="protein-reverse" >protein-reverse</option>
-                    </param>
-                    <param name="tide_keep_terminals" label="TIDE: Keep Terminals" type="select" help="Select to keep the terminal amino acids when creating decoys">
-                        <option value="N" >N</option>
-                        <option value="C" >C</option>
-                        <option value="NC" selected="True">NC</option>
-                        <option value="non" >none</option>
-                    </param>
-                    <param name="tide_decoy_seed" type="integer" value="1"
-                        label="TIDE: Decoy Seed" help="Set the decoy seed"/>
-                    <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"
-                        label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/>
-                    <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress">
-                        <option value="0" >0</option>
-                        <option value="10" >10</option>
-                        <option value="20" >20</option>
-                        <option value="30" selected="True">30</option>
-                        <option value="40" >40</option>
-                        <option value="50" >50</option>
-                        <option value="60" >60</option>
-                    </param>
-
-                    <param name="tide_monoisotopic" type="boolean" truevalue="1" falsevalue="0" checked="true"
-                        label="TIDE: Monoisotopic" help="If true, the precursor mass is monoisotopic"/>
-                    <param name="tide_clip_n_term" type="boolean" truevalue="1" falsevalue="0" checked="false"
-                        label="TIDE: Clip Nterm Methionine" help="If true, the Nterm Methionine will be clipped"/>
-                    <param name="tide_digestion_type" label="TIDE: Digestion Type" type="select" help="Either both ends (full-digest) or at least one end (partial-digest) of a peptide must conform to enzyme specificity rules">
-                        <option value="full-digest" selected="True">full-digest</option>
-                        <option value="partial-digest" >partial-digest</option>
-                    </param>
-                    <param name="tide_compute_sp" type="boolean" truevalue="1" falsevalue="0" checked="false"
-                        label="TIDE: Compute SP" help="If true, the SP-score is calculated"/>
-                    <param name="tide_max_psms" type="integer" value="10"
-                        label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/>
-                    <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false"
-                        label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/>
-                    <param name="tide_min_spectrum_mz" type="float" value="0.0"
-                        label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/>
-                    <param name="tide_max_spectrum_mz" type="float" value="" optional="true"
-                        label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/>
-                    <param name="tide_min_spectrum_peaks" type="integer" value="20"
-                        label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/>
-                    <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching">
-                        <option value="1" >1</option>
-                        <option value="2" >2</option>
-                        <option value="3" >3</option>
-                        <option value="all" selected="True">all</option>
-                    </param>
-                    <param name="tide_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
-                        label="TIDE: Remove Precursor" help="If true, the peak that corresponds to the precursor mass is excluded"/>
-                    <param name="tide_remove_prec_tol" type="float" value="1.5"
-                        label="TIDE: Remove Precursor Tolerance" help="Choose the threshold for precursor mass searching (for precursor peak removal)"/>
-                    <param name="tide_progress_indicator" type="integer" value="1000"
-                        label="TIDE: Progress Indicator" help="Choose the progress indicator frequency  (in number of fragmentation spectra processed)"/>
-                    <param name="tide_use_flanking" type="boolean" truevalue="1" falsevalue="0" checked="false"
-                        label="TIDE: Use Flanking" help="Includes two flanking peaks on either side of each b- and y-ion to compute the XCorr"/>
-                    <param name="tide_use_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="false"
-                        label="TIDE: Neutral Losses" help="Includes fragment peaks with neutral losses to perform the matching"/>
-                    <param name="tide_mz_bin_width" type="float" value="0.02"
-                        label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/>
-                    <param name="tide_mz_bin_offset" type="float" value="0.0"
-                        label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/>
-                    <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false"
-                        label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/>
-
-                    <param name="tide_export" label="TIDE: Output Format" type="select" help="Choose the output format">
-                        <option value="tide_export_text" selected="True">Text</option>
-                        <option value="tide_export_sqt" >SQT</option>
-                        <option value="tide_export_pepxml" >pepxml</option>
-                        <option value="tide_export_mzid" >MzIdentML</option>
-                        <option value="tide_export_pin" >Percolator input file</option>
-                    </param>
-
-                    <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"
-                        label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>
-                </when>
-            </conditional>
-
-
-            <!-- MyriMatch ADVANCED PARAMETERS -->
-            <conditional name="myrimatch">
-                <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
-                    <option value="yes">Advanced</option>
-                    <option value="no" selected="True">Default</option>
-                </param>
-                <when value="no" />
-                <when value="yes">
-                    <param name="myrimatch_min_pep_length"  type="integer" value="8"
-                        label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" />
-                    <param name="myrimatch_max_pep_length"  type="integer" value="30"
-                        label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" />
-                    <param name="myrimatch_min_prec_mass"  type="float" value="600.0"
-                        label="MyriMatch: Minimum Precursor Mass" help="Minimum precursor mass of parent ion to be considered" />
-                    <param name="myrimatch_max_prec_mass"  type="float" value="5000.0"
-                        label="MyriMatch: Maximum Precursor Mass" help="Maximum precursor mass of parent ion to be considered" />
-                    <param name="myrimatch_num_matches"  type="integer" value="10"
-                        label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
-                    <param name="myrimatch_num_ptms"  type="integer" value="2"
-                        label="MyriMatch: Max Variable PTMs per Peptide" help="Set the number of PTMS allowed per peptide" />
-                    <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)">
-                        <option value="CID" selected="True">CID</option>
-                        <option value="HCD" >HCD</option>
-                        <option value="ETD" >ETD</option>
-                    </param>
-                    <param name="myrimatch_termini" label="MyriMatch: Enzymatic Terminals" type="select" help="Select the number of enzymatic terminals">
-                        <option value="0">None required</option>
-                        <option value="1">At least one</option>
-                        <option value="2" selected="True" >Both</option>
-                    </param>
-                    <param name="myrimatch_plus_three"  type="boolean" truevalue="1" falsevalue="0" checked="true"
-                        label="MyriMatch: Use Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" />
-                    <param name="myrimatch_xcorr"  type="boolean" truevalue="1" falsevalue="0" checked="false"
-                        label="MyriMatch: Compute Xcorr" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" />
-                    <param name="myrimatch_tic_cutoff"  type="float" value="0.98"
-                        label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained (0.0 - 1.0)" />
-                    <param name="myrimatch_intensity_classes"  type="integer" value="3"
-                        label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" />
-                    <param name="myrimatch_class_multiplier"  type="integer" value="2"
-                        label="MyriMatch: Class Size Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" />
-                    <param name="myrimatch_num_batches"  type="integer" value="50"
-                        label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" />
-                    <param name="myrimatch_max_peak"  type="integer" value="100"
-                        label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
-                </when>
-            </conditional>
-
-
-            <!-- Andromeda ADVANCED PARAMETERS -->
-            <!-- Windows only
-            <conditional name="andromeda">
-                <param name="andromeda_advanced" type="select" label="Andromeda Options">
-                    <option value="yes">Advanced</option>
-                    <option value="no" selected="True">Default</option>
-                </param>
-                <when value="no" />
-                <when value="yes">
-                    <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" />
-                    <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" />
-                    <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" />
-                    <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" />
-                    <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" />
-                    <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" />
-                    <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" />
-                    <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" />
-                    <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" />
-                    <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" />
-                    <param name="andromeda_equal_il" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda whether I and L should be considered indistinguishable, default is: false" />
-                    <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." >
-                       <option value="CID" selected="true">CID</option>
-                       <option value="HCD">HCD</option>
-                       <option value="EDT">EDT</option>
-                    </param>
-                    <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" />
-                    <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" />
-                    <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" />
-                    <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" />
-                    <param name="andromeda_decoy_mode" type="boolean" truevalue="decoy" falsevalue="none" checked="false" label="Andromeda decoy mode" />
-                </when>
-            </conditional>
-            -->
-
-            <!-- Comet ADVANCED PARAMETERS -->
-            <conditional name="comet">
-                <param name="comet_advanced" type="select" label="Comet Options">
-                    <option value="yes">Advanced</option>
-                    <option value="no" selected="True">Default</option>
-                </param>
-                <when value="no" />
-                <when value="yes">
-                    <!-- Spectrum Related parameters -->
-                    <conditional name="comet_spectrum">
-                        <param name="comet_spectrum_selector" type="select" label="Comet: Spectrum Related">
-                            <option value="yes">Set Spectrum Parameters</option>
-                            <option value="no" selected="True">Keep Default Spectrum Parameters</option>
-                        </param>
-                        <when value="no" />
-                        <when value="yes">
-                            <param name="comet_min_peaks"  type="integer" value="10"
-                                label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" />
-                            <param name="comet_min_peak_int"  type="float" value="0.0"
-                                label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" />
-                            <conditional name="comet_prec">
-                                <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal">
-                                    <option value="0"  selected="True" >off</option>
-                                    <option value="1">on</option>
-                                    <option value="2">as expected for ETD/ECD spectra</option>
-                                </param>
-                                <when value="0" />
-                                <when value="1">
-                                    <param name="comet_remove_prec_tol"  type="float" value="1.5"
-                                        label="Comet: Remove Precursor Tolerance" />
-                                </when>
-                                <when value="2">
-                                    <param name="comet_remove_prec_tol"  type="float" value="1.5"
-                                        label="Comet: Remove Precursor Tolerance" />
-                                </when>
-                            </conditional>
-                            <param name="comet_clear_mz_range_lower"  type="float" value="0.0"
-                                label="Comet: Minimum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, lower m/z range" />
-                            <param name="comet_clear_mz_range_upper"  type="float" value="0.0"
-                                label="Comet: Maximum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, upper m/z range" />
-                        </when>
-                    </conditional>
-                      <!-- Search Related parameters -->
-                    <conditional name="comet_search">
-                        <param name="comet_search_selector" type="select" label="Comet: Search Related">
-                            <option value="yes">Set Search Parameters</option>
-                            <option value="no" selected="True">Keep Default Search Parameters</option>
-                        </param>
-                        <when value="no" />
-                        <when value="yes">
-                            <param name="comet_enzyme_type" label="Comet: Enzyme Type" type="select" help="Specifies the number of enzyme termini a peptide must have">
-                                <option value="1">semi-specific</option>
-                                <option value="2" selected="True">full-enzyme</option>
-                                <option value="8">unspecific N-term</option>
-                                <option value="9">unspecific C-term</option>
-                            </param>
-                            <param name="comet_isotope_correction" label="Comet: Isotope Correction" type="select" help="Controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement">
-                                <option value="0" selected="True">off</option>
-                                <option value="1">-1,0,+1,+2,+3</option>
-                                <option value="2">-8,-4,0,+4,+8</option>
-                            </param>
-                            <param name="comet_min_prec_mass"  type="float" value="0.0"
-                                label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" />
-                            <param name="comet_max_prec_mass"  type="float" value="10000.0"
-                                label="Comet: Maximum Precursor Mass" help="The maximum precursor mass considered" />
-                            <param name="comet_num_matches"  type="integer" value="10"
-                                label="Comet: Maximum Number of Matches" help="The maximum number of peptide matches per spectrum" />
-                            <param name="comet_max_frag_charge"  type="integer" value="3"
-                                label="Comet: Maximum Fragment Charge" help="Sets the maximum fragment charge (fill value between 1 and 5)" />
-                            <param name="comet_remove_meth"  type="boolean" truevalue="1" falsevalue="0" checked="false"
-                                label="Comet: Remove Methionine" help="Specifies whether the N-terminal methionine is cleaved prior to matching" />
-                            <param name="comet_batch_size"  type="integer" value="0"
-                                label="Comet: Batch Size" help="0 means load and search all spectra at once, otherwise spectra are loaded and searched in batches of the number specified" />
-                            <param name="comet_num_ptms"  type="integer" value="10"
-                                label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" />
-                        </when>
-                    </conditional>
-                    <!-- Fragment Ions Related parameters -->
-                    <conditional name="comet_fragment_ions">
-                        <param name="comet_fragment_ions_selector" type="select" label="Comet: Fragment Ions Related">
-                            <option value="yes">Set Fragment Ions Parameters</option>
-                            <option value="no" selected="True">Keep Default Fragment Ions Parameters</option>
-                        </param>
-                        <when value="no" />
-                        <when value="yes">
-                            <param name="comet_frag_bin_offset"  type="float" value="0.4"
-                                label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" />
-                            <param name="comet_theoretical_fragment_ions"  type="integer" value="0"
-                                label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" />
-                        </when>
-                    </conditional>
-                </when>
-            </conditional>
-            <conditional name="directtag">
-                <param name="directtag_advanced" type="select" label="DirectTag Options">
-                    <option value="yes">Advanced</option>
-                    <option value="no" selected="True">Default</option>
-                </param>
-                <when value="no" />
-                <when value="yes">
-                    <param name="directag_tic_cutoff" type="integer" value="85" label="DirecTag TIC cutoff in percent, default is '85'."/>
-                    <param name="directag_max_peak_count" type="integer" value="400" label="DirecTag max peak count, default is '400'."/>
-                    <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses, default is '3'."/>
-                    <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor, default is false."/>
-                    <param name="directag_min_adjustment" type="float" value="-2.5" label="DirecTag minimum precursor adjustment, default is '-2.5'."/>
-                    <param name="directag_max_adjustment" type="float" value="2.5" label="DirecTag maximum precursor adjustment, default is '2.5'."/>
-                    <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step, default is '0.1'."/>
-                    <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered, default is '3'."/>
-                    <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix, default is no suffix."/>
-                    <param name="directag_ms_charge_state" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag use charge state from M spectrum, default is false."/>
-                    <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge, default is true."/>
-                    <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode, default is no deisotoping">
-                        <option value="0" selected="true">no deisotoping</option>
-                        <option value="1">precursor only</option>
-                        <option value="2">precursor and candidate</option>
-                    </param>
-                    <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is '0.25'."/>
-                    <param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is '0.5'."/>
-                    <param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is '3'."/>
-                    <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is '2'."/>
-                    <param name="directag_max_tag_count" type="integer" value="20" label="DirecTag maximum tag count, default is '20'."/>
-                    <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight, default is '1.0'."/>
-                    <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight, default is '1.0'."/>
-                    <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight, default is '1.0'."/>
-                </when>
-            </conditional>
-
-            <conditional name="novor">
-                <param name="novor_advanced" type="select" label="Novor Options">
-                    <option value="yes">Advanced</option>
-                    <option value="no" selected="True">Default</option>
-                </param>
-                <when value="no" />
-                <when value="yes">
-                    <param name="novor_fragmentation" type="select" label="Novor fragmentation method">
-                        <option value="HCD" selected="True">HCD</option>
-                        <option value="CID">CID</option>
-                    </param>
-                    <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra">
-                        <option value="FT" selected="True">FT</option>
-                        <option value="Trap" >Trap</option>
-                        <option value="TOF" >TOF</option>
-                    </param>
-                </when>
-            </conditional>
-        </section>
     </inputs>
     <outputs>
         <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
     </outputs>
     <tests>
 
-        <!-- Test that specifying non-default search engines works -->
+        <!-- Test that specifying non-default search engines with default parameters works -->
+        <test>
+            <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
+            <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
+            <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
+            <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
+            <output name="searchgui_results" file="searchgui_tiny_result_default_4engines.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
+        </test>
+
+        <!-- Test that search works with MSAmanda with default parameters works-->
         <test>
-            <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
-            <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
-            <param name="precursor_ion_tol" value="100"/>
-            <param name="min_charge" value="1"/>
-            <param name="max_charge" value="3"/>
-            <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
-            <param name="xtandem|xtandem_advanced" value="yes"/>
-            <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/>
-            <output name="searchgui_results" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
+            <param name="peak_lists_files" value="searchgui_smallspectra.mgf"/>
+            <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
+            <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
+            <param name="engines" value="MS_Amanda"/>
+            <output name="searchgui_results" ftype="searchgui_archive">
+                <assert_contents>
+                    <has_size value="635138" delta="5000"/>
+                </assert_contents>
+            </output>
         </test>
-        <!-- Test that search works with MSAmanda -->
+
+		    <!-- Test that specifying non-default search engines with non-default parameters works -->
         <test>
-            <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
-            <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
+           <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
+           <param name="input_parameters_file" value="Identification_Parameters_specific.par"/>
+           <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
+           <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
+           <output name="searchgui_results" ftype="searchgui_archive">
+               <assert_contents>
+                   <has_size value="159330" delta="20000"/>
+               </assert_contents>
+           </output>
+        </test>
+
+        <!--
+            NOTE: Identification_Parameters_specific.par is equivalent to the default .par plus these parameters:
             <param name="precursor_ion_tol" value="100"/>
             <param name="min_charge" value="1"/>
             <param name="max_charge" value="3"/>
+            <param name="xtandem|xtandem_advanced" value="yes"/>
+            <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/>
+        -->
+
+        <!-- Test that specifying MsAmanda as search engine with non-default parameters works -->
+        <test>
+            <param name="peak_lists_files" value="searchgui_smallspectra.mgf"/>
+            <param name="input_parameters_file" value="Identification_Parameters_specific.par"/>
+            <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
             <param name="engines" value="MS_Amanda"/>
-            <output name="searchgui_results" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
+            <output name="searchgui_results" ftype="searchgui_archive">
+                <assert_contents>
+                    <has_size value="635158" delta="5000"/>
+                </assert_contents>
+            </output>
         </test>
 
-        <!-- Test that specifying non-default search engines works using modifications -->
+        <!-- Test that specifying non-default search engines with default parameters works using modifications -->
         <test>
-            <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
-            <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
-            <param name="precursor_ion_tol" value="100"/>
-            <param name="fixed_modifications" value="Carbamidomethylation of C"/>
-            <param name="variable_modifications" value="Oxidation of M"/>
-            <param name="min_charge" value="1"/>
-            <param name="max_charge" value="3"/>
-            <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
-            <param name="xtandem|xtandem_advanced" value="yes"/>
-            <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/>
-            <output name="searchgui_results" file="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
+            <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
+            <param name="input_parameters_file" value="Identification_Parameters_default_modifications.par"/>
+            <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
+            <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
+            <output name="searchgui_results" file="searchgui_tiny_result_default_4engines_modifications.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
         </test>
-        <!-- Test that search works with MSAmanda - with modifications -->
+
+        <!--
+            NOTE: Identification_Parameters_default_modifications.par adds:
+            - "Carbamidomethylation of C" as fixed modification
+            - "Oxidation of M" as variable modification
+          -->
+
+        <!-- Test that search works with MSAmanda with default default parameters - with modifications -->
         <test>
-            <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
-            <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
-            <param name="precursor_ion_tol" value="100"/>
-            <param name="fixed_modifications" value="Carbamidomethylation of C"/>
-            <param name="variable_modifications" value="Oxidation of M"/>
-            <param name="min_charge" value="1"/>
-            <param name="max_charge" value="3"/>
+            <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
+            <param name="input_parameters_file" value="Identification_Parameters_default_modifications.par"/>
+            <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
             <param name="engines" value="MS_Amanda"/>
-            <output name="searchgui_results" file="tiny_searchgui_modifications_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
+            <output name="searchgui_results" ftype="searchgui_archive">
+                <assert_contents>
+                    <has_size value="118136" delta="30000"/>
+                </assert_contents>
+            </output>
         </test>
+
     </tests>
     <help>
 **What it does**
 
-Runs multiple search engines on any number of MGF peak lists using the SearchGUI.
-Default:     X! Tandem, OMSSA and MS-GF+ are executed.
-Optional:     MyriMatch, MS-Amanda, Comet and Tide can be executed.
+Runs multiple search engines on any number of MGF peak lists using SearchGUI.
+
+Default:     X! Tandem and MS-GF+ are executed.
+
+Optional:     MyriMatch, MS-Amanda, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed.
 
     </help>
     <expand macro="citations" />
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/Identification_Parameters_default.par
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Identification_Parameters_default.par	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,662 @@
+{
+  "marshallableParameterType": "identification_parameters",
+  "version": "5.0.1",
+  "name": "IdentificationParametersOutput",
+  "description": "Fragment Tolerance: 0.5 Da.\n",
+  "defaultDescription": true,
+  "searchParameters": {
+    "version": "5.0.1",
+    "precursorAccuracyType": "PPM",
+    "fragmentAccuracyType": "DA",
+    "precursorTolerance": 10.0,
+    "fragmentIonMZTolerance": 0.5,
+    "modificationParameters": {
+      "fixedModifications": [],
+      "variableModifications": [],
+      "refinementVariableModifications": [],
+      "refinementFixedModifications": [],
+      "colors": {},
+      "backUp": {},
+      "id": 0
+    },
+    "digestionParameters": {
+      "cleavageParameter": "enzyme",
+      "enzymes": [
+        {
+          "name": "Trypsin",
+          "aminoAcidBefore": [
+            "R",
+            "K"
+          ],
+          "aminoAcidAfter": [],
+          "restrictionBefore": [],
+          "restrictionAfter": [
+            "P"
+          ],
+          "cvTerm": {
+            "ontology": "PSI-MS",
+            "accession": "MS:1001251",
+            "name": "Trypsin",
+            "id": 0
+          },
+          "id": 0
+        }
+      ],
+      "nMissedCleavages": {
+        "Trypsin": 2
+      },
+      "specificity": {
+        "Trypsin": "specific"
+      },
+      "id": 0
+    },
+    "forwardIons": [
+      1
+    ],
+    "rewindIons": [
+      4
+    ],
+    "minChargeSearched": 2,
+    "maxChargeSearched": 4,
+    "minIsotopicCorrection": 0,
+    "maxIsotopicCorrection": 1,
+    "refMass": 2000.0,
+    "algorithmParameters": {
+      "1": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.OmssaParameters",
+        "data": {
+          "maxEValue": 100.0,
+          "hitListLength": 10,
+          "minimalChargeForMultipleChargedFragments": 3,
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "removePrecursor": false,
+          "scalePrecursor": true,
+          "estimateCharge": true,
+          "selectedOutput": "OMX",
+          "memoryMappedSequenceLibraries": false,
+          "neutronThreshold": 1446.94,
+          "lowIntensityCutOff": 0.0,
+          "highIntensityCutOff": 0.2,
+          "intensityCutOffIncrement": 5.0E-4,
+          "singleChargeWindow": 27,
+          "doubleChargeWindow": 14,
+          "nPeaksInSingleChargeWindow": 2,
+          "nPeaksIndoubleChargeWindow": 2,
+          "maxHitsPerSpectrumPerCharge": 30,
+          "nAnnotatedMostIntensePeaks": 6,
+          "minAnnotatedPeaks": 2,
+          "minPeaks": 4,
+          "cleaveNtermMethionine": true,
+          "maxMzLadders": 128,
+          "maxFragmentCharge": 2,
+          "fractionOfPeaksForChargeEstimation": 0.95,
+          "determineChargePlusOneAlgorithmically": true,
+          "searchPositiveIons": true,
+          "minPrecPerSpectrum": 1,
+          "searchForwardFragmentFirst": false,
+          "searchRewindFragments": true,
+          "maxFragmentPerSeries": 100,
+          "useCorrelationCorrectionScore": true,
+          "consecutiveIonProbability": 0.5,
+          "iterativeSequenceEvalue": 0.0,
+          "iterativeReplaceEvalue": 0.0,
+          "iterativeSpectrumEvalue": 0.01,
+          "noProlineRuleSeries": [],
+          "ptmIndexes": {},
+          "id": 0
+        }
+      },
+      "33": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters",
+        "data": {
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "searchType": "Classic",
+          "totalPartitions": 1,
+          "dissociationType": "HCD",
+          "maxModsForPeptide": 2,
+          "initiatorMethionineBehavior": "Variable",
+          "scoreCutoff": 5.0,
+          "useDeltaScore": false,
+          "fragmentationTerminus": "Both",
+          "maxFragmentSize": 30000.0,
+          "massDiffAcceptorType": "OneMM",
+          "writeMzId": true,
+          "writePepXml": false,
+          "useProvidedPrecursorInfo": true,
+          "doPrecursorDeconvolution": true,
+          "deconvolutionIntensityRatio": 3.0,
+          "deconvolutionMassTolerance": 4.0,
+          "deconvolutionMassToleranceType": "PPM",
+          "trimMs1Peaks": false,
+          "trimMsMsPeaks": true,
+          "numberOfPeaksToKeepPerWindow": 200,
+          "minAllowedIntensityRatioToBasePeak": 0.01,
+          "normalizePeaksAcrossAllWindows": false,
+          "modPeptidesAreDifferent": false,
+          "noOneHitWonders": false,
+          "searchTarget": true,
+          "decoyType": "None",
+          "maxModificationIsoforms": 1024,
+          "minVariantDepth": 1,
+          "maxHeterozygousVariants": 4,
+          "runGptm": false,
+          "gPtmCategories": [
+            "Common_Biological",
+            "Common_Artifact",
+            "Metal"
+          ],
+          "id": 0
+        }
+      },
+      "2": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.XtandemParameters",
+        "data": {
+          "maxEValue": 0.01,
+          "outputResults": "all",
+          "dynamicRange": 100.0,
+          "nPeaks": 50,
+          "minPrecursorMass": 500.0,
+          "minFragmentMz": 200.0,
+          "minPeaksPerSpectrum": 5,
+          "proteinQuickAcetyl": true,
+          "quickPyrolidone": true,
+          "refine": true,
+          "refineSemi": false,
+          "refinePointMutations": false,
+          "refineSpectrumSynthesis": true,
+          "refineUnanticipatedCleavages": true,
+          "refineSnaps": true,
+          "maximumExpectationValueRefinement": 0.01,
+          "potentialModificationsForFullRefinment": false,
+          "skylinePath": "",
+          "outputProteins": true,
+          "outputSequences": false,
+          "outputSpectra": true,
+          "outputHistograms": false,
+          "stpBias": false,
+          "useNoiseSuppression": false,
+          "proteinPtmComplexity": 6.0,
+          "parentMonoisotopicMassIsotopeError": true,
+          "id": 0
+        }
+      },
+      "3": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.PepnovoParameters",
+        "data": {
+          "hitListLength": 10,
+          "estimateCharge": true,
+          "correctPrecursorMass": false,
+          "discardLowQualitySpectra": true,
+          "fragmentationModel": "CID_IT_TRYP",
+          "generateQuery": false,
+          "id": 0
+        }
+      },
+      "4": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.AndromedaParameters",
+        "data": {
+          "maxPeptideMass": 4600.0,
+          "maxCombinations": 250,
+          "topPeaks": 8,
+          "topPeaksWindow": 100,
+          "includeWater": true,
+          "includeAmmonia": true,
+          "dependentLosses": true,
+          "fragmentAll": false,
+          "empiricalCorrection": true,
+          "higherCharge": true,
+          "fragmentationMethod": "CID",
+          "maxNumberOfModifications": 5,
+          "minPeptideLengthNoEnzyme": 8,
+          "maxPeptideLengthNoEnzyme": 30,
+          "equalIL": false,
+          "numberOfCandidates": 10,
+          "ptmIndexes": {},
+          "decoyMode": "none",
+          "id": 0
+        }
+      },
+      "5": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters",
+        "data": {
+          "generateDecoy": false,
+          "reportBothBestHitsForTD": true,
+          "instrumentID": "b, y",
+          "maxRank": 10,
+          "monoisotopic": true,
+          "lowMemoryMode": true,
+          "performDeisotoping": true,
+          "maxModifications": 3,
+          "maxVariableModifications": 4,
+          "maxModificationSites": 6,
+          "maxNeutralLosses": 1,
+          "maxNeutralLossesPerModification": 2,
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "maxLoadedProteins": 100000,
+          "maxLoadedSpectra": 2000,
+          "outputFormat": "csv",
+          "id": 0
+        }
+      },
+      "7": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.MsgfParameters",
+        "data": {
+          "searchDecoyDatabase": false,
+          "instrumentID": 3,
+          "fragmentationType": 3,
+          "protocol": 0,
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "numberOfSpectrumMarches": 10,
+          "additionalOutput": false,
+          "numberTolerableTermini": 2,
+          "numberOfModificationsPerPeptide": 2,
+          "id": 0
+        }
+      },
+      "8": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.DirecTagParameters",
+        "data": {
+          "ticCutoffPercentage": 100.0,
+          "maxPeakCount": 100,
+          "numIntensityClasses": 3,
+          "adjustPrecursorMass": false,
+          "minPrecursorAdjustment": -0.5,
+          "maxPrecursorAdjustment": 1.5,
+          "precursorAdjustmentStep": 0.1,
+          "numChargeStates": 3,
+          "outputSuffix": "",
+          "useChargeStateFromMS": true,
+          "duplicateSpectra": true,
+          "deisotopingMode": 0,
+          "isotopeMzTolerance": 0.25,
+          "complementMzTolerance": 0.1,
+          "tagLength": 4,
+          "maxDynamicMods": 2,
+          "maxTagCount": 10,
+          "intensityScoreWeight": 1.0,
+          "mzFidelityScoreWeight": 1.0,
+          "complementScoreWeight": 1.0,
+          "variableModifications": [],
+          "id": 0
+        }
+      },
+      "10": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.CometParameters",
+        "data": {
+          "numberOfSpectrumMatches": 10,
+          "maxVariableMods": 10,
+          "requireVariableMods": false,
+          "minPeaks": 10,
+          "minPeakIntensity": 0.0,
+          "removePrecursor": 0,
+          "removePrecursorTolerance": 1.5,
+          "lowerClearMzRange": 0.0,
+          "upperClearMzRange": 0.0,
+          "enzymeType": 2,
+          "isotopeCorrection": 3,
+          "minPrecursorMass": 600.0,
+          "maxPrecursorMass": 5000.0,
+          "maxFragmentCharge": 3,
+          "removeMethionine": false,
+          "batchSize": 0,
+          "theoreticalFragmentIonsSumOnly": false,
+          "fragmentBinOffset": 0.0,
+          "useSparseMatrix": true,
+          "selectedOutputFormat": "PepXML",
+          "printExpectScore": true,
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "id": 0
+        }
+      },
+      "13": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters",
+        "data": {
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "numberOfSpectrumMatches": 10,
+          "ticCutoffPercentage": 0.98,
+          "maxDynamicMods": 2,
+          "minTerminiCleavages": 2,
+          "minPrecursorMass": 600.0,
+          "maxPrecursorMass": 5000.0,
+          "useSmartPlusThreeModel": false,
+          "computeXCorr": false,
+          "numIntensityClasses": 3,
+          "classSizeMultiplier": 2,
+          "numberOfBatches": 50,
+          "lowerIsotopeCorrection": -1,
+          "upperIsotopeCorrection": 2,
+          "fragmentationRule": "CID",
+          "maxPeakCount": 300,
+          "outputFormat": "mzIdentML",
+          "id": 0
+        }
+      },
+      "27": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.PNovoParameters",
+        "data": {
+          "numberOfPeptides": 10,
+          "lowerPrecursorMass": 300,
+          "upperPrecursorMass": 5000,
+          "acticationType": "HCD",
+          "id": 0
+        }
+      },
+      "28": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.TideParameters",
+        "data": {
+          "fastIndexFolderName": "fasta-index",
+          "maxVariableModificationsPerPeptide": 255,
+          "maxVariableModificationsPerTypePerPeptide": 2,
+          "minPeptideLength": 6,
+          "maxPeptideLength": 30,
+          "minPrecursorMass": 200.0,
+          "maxPrecursorMass": 7200.0,
+          "decoyFormat": "none",
+          "keepTerminalAminoAcids": "NC",
+          "decoySeed": 1,
+          "outputFolderName": "crux-output",
+          "printPeptides": false,
+          "verbosity": 30,
+          "monoisotopicPrecursor": true,
+          "clipNtermMethionine": false,
+          "digestionType": "full-digest",
+          "computeSpScore": false,
+          "numberOfSpectrumMatches": 10,
+          "computeExactPValues": false,
+          "minSpectrumMz": 0.0,
+          "minSpectrumPeaks": 20,
+          "spectrumCharges": "all",
+          "removePrecursor": false,
+          "removePrecursorTolerance": 1.5,
+          "printProgressIndicatorSize": 1000,
+          "useFlankingPeaks": false,
+          "useNeutralLossPeaks": false,
+          "mzBinWidth": 0.02,
+          "mzBinOffset": 0.0,
+          "concatenateTargetDecoy": false,
+          "textOutput": true,
+          "sqtOutput": false,
+          "pepXmlOutput": false,
+          "mzidOutput": false,
+          "pinOutput": false,
+          "removeTempFolders": true,
+          "id": 0
+        }
+      },
+      "29": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.NovorParameters",
+        "data": {
+          "fragmentationMethod": "HCD",
+          "massAnalyzer": "FT",
+          "id": 0
+        }
+      }
+    },
+    "flanking": false,
+    "id": 0
+  },
+  "annotationParameters": {
+    "yAxisZoomExcludesBackgroundPeaks": true,
+    "showAllPeaks": false,
+    "intensityThresholdType": "percentile",
+    "intensityLimit": 0.75,
+    "automaticAnnotation": true,
+    "selectedIonsMap": {
+      "PEPTIDE_FRAGMENT_ION": [
+        4,
+        1
+      ],
+      "REPORTER_ION": [],
+      "IMMONIUM_ION": [
+        0,
+        1,
+        2,
+        3,
+        4,
+        5,
+        6,
+        7,
+        8,
+        9,
+        10,
+        11,
+        12,
+        13,
+        14,
+        15,
+        16,
+        17,
+        18,
+        19,
+        20
+      ],
+      "RELATED_ION": [
+        0,
+        1,
+        2,
+        3,
+        4,
+        5,
+        6,
+        7,
+        8,
+        9,
+        10,
+        11,
+        12,
+        13,
+        14,
+        15,
+        16,
+        17,
+        18
+      ],
+      "TAG_FRAGMENT_ION": [
+        4,
+        1
+      ],
+      "PRECURSOR_ION": [
+        0
+      ]
+    },
+    "neutralLossesList": [
+      {
+        "composition": {
+          "atomChain": [
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "O",
+              "isotope": 0,
+              "id": 0
+            }
+          ],
+          "mass": -1.0,
+          "id": 0
+        },
+        "name": "H2O",
+        "fixed": false,
+        "aminoAcids": [
+          "D",
+          "E",
+          "S",
+          "T"
+        ],
+        "id": 0
+      },
+      {
+        "composition": {
+          "atomChain": [
+            {
+              "atomSymbol": "N",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            }
+          ],
+          "mass": -1.0,
+          "id": 0
+        },
+        "name": "NH3",
+        "fixed": false,
+        "aminoAcids": [
+          "K",
+          "N",
+          "Q",
+          "R"
+        ],
+        "id": 0
+      }
+    ],
+    "neutralLossesAuto": true,
+    "reporterIons": true,
+    "relatedIons": true,
+    "fragmentIonAccuracy": 10.0,
+    "fragmentIonPpm": false,
+    "showForwardIonDeNovoTags": false,
+    "showRewindIonDeNovoTags": false,
+    "deNovoCharge": 1,
+    "tiesResolution": "mostAccurateMz",
+    "id": 0
+  },
+  "sequenceMatchingParameters": {
+    "sequenceMatchingType": "indistiguishableAminoAcids",
+    "limitX": 0.25,
+    "enzymaticTagsOnly": false,
+    "maxPtmsPerTagPeptide": 3,
+    "minAminoAcidScore": 30,
+    "minTagLength": 3,
+    "id": 0
+  },
+  "peptideVariantsParameters": {
+    "variantType": "NO_VARIANT",
+    "nVariants": 0,
+    "nAaDeletions": 0,
+    "nAaInsertions": 0,
+    "nAaSubstitutions": 0,
+    "nAaSwap": 0,
+    "aaSubstitutionMatrix": {
+      "name": "No Substitution",
+      "description": "No substitution",
+      "substitutions": {},
+      "reverseMap": {},
+      "id": 0
+    },
+    "fixedVariants": {},
+    "id": 0
+  },
+  "geneParameters": {
+    "autoUpdate": false,
+    "useGeneMapping": false,
+    "id": 0
+  },
+  "psmScoringParameters": {
+    "spectrumMatchingScores": {
+      "8": [
+        1
+      ],
+      "3": [
+        1
+      ],
+      "27": [
+        1
+      ]
+    },
+    "defaultScores": [
+      -1
+    ],
+    "minDecoysInBin": 10,
+    "id": 0
+  },
+  "peptideAssumptionFilter": {
+    "minPepLength": 8,
+    "maxPepLength": 30,
+    "maxMassDeviation": 10.0,
+    "isPpm": true,
+    "unknownModification": true,
+    "minIsotopes": 0,
+    "maxIsotopes": 1,
+    "id": 0
+  },
+  "modificationLocalizationParameters": {
+    "probabilisticScoreCalculation": true,
+    "selectedProbabilisticScore": "PhosphoRS",
+    "dScoreThreshold": 95.0,
+    "probabilisticScoreThreshold": 95.0,
+    "probabilisticScoreNeutralLosses": false,
+    "sequenceMatchingParameters": {
+      "sequenceMatchingType": "aminoAcid",
+      "limitX": 0.25,
+      "enzymaticTagsOnly": false,
+      "maxPtmsPerTagPeptide": 3,
+      "minAminoAcidScore": 30,
+      "minTagLength": 3,
+      "id": 0
+    },
+    "alignNonConfidentModifications": true,
+    "id": 0
+  },
+  "proteinInferenceParameters": {
+    "modificationRefinement": true,
+    "simplifyProteinGroups": true,
+    "simplifyGroupsEvidence": true,
+    "simplifyGroupsConfidence": true,
+    "simplifyGroupsEnzymaticity": true,
+    "simplifyGroupsVariants": true,
+    "confidenceThreshold": 0.05,
+    "id": 0
+  },
+  "idValidationParameters": {
+    "defaultProteinFDR": 1.0,
+    "defaultPeptideFDR": 1.0,
+    "defaultPsmFDR": 1.0,
+    "validationQCPreferences": {
+      "dbSize": false,
+      "firstDecoy": true,
+      "confidenceMargin": 1.0,
+      "id": 0
+    },
+    "id": 0
+  },
+  "fractionParameters": {
+    "proteinConfidenceMwPlots": 95.0,
+    "fractionMolecularWeightRanges": {},
+    "id": 0
+  },
+  "fastaParameters": {
+    "targetDecoy": true,
+    "decoyFlag": "-REVERSED",
+    "decoySuffix": true,
+    "targetDecoyFileNameTag": "_concatenated_target_decoy",
+    "id": 0
+  },
+  "id": 0
+}
\ No newline at end of file
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/Identification_Parameters_default_modifications.par
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Identification_Parameters_default_modifications.par	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,882 @@
+{
+  "marshallableParameterType": "identification_parameters",
+  "version": "5.0.1",
+  "name": "IdentificationParametersOutput",
+  "description": "Fixed: Carbamidomethylation of C.\nVariable: Oxidation of M.\nFragment Tolerance: 0.5 Da.\n",
+  "defaultDescription": true,
+  "searchParameters": {
+    "version": "5.0.1",
+    "precursorAccuracyType": "PPM",
+    "fragmentAccuracyType": "DA",
+    "precursorTolerance": 10.0,
+    "fragmentIonMZTolerance": 0.5,
+    "modificationParameters": {
+      "fixedModifications": [
+        "Carbamidomethylation of C"
+      ],
+      "variableModifications": [
+        "Oxidation of M"
+      ],
+      "refinementVariableModifications": [],
+      "refinementFixedModifications": [],
+      "colors": {},
+      "backUp": {
+        "Carbamidomethylation of C": {
+          "modificationType": "modaa",
+          "name": "Carbamidomethylation of C",
+          "shortName": "cmm",
+          "neutralLosses": [],
+          "reporterIons": [],
+          "pattern": {
+            "length": 0,
+            "residueTargeted": {
+              "0": [
+                "C"
+              ]
+            },
+            "id": 0
+          },
+          "atomChainAdded": {
+            "atomChain": [
+              {
+                "atomSymbol": "C",
+                "isotope": 0,
+                "id": 0
+              },
+              {
+                "atomSymbol": "C",
+                "isotope": 0,
+                "id": 0
+              },
+              {
+                "atomSymbol": "H",
+                "isotope": 0,
+                "id": 0
+              },
+              {
+                "atomSymbol": "H",
+                "isotope": 0,
+                "id": 0
+              },
+              {
+                "atomSymbol": "H",
+                "isotope": 0,
+                "id": 0
+              },
+              {
+                "atomSymbol": "N",
+                "isotope": 0,
+                "id": 0
+              },
+              {
+                "atomSymbol": "O",
+                "isotope": 0,
+                "id": 0
+              }
+            ],
+            "mass": -1.0,
+            "id": 0
+          },
+          "atomChainRemoved": {
+            "atomChain": [],
+            "mass": -1.0,
+            "id": 0
+          },
+          "unimodCvTerm": {
+            "ontology": "UNIMOD",
+            "accession": "UNIMOD:4",
+            "name": "Carbamidomethyl",
+            "id": 0
+          },
+          "psiModCvTerm": {
+            "ontology": "MOD",
+            "accession": "MOD:01060",
+            "name": "S-carboxamidomethyl-L-cysteine",
+            "id": 0
+          },
+          "category": "Common",
+          "id": 0
+        },
+        "Oxidation of M": {
+          "modificationType": "modaa",
+          "name": "Oxidation of M",
+          "shortName": "ox",
+          "neutralLosses": [
+            {
+              "composition": {
+                "atomChain": [
+                  {
+                    "atomSymbol": "C",
+                    "isotope": 0,
+                    "id": 0
+                  },
+                  {
+                    "atomSymbol": "H",
+                    "isotope": 0,
+                    "id": 0
+                  },
+                  {
+                    "atomSymbol": "H",
+                    "isotope": 0,
+                    "id": 0
+                  },
+                  {
+                    "atomSymbol": "H",
+                    "isotope": 0,
+                    "id": 0
+                  },
+                  {
+                    "atomSymbol": "H",
+                    "isotope": 0,
+                    "id": 0
+                  },
+                  {
+                    "atomSymbol": "O",
+                    "isotope": 0,
+                    "id": 0
+                  },
+                  {
+                    "atomSymbol": "S",
+                    "isotope": 0,
+                    "id": 0
+                  }
+                ],
+                "mass": -1.0,
+                "id": 0
+              },
+              "name": "CH4OS",
+              "fixed": false,
+              "id": 0
+            }
+          ],
+          "reporterIons": [],
+          "pattern": {
+            "length": 0,
+            "residueTargeted": {
+              "0": [
+                "M"
+              ]
+            },
+            "id": 0
+          },
+          "atomChainAdded": {
+            "atomChain": [
+              {
+                "atomSymbol": "O",
+                "isotope": 0,
+                "id": 0
+              }
+            ],
+            "mass": -1.0,
+            "id": 0
+          },
+          "atomChainRemoved": {
+            "atomChain": [],
+            "mass": -1.0,
+            "id": 0
+          },
+          "unimodCvTerm": {
+            "ontology": "UNIMOD",
+            "accession": "UNIMOD:35",
+            "name": "Oxidation",
+            "id": 0
+          },
+          "psiModCvTerm": {
+            "ontology": "MOD",
+            "accession": "MOD:00719",
+            "name": "L-methionine sulfoxide",
+            "id": 0
+          },
+          "category": "Common",
+          "id": 0
+        }
+      },
+      "id": 0
+    },
+    "digestionParameters": {
+      "cleavageParameter": "enzyme",
+      "enzymes": [
+        {
+          "name": "Trypsin",
+          "aminoAcidBefore": [
+            "R",
+            "K"
+          ],
+          "aminoAcidAfter": [],
+          "restrictionBefore": [],
+          "restrictionAfter": [
+            "P"
+          ],
+          "cvTerm": {
+            "ontology": "PSI-MS",
+            "accession": "MS:1001251",
+            "name": "Trypsin",
+            "id": 0
+          },
+          "id": 0
+        }
+      ],
+      "nMissedCleavages": {
+        "Trypsin": 2
+      },
+      "specificity": {
+        "Trypsin": "specific"
+      },
+      "id": 0
+    },
+    "forwardIons": [
+      1
+    ],
+    "rewindIons": [
+      4
+    ],
+    "minChargeSearched": 2,
+    "maxChargeSearched": 4,
+    "minIsotopicCorrection": 0,
+    "maxIsotopicCorrection": 1,
+    "refMass": 2000.0,
+    "algorithmParameters": {
+      "1": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.OmssaParameters",
+        "data": {
+          "maxEValue": 100.0,
+          "hitListLength": 10,
+          "minimalChargeForMultipleChargedFragments": 3,
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "removePrecursor": false,
+          "scalePrecursor": true,
+          "estimateCharge": true,
+          "selectedOutput": "OMX",
+          "memoryMappedSequenceLibraries": false,
+          "neutronThreshold": 1446.94,
+          "lowIntensityCutOff": 0.0,
+          "highIntensityCutOff": 0.2,
+          "intensityCutOffIncrement": 5.0E-4,
+          "singleChargeWindow": 27,
+          "doubleChargeWindow": 14,
+          "nPeaksInSingleChargeWindow": 2,
+          "nPeaksIndoubleChargeWindow": 2,
+          "maxHitsPerSpectrumPerCharge": 30,
+          "nAnnotatedMostIntensePeaks": 6,
+          "minAnnotatedPeaks": 2,
+          "minPeaks": 4,
+          "cleaveNtermMethionine": true,
+          "maxMzLadders": 128,
+          "maxFragmentCharge": 2,
+          "fractionOfPeaksForChargeEstimation": 0.95,
+          "determineChargePlusOneAlgorithmically": true,
+          "searchPositiveIons": true,
+          "minPrecPerSpectrum": 1,
+          "searchForwardFragmentFirst": false,
+          "searchRewindFragments": true,
+          "maxFragmentPerSeries": 100,
+          "useCorrelationCorrectionScore": true,
+          "consecutiveIonProbability": 0.5,
+          "iterativeSequenceEvalue": 0.0,
+          "iterativeReplaceEvalue": 0.0,
+          "iterativeSpectrumEvalue": 0.01,
+          "noProlineRuleSeries": [],
+          "ptmIndexes": {},
+          "id": 0
+        }
+      },
+      "33": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters",
+        "data": {
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "searchType": "Classic",
+          "totalPartitions": 1,
+          "dissociationType": "HCD",
+          "maxModsForPeptide": 2,
+          "initiatorMethionineBehavior": "Variable",
+          "scoreCutoff": 5.0,
+          "useDeltaScore": false,
+          "fragmentationTerminus": "Both",
+          "maxFragmentSize": 30000.0,
+          "massDiffAcceptorType": "OneMM",
+          "writeMzId": true,
+          "writePepXml": false,
+          "useProvidedPrecursorInfo": true,
+          "doPrecursorDeconvolution": true,
+          "deconvolutionIntensityRatio": 3.0,
+          "deconvolutionMassTolerance": 4.0,
+          "deconvolutionMassToleranceType": "PPM",
+          "trimMs1Peaks": false,
+          "trimMsMsPeaks": true,
+          "numberOfPeaksToKeepPerWindow": 200,
+          "minAllowedIntensityRatioToBasePeak": 0.01,
+          "normalizePeaksAcrossAllWindows": false,
+          "modPeptidesAreDifferent": false,
+          "noOneHitWonders": false,
+          "searchTarget": true,
+          "decoyType": "None",
+          "maxModificationIsoforms": 1024,
+          "minVariantDepth": 1,
+          "maxHeterozygousVariants": 4,
+          "runGptm": false,
+          "gPtmCategories": [
+            "Common_Biological",
+            "Common_Artifact",
+            "Metal"
+          ],
+          "id": 0
+        }
+      },
+      "2": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.XtandemParameters",
+        "data": {
+          "maxEValue": 0.01,
+          "outputResults": "all",
+          "dynamicRange": 100.0,
+          "nPeaks": 50,
+          "minPrecursorMass": 500.0,
+          "minFragmentMz": 200.0,
+          "minPeaksPerSpectrum": 5,
+          "proteinQuickAcetyl": true,
+          "quickPyrolidone": true,
+          "refine": true,
+          "refineSemi": false,
+          "refinePointMutations": false,
+          "refineSpectrumSynthesis": true,
+          "refineUnanticipatedCleavages": true,
+          "refineSnaps": true,
+          "maximumExpectationValueRefinement": 0.01,
+          "potentialModificationsForFullRefinment": false,
+          "skylinePath": "",
+          "outputProteins": true,
+          "outputSequences": false,
+          "outputSpectra": true,
+          "outputHistograms": false,
+          "stpBias": false,
+          "useNoiseSuppression": false,
+          "proteinPtmComplexity": 6.0,
+          "parentMonoisotopicMassIsotopeError": true,
+          "id": 0
+        }
+      },
+      "3": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.PepnovoParameters",
+        "data": {
+          "hitListLength": 10,
+          "estimateCharge": true,
+          "correctPrecursorMass": false,
+          "discardLowQualitySpectra": true,
+          "fragmentationModel": "CID_IT_TRYP",
+          "generateQuery": false,
+          "id": 0
+        }
+      },
+      "4": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.AndromedaParameters",
+        "data": {
+          "maxPeptideMass": 4600.0,
+          "maxCombinations": 250,
+          "topPeaks": 8,
+          "topPeaksWindow": 100,
+          "includeWater": true,
+          "includeAmmonia": true,
+          "dependentLosses": true,
+          "fragmentAll": false,
+          "empiricalCorrection": true,
+          "higherCharge": true,
+          "fragmentationMethod": "CID",
+          "maxNumberOfModifications": 5,
+          "minPeptideLengthNoEnzyme": 8,
+          "maxPeptideLengthNoEnzyme": 30,
+          "equalIL": false,
+          "numberOfCandidates": 10,
+          "ptmIndexes": {},
+          "decoyMode": "none",
+          "id": 0
+        }
+      },
+      "5": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters",
+        "data": {
+          "generateDecoy": false,
+          "reportBothBestHitsForTD": true,
+          "instrumentID": "b, y",
+          "maxRank": 10,
+          "monoisotopic": true,
+          "lowMemoryMode": true,
+          "performDeisotoping": true,
+          "maxModifications": 3,
+          "maxVariableModifications": 4,
+          "maxModificationSites": 6,
+          "maxNeutralLosses": 1,
+          "maxNeutralLossesPerModification": 2,
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "maxLoadedProteins": 100000,
+          "maxLoadedSpectra": 2000,
+          "outputFormat": "csv",
+          "id": 0
+        }
+      },
+      "7": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.MsgfParameters",
+        "data": {
+          "searchDecoyDatabase": false,
+          "instrumentID": 3,
+          "fragmentationType": 3,
+          "protocol": 0,
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "numberOfSpectrumMarches": 10,
+          "additionalOutput": false,
+          "numberTolerableTermini": 2,
+          "numberOfModificationsPerPeptide": 2,
+          "id": 0
+        }
+      },
+      "8": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.DirecTagParameters",
+        "data": {
+          "ticCutoffPercentage": 100.0,
+          "maxPeakCount": 100,
+          "numIntensityClasses": 3,
+          "adjustPrecursorMass": false,
+          "minPrecursorAdjustment": -0.5,
+          "maxPrecursorAdjustment": 1.5,
+          "precursorAdjustmentStep": 0.1,
+          "numChargeStates": 3,
+          "outputSuffix": "",
+          "useChargeStateFromMS": true,
+          "duplicateSpectra": true,
+          "deisotopingMode": 0,
+          "isotopeMzTolerance": 0.25,
+          "complementMzTolerance": 0.1,
+          "tagLength": 4,
+          "maxDynamicMods": 2,
+          "maxTagCount": 10,
+          "intensityScoreWeight": 1.0,
+          "mzFidelityScoreWeight": 1.0,
+          "complementScoreWeight": 1.0,
+          "variableModifications": [],
+          "id": 0
+        }
+      },
+      "10": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.CometParameters",
+        "data": {
+          "numberOfSpectrumMatches": 10,
+          "maxVariableMods": 10,
+          "requireVariableMods": false,
+          "minPeaks": 10,
+          "minPeakIntensity": 0.0,
+          "removePrecursor": 0,
+          "removePrecursorTolerance": 1.5,
+          "lowerClearMzRange": 0.0,
+          "upperClearMzRange": 0.0,
+          "enzymeType": 2,
+          "isotopeCorrection": 3,
+          "minPrecursorMass": 600.0,
+          "maxPrecursorMass": 5000.0,
+          "maxFragmentCharge": 3,
+          "removeMethionine": false,
+          "batchSize": 0,
+          "theoreticalFragmentIonsSumOnly": false,
+          "fragmentBinOffset": 0.0,
+          "useSparseMatrix": true,
+          "selectedOutputFormat": "PepXML",
+          "printExpectScore": true,
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "id": 0
+        }
+      },
+      "13": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters",
+        "data": {
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "numberOfSpectrumMatches": 10,
+          "ticCutoffPercentage": 0.98,
+          "maxDynamicMods": 2,
+          "minTerminiCleavages": 2,
+          "minPrecursorMass": 600.0,
+          "maxPrecursorMass": 5000.0,
+          "useSmartPlusThreeModel": false,
+          "computeXCorr": false,
+          "numIntensityClasses": 3,
+          "classSizeMultiplier": 2,
+          "numberOfBatches": 50,
+          "lowerIsotopeCorrection": -1,
+          "upperIsotopeCorrection": 2,
+          "fragmentationRule": "CID",
+          "maxPeakCount": 300,
+          "outputFormat": "mzIdentML",
+          "id": 0
+        }
+      },
+      "27": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.PNovoParameters",
+        "data": {
+          "numberOfPeptides": 10,
+          "lowerPrecursorMass": 300,
+          "upperPrecursorMass": 5000,
+          "acticationType": "HCD",
+          "id": 0
+        }
+      },
+      "28": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.TideParameters",
+        "data": {
+          "fastIndexFolderName": "fasta-index",
+          "maxVariableModificationsPerPeptide": 255,
+          "maxVariableModificationsPerTypePerPeptide": 2,
+          "minPeptideLength": 6,
+          "maxPeptideLength": 30,
+          "minPrecursorMass": 200.0,
+          "maxPrecursorMass": 7200.0,
+          "decoyFormat": "none",
+          "keepTerminalAminoAcids": "NC",
+          "decoySeed": 1,
+          "outputFolderName": "crux-output",
+          "printPeptides": false,
+          "verbosity": 30,
+          "monoisotopicPrecursor": true,
+          "clipNtermMethionine": false,
+          "digestionType": "full-digest",
+          "computeSpScore": false,
+          "numberOfSpectrumMatches": 10,
+          "computeExactPValues": false,
+          "minSpectrumMz": 0.0,
+          "minSpectrumPeaks": 20,
+          "spectrumCharges": "all",
+          "removePrecursor": false,
+          "removePrecursorTolerance": 1.5,
+          "printProgressIndicatorSize": 1000,
+          "useFlankingPeaks": false,
+          "useNeutralLossPeaks": false,
+          "mzBinWidth": 0.02,
+          "mzBinOffset": 0.0,
+          "concatenateTargetDecoy": false,
+          "textOutput": true,
+          "sqtOutput": false,
+          "pepXmlOutput": false,
+          "mzidOutput": false,
+          "pinOutput": false,
+          "removeTempFolders": true,
+          "id": 0
+        }
+      },
+      "29": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.NovorParameters",
+        "data": {
+          "fragmentationMethod": "HCD",
+          "massAnalyzer": "FT",
+          "id": 0
+        }
+      }
+    },
+    "flanking": false,
+    "id": 0
+  },
+  "annotationParameters": {
+    "yAxisZoomExcludesBackgroundPeaks": true,
+    "showAllPeaks": false,
+    "intensityThresholdType": "percentile",
+    "intensityLimit": 0.75,
+    "automaticAnnotation": true,
+    "selectedIonsMap": {
+      "IMMONIUM_ION": [
+        0,
+        1,
+        2,
+        3,
+        4,
+        5,
+        6,
+        7,
+        8,
+        9,
+        10,
+        11,
+        12,
+        13,
+        14,
+        15,
+        16,
+        17,
+        18,
+        19,
+        20
+      ],
+      "PEPTIDE_FRAGMENT_ION": [
+        4,
+        1
+      ],
+      "PRECURSOR_ION": [
+        0
+      ],
+      "TAG_FRAGMENT_ION": [
+        4,
+        1
+      ],
+      "REPORTER_ION": [],
+      "RELATED_ION": [
+        0,
+        1,
+        2,
+        3,
+        4,
+        5,
+        6,
+        7,
+        8,
+        9,
+        10,
+        11,
+        12,
+        13,
+        14,
+        15,
+        16,
+        17,
+        18
+      ]
+    },
+    "neutralLossesList": [
+      {
+        "composition": {
+          "atomChain": [
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "O",
+              "isotope": 0,
+              "id": 0
+            }
+          ],
+          "mass": -1.0,
+          "id": 0
+        },
+        "name": "H2O",
+        "fixed": false,
+        "aminoAcids": [
+          "D",
+          "E",
+          "S",
+          "T"
+        ],
+        "id": 0
+      },
+      {
+        "composition": {
+          "atomChain": [
+            {
+              "atomSymbol": "N",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            }
+          ],
+          "mass": -1.0,
+          "id": 0
+        },
+        "name": "NH3",
+        "fixed": false,
+        "aminoAcids": [
+          "K",
+          "N",
+          "Q",
+          "R"
+        ],
+        "id": 0
+      },
+      {
+        "composition": {
+          "atomChain": [
+            {
+              "atomSymbol": "C",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "O",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "S",
+              "isotope": 0,
+              "id": 0
+            }
+          ],
+          "mass": -1.0,
+          "id": 0
+        },
+        "name": "CH4OS",
+        "fixed": false,
+        "id": 0
+      }
+    ],
+    "neutralLossesAuto": true,
+    "reporterIons": true,
+    "relatedIons": true,
+    "fragmentIonAccuracy": 10.0,
+    "fragmentIonPpm": false,
+    "showForwardIonDeNovoTags": false,
+    "showRewindIonDeNovoTags": false,
+    "deNovoCharge": 1,
+    "tiesResolution": "mostAccurateMz",
+    "id": 0
+  },
+  "sequenceMatchingParameters": {
+    "sequenceMatchingType": "indistiguishableAminoAcids",
+    "limitX": 0.25,
+    "enzymaticTagsOnly": false,
+    "maxPtmsPerTagPeptide": 3,
+    "minAminoAcidScore": 30,
+    "minTagLength": 3,
+    "id": 0
+  },
+  "peptideVariantsParameters": {
+    "variantType": "NO_VARIANT",
+    "nVariants": 0,
+    "nAaDeletions": 0,
+    "nAaInsertions": 0,
+    "nAaSubstitutions": 0,
+    "nAaSwap": 0,
+    "aaSubstitutionMatrix": {
+      "name": "No Substitution",
+      "description": "No substitution",
+      "substitutions": {},
+      "reverseMap": {},
+      "id": 0
+    },
+    "fixedVariants": {},
+    "id": 0
+  },
+  "geneParameters": {
+    "autoUpdate": false,
+    "useGeneMapping": false,
+    "id": 0
+  },
+  "psmScoringParameters": {
+    "spectrumMatchingScores": {
+      "8": [
+        1
+      ],
+      "3": [
+        1
+      ],
+      "27": [
+        1
+      ]
+    },
+    "defaultScores": [
+      -1
+    ],
+    "minDecoysInBin": 10,
+    "id": 0
+  },
+  "peptideAssumptionFilter": {
+    "minPepLength": 8,
+    "maxPepLength": 30,
+    "maxMassDeviation": 10.0,
+    "isPpm": true,
+    "unknownModification": true,
+    "minIsotopes": 0,
+    "maxIsotopes": 1,
+    "id": 0
+  },
+  "modificationLocalizationParameters": {
+    "probabilisticScoreCalculation": true,
+    "selectedProbabilisticScore": "PhosphoRS",
+    "dScoreThreshold": 95.0,
+    "probabilisticScoreThreshold": 95.0,
+    "probabilisticScoreNeutralLosses": false,
+    "sequenceMatchingParameters": {
+      "sequenceMatchingType": "aminoAcid",
+      "limitX": 0.25,
+      "enzymaticTagsOnly": false,
+      "maxPtmsPerTagPeptide": 3,
+      "minAminoAcidScore": 30,
+      "minTagLength": 3,
+      "id": 0
+    },
+    "alignNonConfidentModifications": true,
+    "id": 0
+  },
+  "proteinInferenceParameters": {
+    "modificationRefinement": true,
+    "simplifyProteinGroups": true,
+    "simplifyGroupsEvidence": true,
+    "simplifyGroupsConfidence": true,
+    "simplifyGroupsEnzymaticity": true,
+    "simplifyGroupsVariants": true,
+    "confidenceThreshold": 0.05,
+    "id": 0
+  },
+  "idValidationParameters": {
+    "defaultProteinFDR": 1.0,
+    "defaultPeptideFDR": 1.0,
+    "defaultPsmFDR": 1.0,
+    "validationQCPreferences": {
+      "dbSize": false,
+      "firstDecoy": true,
+      "confidenceMargin": 1.0,
+      "id": 0
+    },
+    "id": 0
+  },
+  "fractionParameters": {
+    "proteinConfidenceMwPlots": 95.0,
+    "fractionMolecularWeightRanges": {},
+    "id": 0
+  },
+  "fastaParameters": {
+    "targetDecoy": true,
+    "decoyFlag": "-REVERSED",
+    "decoySuffix": true,
+    "targetDecoyFileNameTag": "_concatenated_target_decoy",
+    "id": 0
+  },
+  "id": 0
+}
\ No newline at end of file
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/Identification_Parameters_specific.par
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Identification_Parameters_specific.par	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,882 @@
+{
+  "marshallableParameterType": "identification_parameters",
+  "version": "5.0.1",
+  "name": "IdentificationParametersOutput",
+  "description": "Fixed: Carbamidomethylation of C.\nVariable: Oxidation of M.\nPrecursor Tolerance: 100.0 ppm.\nFragment Tolerance: 0.5 Da.\nCharge: 1-3.\n",
+  "defaultDescription": true,
+  "searchParameters": {
+    "version": "5.0.1",
+    "precursorAccuracyType": "PPM",
+    "fragmentAccuracyType": "DA",
+    "precursorTolerance": 100.0,
+    "fragmentIonMZTolerance": 0.5,
+    "modificationParameters": {
+      "fixedModifications": [
+        "Carbamidomethylation of C"
+      ],
+      "variableModifications": [
+        "Oxidation of M"
+      ],
+      "refinementVariableModifications": [],
+      "refinementFixedModifications": [],
+      "colors": {},
+      "backUp": {
+        "Carbamidomethylation of C": {
+          "modificationType": "modaa",
+          "name": "Carbamidomethylation of C",
+          "shortName": "cmm",
+          "neutralLosses": [],
+          "reporterIons": [],
+          "pattern": {
+            "length": 0,
+            "residueTargeted": {
+              "0": [
+                "C"
+              ]
+            },
+            "id": 0
+          },
+          "atomChainAdded": {
+            "atomChain": [
+              {
+                "atomSymbol": "C",
+                "isotope": 0,
+                "id": 0
+              },
+              {
+                "atomSymbol": "C",
+                "isotope": 0,
+                "id": 0
+              },
+              {
+                "atomSymbol": "H",
+                "isotope": 0,
+                "id": 0
+              },
+              {
+                "atomSymbol": "H",
+                "isotope": 0,
+                "id": 0
+              },
+              {
+                "atomSymbol": "H",
+                "isotope": 0,
+                "id": 0
+              },
+              {
+                "atomSymbol": "N",
+                "isotope": 0,
+                "id": 0
+              },
+              {
+                "atomSymbol": "O",
+                "isotope": 0,
+                "id": 0
+              }
+            ],
+            "mass": -1.0,
+            "id": 0
+          },
+          "atomChainRemoved": {
+            "atomChain": [],
+            "mass": -1.0,
+            "id": 0
+          },
+          "unimodCvTerm": {
+            "ontology": "UNIMOD",
+            "accession": "UNIMOD:4",
+            "name": "Carbamidomethyl",
+            "id": 0
+          },
+          "psiModCvTerm": {
+            "ontology": "MOD",
+            "accession": "MOD:01060",
+            "name": "S-carboxamidomethyl-L-cysteine",
+            "id": 0
+          },
+          "category": "Common",
+          "id": 0
+        },
+        "Oxidation of M": {
+          "modificationType": "modaa",
+          "name": "Oxidation of M",
+          "shortName": "ox",
+          "neutralLosses": [
+            {
+              "composition": {
+                "atomChain": [
+                  {
+                    "atomSymbol": "C",
+                    "isotope": 0,
+                    "id": 0
+                  },
+                  {
+                    "atomSymbol": "H",
+                    "isotope": 0,
+                    "id": 0
+                  },
+                  {
+                    "atomSymbol": "H",
+                    "isotope": 0,
+                    "id": 0
+                  },
+                  {
+                    "atomSymbol": "H",
+                    "isotope": 0,
+                    "id": 0
+                  },
+                  {
+                    "atomSymbol": "H",
+                    "isotope": 0,
+                    "id": 0
+                  },
+                  {
+                    "atomSymbol": "O",
+                    "isotope": 0,
+                    "id": 0
+                  },
+                  {
+                    "atomSymbol": "S",
+                    "isotope": 0,
+                    "id": 0
+                  }
+                ],
+                "mass": -1.0,
+                "id": 0
+              },
+              "name": "CH4OS",
+              "fixed": false,
+              "id": 0
+            }
+          ],
+          "reporterIons": [],
+          "pattern": {
+            "length": 0,
+            "residueTargeted": {
+              "0": [
+                "M"
+              ]
+            },
+            "id": 0
+          },
+          "atomChainAdded": {
+            "atomChain": [
+              {
+                "atomSymbol": "O",
+                "isotope": 0,
+                "id": 0
+              }
+            ],
+            "mass": -1.0,
+            "id": 0
+          },
+          "atomChainRemoved": {
+            "atomChain": [],
+            "mass": -1.0,
+            "id": 0
+          },
+          "unimodCvTerm": {
+            "ontology": "UNIMOD",
+            "accession": "UNIMOD:35",
+            "name": "Oxidation",
+            "id": 0
+          },
+          "psiModCvTerm": {
+            "ontology": "MOD",
+            "accession": "MOD:00719",
+            "name": "L-methionine sulfoxide",
+            "id": 0
+          },
+          "category": "Common",
+          "id": 0
+        }
+      },
+      "id": 0
+    },
+    "digestionParameters": {
+      "cleavageParameter": "enzyme",
+      "enzymes": [
+        {
+          "name": "Trypsin",
+          "aminoAcidBefore": [
+            "R",
+            "K"
+          ],
+          "aminoAcidAfter": [],
+          "restrictionBefore": [],
+          "restrictionAfter": [
+            "P"
+          ],
+          "cvTerm": {
+            "ontology": "PSI-MS",
+            "accession": "MS:1001251",
+            "name": "Trypsin",
+            "id": 0
+          },
+          "id": 0
+        }
+      ],
+      "nMissedCleavages": {
+        "Trypsin": 2
+      },
+      "specificity": {
+        "Trypsin": "specific"
+      },
+      "id": 0
+    },
+    "forwardIons": [
+      1
+    ],
+    "rewindIons": [
+      4
+    ],
+    "minChargeSearched": 1,
+    "maxChargeSearched": 3,
+    "minIsotopicCorrection": 0,
+    "maxIsotopicCorrection": 1,
+    "refMass": 2000.0,
+    "algorithmParameters": {
+      "1": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.OmssaParameters",
+        "data": {
+          "maxEValue": 100.0,
+          "hitListLength": 10,
+          "minimalChargeForMultipleChargedFragments": 3,
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "removePrecursor": false,
+          "scalePrecursor": true,
+          "estimateCharge": true,
+          "selectedOutput": "OMX",
+          "memoryMappedSequenceLibraries": false,
+          "neutronThreshold": 1446.94,
+          "lowIntensityCutOff": 0.0,
+          "highIntensityCutOff": 0.2,
+          "intensityCutOffIncrement": 5.0E-4,
+          "singleChargeWindow": 27,
+          "doubleChargeWindow": 14,
+          "nPeaksInSingleChargeWindow": 2,
+          "nPeaksIndoubleChargeWindow": 2,
+          "maxHitsPerSpectrumPerCharge": 30,
+          "nAnnotatedMostIntensePeaks": 6,
+          "minAnnotatedPeaks": 2,
+          "minPeaks": 4,
+          "cleaveNtermMethionine": true,
+          "maxMzLadders": 128,
+          "maxFragmentCharge": 2,
+          "fractionOfPeaksForChargeEstimation": 0.95,
+          "determineChargePlusOneAlgorithmically": true,
+          "searchPositiveIons": true,
+          "minPrecPerSpectrum": 1,
+          "searchForwardFragmentFirst": false,
+          "searchRewindFragments": true,
+          "maxFragmentPerSeries": 100,
+          "useCorrelationCorrectionScore": true,
+          "consecutiveIonProbability": 0.5,
+          "iterativeSequenceEvalue": 0.0,
+          "iterativeReplaceEvalue": 0.0,
+          "iterativeSpectrumEvalue": 0.01,
+          "noProlineRuleSeries": [],
+          "ptmIndexes": {},
+          "id": 0
+        }
+      },
+      "33": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters",
+        "data": {
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "searchType": "Classic",
+          "totalPartitions": 1,
+          "dissociationType": "HCD",
+          "maxModsForPeptide": 2,
+          "initiatorMethionineBehavior": "Variable",
+          "scoreCutoff": 5.0,
+          "useDeltaScore": false,
+          "fragmentationTerminus": "Both",
+          "maxFragmentSize": 30000.0,
+          "massDiffAcceptorType": "OneMM",
+          "writeMzId": true,
+          "writePepXml": false,
+          "useProvidedPrecursorInfo": true,
+          "doPrecursorDeconvolution": true,
+          "deconvolutionIntensityRatio": 3.0,
+          "deconvolutionMassTolerance": 4.0,
+          "deconvolutionMassToleranceType": "PPM",
+          "trimMs1Peaks": false,
+          "trimMsMsPeaks": true,
+          "numberOfPeaksToKeepPerWindow": 200,
+          "minAllowedIntensityRatioToBasePeak": 0.01,
+          "normalizePeaksAcrossAllWindows": false,
+          "modPeptidesAreDifferent": false,
+          "noOneHitWonders": false,
+          "searchTarget": true,
+          "decoyType": "None",
+          "maxModificationIsoforms": 1024,
+          "minVariantDepth": 1,
+          "maxHeterozygousVariants": 4,
+          "runGptm": false,
+          "gPtmCategories": [
+            "Common_Biological",
+            "Common_Artifact",
+            "Metal"
+          ],
+          "id": 0
+        }
+      },
+      "2": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.XtandemParameters",
+        "data": {
+          "maxEValue": 0.01,
+          "outputResults": "all",
+          "dynamicRange": 100.0,
+          "nPeaks": 50,
+          "minPrecursorMass": 500.0,
+          "minFragmentMz": 200.0,
+          "minPeaksPerSpectrum": 5,
+          "proteinQuickAcetyl": true,
+          "quickPyrolidone": true,
+          "refine": true,
+          "refineSemi": false,
+          "refinePointMutations": false,
+          "refineSpectrumSynthesis": true,
+          "refineUnanticipatedCleavages": true,
+          "refineSnaps": true,
+          "maximumExpectationValueRefinement": 0.01,
+          "potentialModificationsForFullRefinment": true,
+          "skylinePath": "",
+          "outputProteins": true,
+          "outputSequences": false,
+          "outputSpectra": true,
+          "outputHistograms": false,
+          "stpBias": false,
+          "useNoiseSuppression": false,
+          "proteinPtmComplexity": 6.0,
+          "parentMonoisotopicMassIsotopeError": true,
+          "id": 0
+        }
+      },
+      "3": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.PepnovoParameters",
+        "data": {
+          "hitListLength": 10,
+          "estimateCharge": true,
+          "correctPrecursorMass": false,
+          "discardLowQualitySpectra": true,
+          "fragmentationModel": "CID_IT_TRYP",
+          "generateQuery": false,
+          "id": 0
+        }
+      },
+      "4": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.AndromedaParameters",
+        "data": {
+          "maxPeptideMass": 4600.0,
+          "maxCombinations": 250,
+          "topPeaks": 8,
+          "topPeaksWindow": 100,
+          "includeWater": true,
+          "includeAmmonia": true,
+          "dependentLosses": true,
+          "fragmentAll": false,
+          "empiricalCorrection": true,
+          "higherCharge": true,
+          "fragmentationMethod": "CID",
+          "maxNumberOfModifications": 5,
+          "minPeptideLengthNoEnzyme": 8,
+          "maxPeptideLengthNoEnzyme": 30,
+          "equalIL": false,
+          "numberOfCandidates": 10,
+          "ptmIndexes": {},
+          "decoyMode": "none",
+          "id": 0
+        }
+      },
+      "5": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters",
+        "data": {
+          "generateDecoy": false,
+          "reportBothBestHitsForTD": true,
+          "instrumentID": "b, y",
+          "maxRank": 10,
+          "monoisotopic": true,
+          "lowMemoryMode": true,
+          "performDeisotoping": true,
+          "maxModifications": 3,
+          "maxVariableModifications": 4,
+          "maxModificationSites": 6,
+          "maxNeutralLosses": 1,
+          "maxNeutralLossesPerModification": 2,
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "maxLoadedProteins": 100000,
+          "maxLoadedSpectra": 2000,
+          "outputFormat": "csv",
+          "id": 0
+        }
+      },
+      "7": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.MsgfParameters",
+        "data": {
+          "searchDecoyDatabase": false,
+          "instrumentID": 3,
+          "fragmentationType": 3,
+          "protocol": 0,
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "numberOfSpectrumMarches": 10,
+          "additionalOutput": false,
+          "numberTolerableTermini": 2,
+          "numberOfModificationsPerPeptide": 2,
+          "id": 0
+        }
+      },
+      "8": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.DirecTagParameters",
+        "data": {
+          "ticCutoffPercentage": 100.0,
+          "maxPeakCount": 100,
+          "numIntensityClasses": 3,
+          "adjustPrecursorMass": false,
+          "minPrecursorAdjustment": -0.5,
+          "maxPrecursorAdjustment": 1.5,
+          "precursorAdjustmentStep": 0.1,
+          "numChargeStates": 3,
+          "outputSuffix": "",
+          "useChargeStateFromMS": true,
+          "duplicateSpectra": true,
+          "deisotopingMode": 0,
+          "isotopeMzTolerance": 0.25,
+          "complementMzTolerance": 0.1,
+          "tagLength": 4,
+          "maxDynamicMods": 2,
+          "maxTagCount": 10,
+          "intensityScoreWeight": 1.0,
+          "mzFidelityScoreWeight": 1.0,
+          "complementScoreWeight": 1.0,
+          "variableModifications": [],
+          "id": 0
+        }
+      },
+      "10": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.CometParameters",
+        "data": {
+          "numberOfSpectrumMatches": 10,
+          "maxVariableMods": 10,
+          "requireVariableMods": false,
+          "minPeaks": 10,
+          "minPeakIntensity": 0.0,
+          "removePrecursor": 0,
+          "removePrecursorTolerance": 1.5,
+          "lowerClearMzRange": 0.0,
+          "upperClearMzRange": 0.0,
+          "enzymeType": 2,
+          "isotopeCorrection": 3,
+          "minPrecursorMass": 600.0,
+          "maxPrecursorMass": 5000.0,
+          "maxFragmentCharge": 3,
+          "removeMethionine": false,
+          "batchSize": 0,
+          "theoreticalFragmentIonsSumOnly": false,
+          "fragmentBinOffset": 0.0,
+          "useSparseMatrix": true,
+          "selectedOutputFormat": "PepXML",
+          "printExpectScore": true,
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "id": 0
+        }
+      },
+      "13": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters",
+        "data": {
+          "minPeptideLength": 8,
+          "maxPeptideLength": 30,
+          "numberOfSpectrumMatches": 10,
+          "ticCutoffPercentage": 0.98,
+          "maxDynamicMods": 2,
+          "minTerminiCleavages": 2,
+          "minPrecursorMass": 600.0,
+          "maxPrecursorMass": 5000.0,
+          "useSmartPlusThreeModel": false,
+          "computeXCorr": false,
+          "numIntensityClasses": 3,
+          "classSizeMultiplier": 2,
+          "numberOfBatches": 50,
+          "lowerIsotopeCorrection": -1,
+          "upperIsotopeCorrection": 2,
+          "fragmentationRule": "CID",
+          "maxPeakCount": 300,
+          "outputFormat": "mzIdentML",
+          "id": 0
+        }
+      },
+      "27": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.PNovoParameters",
+        "data": {
+          "numberOfPeptides": 10,
+          "lowerPrecursorMass": 300,
+          "upperPrecursorMass": 5000,
+          "acticationType": "HCD",
+          "id": 0
+        }
+      },
+      "28": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.TideParameters",
+        "data": {
+          "fastIndexFolderName": "fasta-index",
+          "maxVariableModificationsPerPeptide": 255,
+          "maxVariableModificationsPerTypePerPeptide": 2,
+          "minPeptideLength": 6,
+          "maxPeptideLength": 30,
+          "minPrecursorMass": 200.0,
+          "maxPrecursorMass": 7200.0,
+          "decoyFormat": "none",
+          "keepTerminalAminoAcids": "NC",
+          "decoySeed": 1,
+          "outputFolderName": "crux-output",
+          "printPeptides": false,
+          "verbosity": 30,
+          "monoisotopicPrecursor": true,
+          "clipNtermMethionine": false,
+          "digestionType": "full-digest",
+          "computeSpScore": false,
+          "numberOfSpectrumMatches": 10,
+          "computeExactPValues": false,
+          "minSpectrumMz": 0.0,
+          "minSpectrumPeaks": 20,
+          "spectrumCharges": "all",
+          "removePrecursor": false,
+          "removePrecursorTolerance": 1.5,
+          "printProgressIndicatorSize": 1000,
+          "useFlankingPeaks": false,
+          "useNeutralLossPeaks": false,
+          "mzBinWidth": 0.02,
+          "mzBinOffset": 0.0,
+          "concatenateTargetDecoy": false,
+          "textOutput": true,
+          "sqtOutput": false,
+          "pepXmlOutput": false,
+          "mzidOutput": false,
+          "pinOutput": false,
+          "removeTempFolders": true,
+          "id": 0
+        }
+      },
+      "29": {
+        "type": "com.compomics.util.parameters.identification.tool_specific.NovorParameters",
+        "data": {
+          "fragmentationMethod": "HCD",
+          "massAnalyzer": "FT",
+          "id": 0
+        }
+      }
+    },
+    "flanking": false,
+    "id": 0
+  },
+  "annotationParameters": {
+    "yAxisZoomExcludesBackgroundPeaks": true,
+    "showAllPeaks": false,
+    "intensityThresholdType": "percentile",
+    "intensityLimit": 0.75,
+    "automaticAnnotation": true,
+    "selectedIonsMap": {
+      "IMMONIUM_ION": [
+        0,
+        1,
+        2,
+        3,
+        4,
+        5,
+        6,
+        7,
+        8,
+        9,
+        10,
+        11,
+        12,
+        13,
+        14,
+        15,
+        16,
+        17,
+        18,
+        19,
+        20
+      ],
+      "PEPTIDE_FRAGMENT_ION": [
+        4,
+        1
+      ],
+      "PRECURSOR_ION": [
+        0
+      ],
+      "TAG_FRAGMENT_ION": [
+        4,
+        1
+      ],
+      "REPORTER_ION": [],
+      "RELATED_ION": [
+        0,
+        1,
+        2,
+        3,
+        4,
+        5,
+        6,
+        7,
+        8,
+        9,
+        10,
+        11,
+        12,
+        13,
+        14,
+        15,
+        16,
+        17,
+        18
+      ]
+    },
+    "neutralLossesList": [
+      {
+        "composition": {
+          "atomChain": [
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "O",
+              "isotope": 0,
+              "id": 0
+            }
+          ],
+          "mass": -1.0,
+          "id": 0
+        },
+        "name": "H2O",
+        "fixed": false,
+        "aminoAcids": [
+          "D",
+          "E",
+          "S",
+          "T"
+        ],
+        "id": 0
+      },
+      {
+        "composition": {
+          "atomChain": [
+            {
+              "atomSymbol": "N",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            }
+          ],
+          "mass": -1.0,
+          "id": 0
+        },
+        "name": "NH3",
+        "fixed": false,
+        "aminoAcids": [
+          "K",
+          "N",
+          "Q",
+          "R"
+        ],
+        "id": 0
+      },
+      {
+        "composition": {
+          "atomChain": [
+            {
+              "atomSymbol": "C",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "H",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "O",
+              "isotope": 0,
+              "id": 0
+            },
+            {
+              "atomSymbol": "S",
+              "isotope": 0,
+              "id": 0
+            }
+          ],
+          "mass": -1.0,
+          "id": 0
+        },
+        "name": "CH4OS",
+        "fixed": false,
+        "id": 0
+      }
+    ],
+    "neutralLossesAuto": true,
+    "reporterIons": true,
+    "relatedIons": true,
+    "fragmentIonAccuracy": 10.0,
+    "fragmentIonPpm": false,
+    "showForwardIonDeNovoTags": false,
+    "showRewindIonDeNovoTags": false,
+    "deNovoCharge": 1,
+    "tiesResolution": "mostAccurateMz",
+    "id": 0
+  },
+  "sequenceMatchingParameters": {
+    "sequenceMatchingType": "indistiguishableAminoAcids",
+    "limitX": 0.25,
+    "enzymaticTagsOnly": false,
+    "maxPtmsPerTagPeptide": 3,
+    "minAminoAcidScore": 30,
+    "minTagLength": 3,
+    "id": 0
+  },
+  "peptideVariantsParameters": {
+    "variantType": "NO_VARIANT",
+    "nVariants": 0,
+    "nAaDeletions": 0,
+    "nAaInsertions": 0,
+    "nAaSubstitutions": 0,
+    "nAaSwap": 0,
+    "aaSubstitutionMatrix": {
+      "name": "No Substitution",
+      "description": "No substitution",
+      "substitutions": {},
+      "reverseMap": {},
+      "id": 0
+    },
+    "fixedVariants": {},
+    "id": 0
+  },
+  "geneParameters": {
+    "autoUpdate": false,
+    "useGeneMapping": false,
+    "id": 0
+  },
+  "psmScoringParameters": {
+    "spectrumMatchingScores": {
+      "8": [
+        1
+      ],
+      "3": [
+        1
+      ],
+      "27": [
+        1
+      ]
+    },
+    "defaultScores": [
+      -1
+    ],
+    "minDecoysInBin": 10,
+    "id": 0
+  },
+  "peptideAssumptionFilter": {
+    "minPepLength": 8,
+    "maxPepLength": 30,
+    "maxMassDeviation": 10.0,
+    "isPpm": true,
+    "unknownModification": true,
+    "minIsotopes": 0,
+    "maxIsotopes": 1,
+    "id": 0
+  },
+  "modificationLocalizationParameters": {
+    "probabilisticScoreCalculation": true,
+    "selectedProbabilisticScore": "PhosphoRS",
+    "dScoreThreshold": 95.0,
+    "probabilisticScoreThreshold": 95.0,
+    "probabilisticScoreNeutralLosses": false,
+    "sequenceMatchingParameters": {
+      "sequenceMatchingType": "aminoAcid",
+      "limitX": 0.25,
+      "enzymaticTagsOnly": false,
+      "maxPtmsPerTagPeptide": 3,
+      "minAminoAcidScore": 30,
+      "minTagLength": 3,
+      "id": 0
+    },
+    "alignNonConfidentModifications": true,
+    "id": 0
+  },
+  "proteinInferenceParameters": {
+    "modificationRefinement": true,
+    "simplifyProteinGroups": true,
+    "simplifyGroupsEvidence": true,
+    "simplifyGroupsConfidence": true,
+    "simplifyGroupsEnzymaticity": true,
+    "simplifyGroupsVariants": true,
+    "confidenceThreshold": 0.05,
+    "id": 0
+  },
+  "idValidationParameters": {
+    "defaultProteinFDR": 1.0,
+    "defaultPeptideFDR": 1.0,
+    "defaultPsmFDR": 1.0,
+    "validationQCPreferences": {
+      "dbSize": false,
+      "firstDecoy": true,
+      "confidenceMargin": 1.0,
+      "id": 0
+    },
+    "id": 0
+  },
+  "fractionParameters": {
+    "proteinConfidenceMwPlots": 95.0,
+    "fractionMolecularWeightRanges": {},
+    "id": 0
+  },
+  "fastaParameters": {
+    "targetDecoy": true,
+    "decoyFlag": "-REVERSED",
+    "decoySuffix": true,
+    "targetDecoyFileNameTag": "_concatenated_target_decoy",
+    "id": 0
+  },
+  "id": 0
+}
\ No newline at end of file
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/fastacli_searchgui_tinydb1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastacli_searchgui_tinydb1.fasta	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,24 @@
+>generic|cds.comp107265_c0_seq1|m.36816 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.94 EValue:9.0e-68
+LKSSFESSFSIKSRDVTFGNSMNITMVPPELEFFKDNRHKEKSEMQDLNTRLESYLSVGKDDSDANLKLMQELEEIKNGIKTETNNIKATFEAELGQLKNLLDDIDHDKNQVIVIGDNNDEMYKDLEQRIKNYNDMEMIHLSKIRQLDNLLSNYGLKMNQLQKKIGFLCEEKDRDIESINKLRADIDVAKNDLSNEILLRTDAQNRCQSLEEDIEFTKEVHQRELSNMIALADYDPVSQSMDWWNDEFARCIKEIQDEYEDRLNNIQYDMDSHYNSKIQDVETTILQSSAKSEMLDQCSMLENSNAEIEDQTSELEKKNAMLKEQNDLLNRGIREIQSQFETLITEKQSEMLEIRKHFEQSLADLQAIVDDNLSLQMEIMSYKKLLECEELRVGIYPESNANENQGDQGQRQNEQITEPITETIPKRKKPERKISYQRSSKGPLTISECKSDGSYILIENMDQYDGQNLGGWRLVQNVDGMEEYDYTFSRYYLGPGESVKIWAENAGPKGVNDLVWDDLKCLGIGEKVITSLMNQKGKEKSSYTQKAIYKV
+>generic|cds.comp307584_c0_seq2|m.40556 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 39.47 EValue:1.0e-14
+DDNYDSLQYSFPKSDHQRKTTYQRSAKGPITITRVQPDGSYIEIENTNIAVNEDISGWKMVQCTDDKIYEYIFDDHVLNGGTCVKIWANGLSGKEENDLVWIDRTCLTTGSVVTTTLMDYNGNEKATFTQ
+>generic|cds.comp376950_c0_seq1|m.42080 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 41.38 EValue:1.0e-32
+KELEDINEDNLGRLRRQDEDVSNYEAQNASLRRKCDNLQADKDRDRNNVEKLKGEVTSLRNDLMMETVSRIDSQNKCQTLREELEFLKDIHSQELKELSPTLGKDPFAKSKEWWSSEFSNCIREIQEEYDNRLDSIKTDMDNYYTLKVQEIQTGAAR
+>generic|cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67
+METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT
+>generic|cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67
+METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT
+>generic|cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10
+SGLAGDSDTMRASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT
+>generic|cds.comp41890_c0_seq1|m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20
+YQSPTPALVKGELQEHSTYRKNNKGPVAISETDRDGSFILLENTSNSHTVDLSGWKIMQNSDNIDISEYEIENLVLKPGGFAKVWANGMGDPNSGDLVWHNKSRLGVGAKVNTVLLNTRGDEKATYNLETTYNL
+>generic|cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91
+MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGTTSITTGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF
+>generic|cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92
+MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF
+>generic|cds.comp55448_c0_seq1|m.24261 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 96.04 EValue:0.0
+MRRIKKKITLDVRVTELIDQLERQQKELEESRTYHQIDQEQIARQNQQLADLEGEISMLRRSIESLEKEKMRQSNILAKMNDELEKLRMDLNNETINHLDAENRRQTLEEELEFQKDVHAQELKELAALAYRDTTAENREFWRNELAQAIRDIQQEYDAKCDQMRGDIEAYYNLKVQEFRTGATKQNMEVTRNKEENTKLRSNMNEVRNRLADLEARNAQLERTNQDLLRDLEEKDRQNELESCQYKEEITKLRGEMESILKELQDLMDIKLSLELEIAAYRKLLEGEESRVGMKQIVEQVVGARPNEAEVLSSILTRSEGGYEATGDSQISMKMMRGELAAKTTYQRTSKGPVSIKEADSQGQFIALETKKEENITGWKIVRKVDDNMVYSYEIPNVVLKTGTVIKIWSKSHQAQARGDDIVSRENDTWGTGSNVVTILQNEKGEEKANYTQNTVYQ
+>generic|cds.comp55448_c0_seq2|m.24262 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 91.49 EValue:5.0e-87
+MSGGFSYSAKIHPRTGYVSRTSQSPYRSSMGSNAAFTRSYEFNYGATAMPGAYANISSTGVNHVKANREREKQDMRDLNERFANYIEKVRFLEAQNKKLAGELEELKSKWGKETSAIKEMYETELEEARKLIDATNKEKNYLGRESN
+>generic|cds.comp8310_c0_seq2|m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16
+FKDTCIRDKTDMKGLNERLSEFIEVARYNAILAKKLEKTIKRFHSQEIPEDVERIYEATIKKLRKLLVVFENERDNERAKNLKLQTECAKLKESLEDLKAKEIENRDRLISKFKILEDLQSKAIRIEKNIEIVAEENVLKNNKIEKLKKHFENLKSKITSERRNRSTHKESYDEVKEDFGIFKELKNQQLSSVRFPKYKDSIKYLRKQWSNEFSKCIKELQNEYESRVSSVKEELESNYCTKTEEIQNYVLKSNYESDFLKNRNLVAEESMNMLKNKFKEAKKENVLLNHEKEELEIEFNKSKNEYDHLAEEKNNEILNFKEYAEKILIQLTEILEINNHLQFEIEYYKTVITSGETKIDFDFDGLDDECMTSINSELP
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,48 @@
+>generic|cds.comp107265_c0_seq1|m.36816 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.94 EValue:9.0e-68
+LKSSFESSFSIKSRDVTFGNSMNITMVPPELEFFKDNRHKEKSEMQDLNTRLESYLSVGKDDSDANLKLMQELEEIKNGIKTETNNIKATFEAELGQLKNLLDDIDHDKNQVIVIGDNNDEMYKDLEQRIKNYNDMEMIHLSKIRQLDNLLSNYGLKMNQLQKKIGFLCEEKDRDIESINKLRADIDVAKNDLSNEILLRTDAQNRCQSLEEDIEFTKEVHQRELSNMIALADYDPVSQSMDWWNDEFARCIKEIQDEYEDRLNNIQYDMDSHYNSKIQDVETTILQSSAKSEMLDQCSMLENSNAEIEDQTSELEKKNAMLKEQNDLLNRGIREIQSQFETLITEKQSEMLEIRKHFEQSLADLQAIVDDNLSLQMEIMSYKKLLECEELRVGIYPESNANENQGDQGQRQNEQITEPITETIPKRKKPERKISYQRSSKGPLTISECKSDGSYILIENMDQYDGQNLGGWRLVQNVDGMEEYDYTFSRYYLGPGESVKIWAENAGPKGVNDLVWDDLKCLGIGEKVITSLMNQKGKEKSSYTQKAIYKV
+>generic|cds.comp107265_c0_seq1_REVERSED|m.36816 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.94 EValue:9.0e-68-REVERSED
+VKYIAKQTYSSKEKGKQNMLSTIVKEGIGLCKLDDWVLDNVGKPGANEAWIKVSEGPGLYYRSFTYDYEEMGDVNQVLRWGGLNQGDYQDMNEILIYSGDSKCESITLPGKSSRQYSIKREPKKRKPITETIPETIQENQRQGQDGQNENANSEPYIGVRLEECELLKKYSMIEMQLSLNDDVIAQLDALSQEFHKRIELMESQKETILTEFQSQIERIGRNLLDNQEKLMANKKELESTQDEIEANSNELMSCQDLMESKASSQLITTEVDQIKSNYHSDMDYQINNLRDEYEDQIEKICRAFEDNWWDMSQSVPDYDALAIMNSLERQHVEKTFEIDEELSQCRNQADTRLLIENSLDNKAVDIDARLKNISEIDRDKEECLFGIKKQLQNMKLGYNSLLNDLQRIKSLHIMEMDNYNKIRQELDKYMEDNNDGIVIVQNKDHDIDDLLNKLQGLEAEFTAKINNTETKIGNKIEELEQMLKLNADSDDKGVSLYSELRTNLDQMESKEKHRNDKFFELEPPVMTINMSNGFTVDRSKISFSSEFSSKL
+>generic|cds.comp307584_c0_seq2|m.40556 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 39.47 EValue:1.0e-14
+DDNYDSLQYSFPKSDHQRKTTYQRSAKGPITITRVQPDGSYIEIENTNIAVNEDISGWKMVQCTDDKIYEYIFDDHVLNGGTCVKIWANGLSGKEENDLVWIDRTCLTTGSVVTTTLMDYNGNEKATFTQ
+>generic|cds.comp307584_c0_seq2_REVERSED|m.40556 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 39.47 EValue:1.0e-14-REVERSED
+QTFTAKENGNYDMLTTTVVSGTTLCTRDIWVLDNEEKGSLGNAWIKVCTGGNLVHDDFIYEYIKDDTCQVMKWGSIDENVAINTNEIEIYSGDPQVRTITIPGKASRQYTTKRQHDSKPFSYQLSDYNDD
+>generic|cds.comp376950_c0_seq1|m.42080 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 41.38 EValue:1.0e-32
+KELEDINEDNLGRLRRQDEDVSNYEAQNASLRRKCDNLQADKDRDRNNVEKLKGEVTSLRNDLMMETVSRIDSQNKCQTLREELEFLKDIHSQELKELSPTLGKDPFAKSKEWWSSEFSNCIREIQEEYDNRLDSIKTDMDNYYTLKVQEIQTGAAR
+>generic|cds.comp376950_c0_seq1_REVERSED|m.42080 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 41.38 EValue:1.0e-32-REVERSED
+RAAGTQIEQVKLTYYNDMDTKISDLRNDYEEQIERICNSFESSWWEKSKAFPDKGLTPSLEKLEQSHIDKLFELEERLTQCKNQSDIRSVTEMMLDNRLSTVEGKLKEVNNRDRDKDAQLNDCKRRLSANQAEYNSVDEDQRRLRGLNDENIDELEK
+>generic|cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67
+METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT
+>generic|cds.comp41779_c0_seq1_REVERSED|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67-REVERSED
+TVVKTSLNAKLADKEDYLSFVSNRNVPGWEDVTAIIDGKKAMKQYNKAWIKISQEGELVVPDKFLFDIKHEPSISTASILRDLKWGKMNVSTKSRGSSTNELTVYQGESEVEGISIVSKSSRQITLRGTLTSTSASDGALGSGSGSGSGGGGGGGGGGSGFELINALNDGAESRFGGINETIYGTSIRNEEGELLKRYAAIELELSLKADMLMQLEEIMSEMEVHLKNVETTRLDKENELDENSRQLQNTITIIEMKMRELQSELEKIRMDKQVSVMGTSKESKTHVAAVPEAHASQRIQSLQSEYRASMEDSIDALRQDYEERLEKMCNSMENNWAASVNTGTDDEKSLMAKYEKIEADTVSRLFELEEELNGVKQQLFIRQQTEDKLDARTAQLQTNVENYKARWHAVQKELEDLKKHLMSCEAERHSNEDILKNVKDQLEDIRDENIRATAHLDEIEEEYTTISIKLEGNEKNADLLLNKAEDIEAQYAEKLPEVDFERRKKSLKLRLQENEAQLSRVKAIYGAFRDNLNQMDKKEGERKVKMTGMDKTAIGGAVGAAMGLSARGGHLSMSQNMSGMSGGGLGAGVVHSRRNVQIFKPQVHATAGMSQRKTVVTSKEKREKTTEM
+>generic|cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67
+METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT
+>generic|cds.comp41779_c0_seq2_REVERSED|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67-REVERSED
+TVVKTSLNAKLADKEDYLSFVSNRNVPGWEDVTAIIDGKKAMKQYNKAWIKISQEGELVVPDKFLFDIKHEPSISTASILRDLKWGKMNVSTKSRGSSTNELTVYQGESEVEGISIVSKSSRQITLRGSDGALGSGSGSGSGGGGGGGGGGSGFELINALNDGAESRFGGINETIYGTSIRNEEGELLKRYAAIELELSLKADMLMQLEEIMSEMEVHLKNVETTRLDKENELDENSRQLQNTITIIEMKMRELQSELEKIRMDKQVSVMGTSKESKTHVAAVPEAHASQRIQSLQSEYRASMEDSIDALRQDYEERLEKMCNSMENNWAASVNTGTDDEKSLMAKYEKIEADTVSRLFELEEELNGVKQQLFIRQQTEDKLDARTAQLQTNVENYKARWHAVQKELEDLKKHLMSCEAERHSNEDILKNVKDQLEDIRDENIRATAHLDEIEEEYTTISIKLEGNEKNADLLLNKAEDIEAQYAEKLPEVDFERRKKSLKLRLQENEAQLSRVKAIYGAFRDNLNQMDKKEGERKVKMTGMDKTAIGGAVGAAMGLSARGGHLSMSQNMSGMSGGGLGAGVVHSRRNVQIFKPQVHATAGMSQRKTVVTSKEKREKTTEM
+>generic|cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10
+SGLAGDSDTMRASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT
+>generic|cds.comp41779_c0_seq3_REVERSED|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10-REVERSED
+TVVKTSLNAKLADKEDYLSFVSNRNVPGWEDVTAIIDGKKAMKQYNKAWIKISQEGELVVPDKFLFDIKHEPSISTASILRDLKWGKMNVSTKSRGSSTNELTVYQGESEVEGISIVSKSSRQITLRGTLTSTSARMTDSDGALGS
+>generic|cds.comp41890_c0_seq1|m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20
+YQSPTPALVKGELQEHSTYRKNNKGPVAISETDRDGSFILLENTSNSHTVDLSGWKIMQNSDNIDISEYEIENLVLKPGGFAKVWANGMGDPNSGDLVWHNKSRLGVGAKVNTVLLNTRGDEKATYNLETTYNL
+>generic|cds.comp41890_c0_seq1_REVERSED|m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20-REVERSED
+LNYTTELNYTAKEDGRTNLLVTNVKAGVGLRSKNHWVLDGSNPDGMGNAWVKAFGGPKLVLNEIEYESIDINDSNQMIKWGSLDVTHSNSTNELLIFSGDRDTESIAVPGKNNKRYTSHEQLEGKVLAPTPSQY
+>generic|cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91
+MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGTTSITTGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF
+>generic|cds.comp52727_c0_seq1_REVERSED|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91-REVERSED
+FVVKITLTAKEVGNEDYLTIISNRNVQGWDAVSSIIDDPKIEPDKEFNKAWVRINQQADLSTDRNIIYEFSLEQLSNTRIFERKIKWGKLNQLRKMRTTSTNDLTVYRGTNDVEAISIVGKSSRQMTVRGTTISTTGSEGMSSSAEFSAGSRELINALADETQGRYGGVMQTMSGISLRNEEVELLKRYAAIELELSLKADMLLQLEKIVGELETNLKQVESVRLTKENDLEATTSDLESTLLHVQSKLKDIQSQLDMMHSDKDTIQSRLRRNEESAQASEANGKTAGLRIENLQVQYKSELDASLLNLQNDYEDRIERMCKSLENNWYERMQPVNDEKMLMAKYEKIEADTVSRLFNLEEELAQARTSEALRQCTEEQLDIRLGQLQTDVHAYKAKWDALQKELEQVKRKLMENDAIRRAIDDNLTDINNQLQDNVDNSHRLQARLDELEDELTNIRVKLNGNDNNADDLLKKAENIEIQYMQKLPEPDFDKKSKNLADRLAKNEAELFRAQEIFNALRENLDQLEKKEGERKLKMSAVGKHSINGLVGAQLHGGLGLGSSMSSRSRQMTSMATGPSLSVRNIVINKSQTFPKYNVSQRSTTVTQRTEVGQKEM
+>generic|cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92
+MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF
+>generic|cds.comp52727_c0_seq2_REVERSED|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92-REVERSED
+FVVKITLTAKEVGNEDYLTIISNRNVQGWDAVSSIIDDPKIEPDKEFNKAWVRINQQADLSTDRNIIYEFSLEQLSNTRIFERKIKWGKLNQLRKMRTTSTNDLTVYRGTNDVEAISIVGKSSRQMTVRGSEGMSSSAEFSAGSRELINALADETQGRYGGVMQTMSGISLRNEEVELLKRYAAIELELSLKADMLLQLEKIVGELETNLKQVESVRLTKENDLEATTSDLESTLLHVQSKLKDIQSQLDMMHSDKDTIQSRLRRNEESAQASEANGKTAGLRIENLQVQYKSELDASLLNLQNDYEDRIERMCKSLENNWYERMQPVNDEKMLMAKYEKIEADTVSRLFNLEEELAQARTSEALRQCTEEQLDIRLGQLQTDVHAYKAKWDALQKELEQVKRKLMENDAIRRAIDDNLTDINNQLQDNVDNSHRLQARLDELEDELTNIRVKLNGNDNNADDLLKKAENIEIQYMQKLPEPDFDKKSKNLADRLAKNEAELFRAQEIFNALRENLDQLEKKEGERKLKMSAVGKHSINGLVGAQLHGGLGLGSSMSSRSRQMTSMATGPSLSVRNIVINKSQTFPKYNVSQRSTTVTQRTEVGQKEM
+>generic|cds.comp55448_c0_seq1|m.24261 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 96.04 EValue:0.0
+MRRIKKKITLDVRVTELIDQLERQQKELEESRTYHQIDQEQIARQNQQLADLEGEISMLRRSIESLEKEKMRQSNILAKMNDELEKLRMDLNNETINHLDAENRRQTLEEELEFQKDVHAQELKELAALAYRDTTAENREFWRNELAQAIRDIQQEYDAKCDQMRGDIEAYYNLKVQEFRTGATKQNMEVTRNKEENTKLRSNMNEVRNRLADLEARNAQLERTNQDLLRDLEEKDRQNELESCQYKEEITKLRGEMESILKELQDLMDIKLSLELEIAAYRKLLEGEESRVGMKQIVEQVVGARPNEAEVLSSILTRSEGGYEATGDSQISMKMMRGELAAKTTYQRTSKGPVSIKEADSQGQFIALETKKEENITGWKIVRKVDDNMVYSYEIPNVVLKTGTVIKIWSKSHQAQARGDDIVSRENDTWGTGSNVVTILQNEKGEEKANYTQNTVYQ
+>generic|cds.comp55448_c0_seq1_REVERSED|m.24261 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 96.04 EValue:0.0-REVERSED
+QYVTNQTYNAKEEGKENQLITVVNSGTGWTDNERSVIDDGRAQAQHSKSWIKIVTGTKLVVNPIEYSYVMNDDVKRVIKWGTINEEKKTELAIFQGQSDAEKISVPGKSTRQYTTKAALEGRMMKMSIQSDGTAEYGGESRTLISSLVEAENPRAGVVQEVIQKMGVRSEEGELLKRYAAIELELSLKIDMLDQLEKLISEMEGRLKTIEEKYQCSELENQRDKEELDRLLDQNTRELQANRAELDALRNRVENMNSRLKTNEEKNRTVEMNQKTAGTRFEQVKLNYYAEIDGRMQDCKADYEQQIDRIAQALENRWFERNEATTDRYALAALEKLEQAHVDKQFELEEELTQRRNEADLHNITENNLDMRLKELEDNMKALINSQRMKEKELSEISRRLMSIEGELDALQQNQRAIQEQDIQHYTRSEELEKQQRELQDILETVRVDLTIKKKIRRM
+>generic|cds.comp55448_c0_seq2|m.24262 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 91.49 EValue:5.0e-87
+MSGGFSYSAKIHPRTGYVSRTSQSPYRSSMGSNAAFTRSYEFNYGATAMPGAYANISSTGVNHVKANREREKQDMRDLNERFANYIEKVRFLEAQNKKLAGELEELKSKWGKETSAIKEMYETELEEARKLIDATNKEKNYLGRESN
+>generic|cds.comp55448_c0_seq2_REVERSED|m.24262 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 91.49 EValue:5.0e-87-REVERSED
+NSERGLYNKEKNTADILKRAEELETEYMEKIASTEKGWKSKLEELEGALKKNQAELFRVKEIYNAFRENLDRMDQKERERNAKVHNVGTSSINAYAGPMATAGYNFEYSRTFAANSGMSSRYPSQSTRSVYGTRPHIKASYSFGGSM
+>generic|cds.comp8310_c0_seq2|m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16
+FKDTCIRDKTDMKGLNERLSEFIEVARYNAILAKKLEKTIKRFHSQEIPEDVERIYEATIKKLRKLLVVFENERDNERAKNLKLQTECAKLKESLEDLKAKEIENRDRLISKFKILEDLQSKAIRIEKNIEIVAEENVLKNNKIEKLKKHFENLKSKITSERRNRSTHKESYDEVKEDFGIFKELKNQQLSSVRFPKYKDSIKYLRKQWSNEFSKCIKELQNEYESRVSSVKEELESNYCTKTEEIQNYVLKSNYESDFLKNRNLVAEESMNMLKNKFKEAKKENVLLNHEKEELEIEFNKSKNEYDHLAEEKNNEILNFKEYAEKILIQLTEILEINNHLQFEIEYYKTVITSGETKIDFDFDGLDDECMTSINSELP
+>generic|cds.comp8310_c0_seq2_REVERSED|m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16-REVERSED
+PLESNISTMCEDDLGDFDFDIKTEGSTIVTKYYEIEFQLHNNIELIETLQILIKEAYEKFNLIENNKEEALHDYENKSKNFEIELEEKEHNLLVNEKKAEKFKNKLMNMSEEAVLNRNKLFDSEYNSKLVYNQIEETKTCYNSELEEKVSSVRSEYENQLEKICKSFENSWQKRLYKISDKYKPFRVSSLQQNKLEKFIGFDEKVEDYSEKHTSRNRRESTIKSKLNEFHKKLKEIKNNKLVNEEAVIEINKEIRIAKSQLDELIKFKSILRDRNEIEKAKLDELSEKLKACETQLKLNKARENDRENEFVVLLKRLKKITAEYIREVDEPIEQSHFRKITKELKKALIANYRAVEIFESLRENLGKMDTKDRICTDKF
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptide_shaker_modifications_result1.cpsx
Binary file test-data/peptide_shaker_modifications_result1.cpsx has changed
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptide_shaker_modifications_result1.output_certificate
--- a/test-data/peptide_shaker_modifications_result1.output_certificate	Thu Feb 20 05:51:38 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
-
-Project Details
-
-1: PeptideShaker Version: 1.16.31
-2: Date: Thu Oct 11 10:41:54 CEST 2018
-3: Experiment: Galaxy_Experiment_2018101110411539247311
-4: Sample: Sample_2018101110411539247311
-5: Replicate Number: 1
-6: Identification Algorithms: OMSSA, X!Tandem, MS-GF+ and Comet
-
-Database Search Parameters
-
-1: Precursor Tolerance Unit: ppm
-2: Precursor Ion m/z Tolerance: 100.0
-3: Fragment Ion Tolerance Unit: Da
-4: Fragment Ion m/z Tolerance: 0.5
-5: Cleavage: Enzyme
-6: Enzyme: Trypsin
-7: Missed Cleavages: 2
-8: Specificity: Specific
-9: Database: input_database.fasta
-10: Forward Ion: b
-11: Rewind Ion: y
-12: Fixed Modifications: Carbamidomethylation of C
-13: Variable Modifications: Oxidation of M
-14: Refinement Variable Modifications: Acetylation of protein N-term, Pyrolidone from E, Pyrolidone from Q, Pyrolidone from carbamidomethylated C
-15: Refinement Fixed Modifications: 
-
-Input Filters
-
-1: Minimal Peptide Length: 1
-2: Maximal Peptide Length: 30
-3: Precursor m/z Tolerance: 10.0
-4: Precursor m/z Tolerance Unit: Yes
-5: Unrecognized Modifications Discarded: Yes
-
-Validation Summary
-
-1: Proteins: #Validated: 2.0
-2: Proteins: Total Possible TP: 2.0
-3: Proteins: FDR Limit [%]: 0.0
-4: Proteins: FNR Limit [%]: 0.0
-5: Proteins: Confidence Limit [%]: 100.0
-6: Proteins: PEP Limit [%]: 0.0
-7: Proteins: Confidence Accuracy [%]: 0.0
-8: Peptides: #Validated: 16.0
-9: Peptides: Total Possible TP: 16.0
-10: Peptides: FDR Limit [%]: 0.0
-11: Peptides: FNR Limit [%]: 0.0
-12: Peptides: Confidence Limit [%]: 100.0
-13: Peptides: PEP Limit [%]: 0.0
-14: Peptides: Confidence Accuracy [%]: 0.0
-15: PSMs: #Validated PSM: 42.0
-16: PSMs: Total Possible TP: 42.0
-17: PSMs: FDR Limit [%]: 0.0
-18: PSMs: FNR Limit [%]: 0.0
-19: PSMs: Confidence Limit [%]: 100.0
-20: PSMs: PEP Limit [%]: 0.0
-21: PSMs: Confidence Accuracy [%]: 0.0
-
-PTM Scoring Settings
-
-1: Probabilistic Score: PhosphoRS
-2: Accounting for Neutral Losses: No
-3: Threshold: 95.0
-
-Spectrum Counting Parameters
-
-1: Method: NSAF
-2: Validated Matches Only: No
-
-Annotation Settings
-
-1: Intensity Limit: 0.75
-2: Automatic Annotation: Yes
-3: Selected Ions: b, y
-4: Neutral Losses: H2O, NH3, CH4OS
-5: Neutral Losses Sequence Dependence: Yes
-6: Fragment Ion m/z Tolerance: 0.5
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptide_shaker_modifications_result1.output_extended_psm
--- a/test-data/peptide_shaker_modifications_result1.output_extended_psm	Thu Feb 20 05:51:38 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-	Protein(s)	Sequence	AAs Before	AAs After	Position	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NK; NK	LS; LS	403; 403	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 1198, +MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560840995904	0	5.225020941769318	0				100.0	Doubtful
-2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	AK; AK	IS; IS	147; 147	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 207,  MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362356486903	0	-9.522902824571501	0				100.0	Doubtful
-3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	VR; VR	LK; LK	110; 110	NH2-SLQAENEQLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 39,  MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942144781802	0	2.063410823544894	0				100.0	Doubtful
-4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	RR; RR	NL; NL	128; 128	NH2-EFDVEPLKEAYQAEIDEAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 736,  MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583092202605	0	-1.1628605151025897	0				100.0	Doubtful
-5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	MK; MK	SN; SN	373; 373	NH2-MEIITITNQLQR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 636, +MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864490053003	0	-3.2324313291878943	0				100.0	Doubtful
-6	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	MR; MR	YQ; YQ	298; 298	NH2-EIRDEYDNQLNLLSADLESK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 748,  MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.14449845571	0	6.2066377342036665	0				100.0	Doubtful
-7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	AR; AR	QS; QS	323; 323	NH2-YESQLSQIR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 67, +MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669371011802	0	6.998127983906467	0				100.0	Doubtful
-8	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	MR; MR	YQ; YQ	298; 298	NH2-EIRDEYDNQLNLLSADLESK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 748, +MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.14449845571	0	6.2066377342036665	0				100.0	Doubtful
-9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	QK; QK	SV; SV	254; 254	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 875,  MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354589782603	0	2.711916908512312	0				100.0	Doubtful
-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	QK; QK	SV; SV	254; 254	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 871,  MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354589782603	0	1.7035983401739305	0				100.0	Doubtful
-11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	AK; AK; AK	NS; NS; NS	590; 583; 108	NH2-KGDIIATVDEWGPVNR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 582,  MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.91079757128	0	1.643983659206309	0				100.0	Doubtful
-12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	SK; SK; SK	SK; SK; SK	511; 504; 29	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 758,  MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.224205328391	0	2.5264056584343257	0				100.0	Doubtful
-13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	LK; LK	IN; IN	161; 161	NH2-ISITTYEEEIEDLHATAR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 752, +MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167787614505	0	6.6562738302421005	0				100.0	Doubtful
-14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	RR; RR	AS; AS	37; 37	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 220,  MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263804604496	0	2.939629370057349	0				100.0	Doubtful
-15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	QK; QK	SV; SV	254; 254	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 871, +MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354589782603	0	1.7035983401739305	0				100.0	Doubtful
-16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NR; NR	SE; SE	442; 442	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 591,  MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7729071161402	0	2.4535863107993414	0				100.0	Doubtful
-17	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	AK; AK	IS; IS	147; 147	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 207, +MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362356486903	0	-9.522902824571501	0				100.0	Doubtful
-18	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	QK; QK	SV; SV	254; 254	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 875, +MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354589782603	0	2.711916908512312	0				100.0	Doubtful
-19	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	GR; GR	DM; DM	63; 63	NH2-ASLGMAAGVAGGIATK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 357,  MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336851564503	0	-2.731669916283406	0				100.0	Doubtful
-20	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NK; NK	LS; LS	403; 403	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 1197,  MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560840995904	0	5.228649666852938	0				100.0	Doubtful
-21	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	AK; AK; AK	NS; NS; NS	590; 583; 108	NH2-KGDIIATVDEWGPVNR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 582, +MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.91079757128	0	1.643983659206309	0				100.0	Doubtful
-22	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	AK; AK	IS; IS	147; 147	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 204, +MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362356486903	0	-6.678955564950069	0				100.0	Doubtful
-23	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NR; NR	SE; SE	442; 442	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 591, +MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7729071161402	0	2.4535863107993414	0				100.0	Doubtful
-24	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	AK; AK	IS; IS	147; 147	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 204,  MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362356486903	0	-6.678955564950069	0				100.0	Doubtful
-25	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NK; NK	LS; LS	403; 403	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 1198,  MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560840995904	0	5.225020941769318	0				100.0	Doubtful
-26	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	DR; DR; DR	ID; ID; ID	549; 542; 67	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 72,  MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928658902905	0	2.0041097707959827	0				100.0	Doubtful
-27	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	GR; GR	DM; DM	63; 63	NH2-ASLGMAAGVAGGIATK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 357, +MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336851564503	0	-2.731669916283406	0				100.0	Doubtful
-28	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	LK; LK	IN; IN	161; 161	NH2-ISITTYEEEIEDLHATAR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 752,  MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167787614505	0	6.6562738302421005	0				100.0	Doubtful
-29	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	DR; DR; DR	ID; ID; ID	549; 542; 67	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 75,  MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928658902905	0	1.481004205034201	0				100.0	Doubtful
-30	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	SK; SK; SK	SK; SK; SK	511; 504; 29	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 758, +MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.224205328391	0	2.5264056584343257	0				100.0	Doubtful
-31	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NK; NK	LS; LS	403; 403	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 1197, +MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560840995904	0	5.228649666852938	0				100.0	Doubtful
-32	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	DR; DR; DR	ID; ID; ID	549; 542; 67	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 72, +MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928658902905	0	2.0041097707959827	0				100.0	Doubtful
-33	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	RR; RR	AS; AS	37; 37	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 220, +MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263804604496	0	2.939629370057349	0				100.0	Doubtful
-34	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	DR; DR; DR	ID; ID; ID	549; 542; 67	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 75, +MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928658902905	0	1.481004205034201	0				100.0	Doubtful
-35	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	AR; AR	QS; QS	323; 323	NH2-YESQLSQIR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 67,  MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669371011802	0	6.998127983906467	0				100.0	Doubtful
-36	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	MK; MK	SN; SN	373; 373	NH2-MEIITITNQLQR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 636,  MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864490053003	0	-3.2324313291878943	0				100.0	Doubtful
-37	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	AR; AR	LI; LI	179; 179	NH2-INEDRIDELQDKVNK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 81, +MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326552146706	0	-1.7720894394949223	0				100.0	Doubtful
-38	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	RR; RR	NL; NL	128; 128	NH2-EFDVEPLKEAYQAEIDEAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 736, +MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583092202605	0	-1.1628605151025897	0				100.0	Doubtful
-39	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	VR; VR	LK; LK	110; 110	NH2-SLQAENEQLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 39, +MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942144781802	0	2.063410823544894	0				100.0	Doubtful
-40	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	AR; AR	LI; LI	179; 179	NH2-INEDRIDELQDKVNK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 81,  MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326552146706	0	-1.7720894394949223	0				100.0	Doubtful
-41	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NR; NR	SE; SE	442; 442	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 588,  MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7729071161402	0	3.113546101111509	0				100.0	Doubtful
-42	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NR; NR	SE; SE	442; 442	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 588, +MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7729071161402	0	3.113546101111509	0				100.0	Doubtful
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptide_shaker_modifications_result1.output_hierarchical
--- a/test-data/peptide_shaker_modifications_result1.output_hierarchical	Thu Feb 20 05:51:38 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
-	Main Accession	Description	MW [kDa]	Possible Coverage [%]	Coverage [%]	Spectrum Counting NSAF	Confidently Localized Modification Sites	# Confidently Localized Modification Sites	Ambiguously Localized Modification Sites	#Ambiguously Localized Modification Sites	Protein Inference	Secondary Accessions	Protein Group	#Validated Peptides	#Peptides	#Unique	#Validated PSMs	#PSMs	Confidence [%]	Decoy	Validation
-1	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91		69.96963713242043	100.0	3.25	0.0032520325203252032					Related Proteins	cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	1	1	1	2	2	100.0	0	Doubtful
-	Protein(s)	Sequence	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#Validated PSMs	#PSMs	Confidence [%]	Decoy	Validation
-1.1	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	MR; MR	YQ; YQ				2	2	100.0	0	Doubtful
-	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-1.1.1	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	NH2-EIRDEYDNQLNLLSADLESK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 748, +MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.14449845571	0	6.2066377342036665	0				100.0	Doubtful
-1.1.2	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	NH2-EIRDEYDNQLNLLSADLESK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 748,  MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.14449845571	0	6.2066377342036665	0				100.0	Doubtful
-2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67		69.88215380565927	92.52	37.58	0.017651472642866785					Related Proteins	cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	15	15	15	40	40	100.0	0	Doubtful
-	Protein(s)	Sequence	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#Validated PSMs	#PSMs	Confidence [%]	Decoy	Validation
-2.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NK; NK	LS; LS				4	4	100.0	0	Doubtful
-	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-2.1.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 1198, +MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560840995904	0	5.225020941769318	0				100.0	Doubtful
-2.1.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 1198,  MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560840995904	0	5.225020941769318	0				100.0	Doubtful
-2.1.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 1197, +MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560840995904	0	5.228649666852938	0				100.0	Doubtful
-2.1.4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 1197,  MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560840995904	0	5.228649666852938	0				100.0	Doubtful
-2.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	AK; AK	IS; IS				4	4	100.0	0	Doubtful
-	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-2.2.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 207,  MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362356486903	0	-9.522902824571501	0				100.0	Doubtful
-2.2.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 204, +MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362356486903	0	-6.678955564950069	0				100.0	Doubtful
-2.2.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 207, +MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362356486903	0	-9.522902824571501	0				100.0	Doubtful
-2.2.4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 204,  MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362356486903	0	-6.678955564950069	0				100.0	Doubtful
-2.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	VR; VR	LK; LK				2	2	100.0	0	Doubtful
-	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-2.3.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	NH2-SLQAENEQLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 39,  MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942144781802	0	2.063410823544894	0				100.0	Doubtful
-2.3.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	NH2-SLQAENEQLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 39, +MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942144781802	0	2.063410823544894	0				100.0	Doubtful
-2.4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	RR; RR	NL; NL				2	2	100.0	0	Doubtful
-	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-2.4.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	NH2-EFDVEPLKEAYQAEIDEAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 736,  MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583092202605	0	-1.1628605151025897	0				100.0	Doubtful
-2.4.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	NH2-EFDVEPLKEAYQAEIDEAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 736, +MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583092202605	0	-1.1628605151025897	0				100.0	Doubtful
-2.5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	MK; MK	SN; SN				2	2	100.0	0	Doubtful
-	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-2.5.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	NH2-MEIITITNQLQR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 636,  MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864490053003	0	-3.2324313291878943	0				100.0	Doubtful
-2.5.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	NH2-MEIITITNQLQR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 636, +MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864490053003	0	-3.2324313291878943	0				100.0	Doubtful
-2.6	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	AR; AR	QS; QS				2	2	100.0	0	Doubtful
-	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-2.6.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	NH2-YESQLSQIR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 67,  MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669371011802	0	6.998127983906467	0				100.0	Doubtful
-2.6.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	NH2-YESQLSQIR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 67, +MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669371011802	0	6.998127983906467	0				100.0	Doubtful
-2.7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	QK; QK	SV; SV				4	4	100.0	0	Doubtful
-	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-2.7.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 875,  MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354589782603	0	2.711916908512312	0				100.0	Doubtful
-2.7.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 871, +MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354589782603	0	1.7035983401739305	0				100.0	Doubtful
-2.7.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 871,  MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354589782603	0	1.7035983401739305	0				100.0	Doubtful
-2.7.4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 875, +MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354589782603	0	2.711916908512312	0				100.0	Doubtful
-2.8	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	LK; LK	IN; IN				2	2	100.0	0	Doubtful
-	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-2.8.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	NH2-ISITTYEEEIEDLHATAR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 752, +MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167787614505	0	6.6562738302421005	0				100.0	Doubtful
-2.8.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	NH2-ISITTYEEEIEDLHATAR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 752,  MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167787614505	0	6.6562738302421005	0				100.0	Doubtful
-2.9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	RR; RR	AS; AS				2	2	100.0	0	Doubtful
-	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-2.9.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 220,  MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263804604496	0	2.939629370057349	0				100.0	Doubtful
-2.9.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 220, +MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263804604496	0	2.939629370057349	0				100.0	Doubtful
-2.10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NR; NR	SE; SE				4	4	100.0	0	Doubtful
-	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-2.10.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 588,  MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7729071161402	0	3.113546101111509	0				100.0	Doubtful
-2.10.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 588, +MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7729071161402	0	3.113546101111509	0				100.0	Doubtful
-2.10.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 591,  MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7729071161402	0	2.4535863107993414	0				100.0	Doubtful
-2.10.4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 591, +MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7729071161402	0	2.4535863107993414	0				100.0	Doubtful
-2.11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	GR; GR	DM; DM				2	2	100.0	0	Doubtful
-	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-2.11.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	NH2-ASLGMAAGVAGGIATK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 357,  MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336851564503	0	-2.731669916283406	0				100.0	Doubtful
-2.11.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	NH2-ASLGMAAGVAGGIATK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 357, +MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336851564503	0	-2.731669916283406	0				100.0	Doubtful
-2.12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	AR; AR	LI; LI				2	2	100.0	0	Doubtful
-	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-2.12.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	NH2-INEDRIDELQDKVNK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 81, +MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326552146706	0	-1.7720894394949223	0				100.0	Doubtful
-2.12.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	NH2-INEDRIDELQDKVNK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 81,  MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326552146706	0	-1.7720894394949223	0				100.0	Doubtful
-2.13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	AK; AK; AK	NS; NS; NS				2	2	100.0	0	Doubtful
-	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-2.13.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	NH2-KGDIIATVDEWGPVNR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 582,  MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.91079757128	0	1.643983659206309	0				100.0	Doubtful
-2.13.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	NH2-KGDIIATVDEWGPVNR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 582, +MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.91079757128	0	1.643983659206309	0				100.0	Doubtful
-2.14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	SK; SK; SK	SK; SK; SK				2	2	100.0	0	Doubtful
-	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-2.14.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 758, +MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.224205328391	0	2.5264056584343257	0				100.0	Doubtful
-2.14.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 758,  MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.224205328391	0	2.5264056584343257	0				100.0	Doubtful
-2.15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	DR; DR; DR	ID; ID; ID				4	4	100.0	0	Doubtful
-	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-2.15.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 75, +MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928658902905	0	1.481004205034201	0				100.0	Doubtful
-2.15.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 72, +MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928658902905	0	2.0041097707959827	0				100.0	Doubtful
-2.15.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 75,  MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928658902905	0	1.481004205034201	0				100.0	Doubtful
-2.15.4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 72,  MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928658902905	0	2.0041097707959827	0				100.0	Doubtful
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptide_shaker_modifications_result1.output_peptides
--- a/test-data/peptide_shaker_modifications_result1.output_peptides	Thu Feb 20 05:51:38 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-	Protein(s)	Protein Group(s)	#Validated Protein Group(s)	Unique Database	Sequence	Modified Sequence	Position	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#Validated PSMs	#PSMs	Confidence [%]	Validation
-1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	SVISIGEVESEGQYVTLENTSSGR	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH	511; 504; 29	SK; SK; SK	SK; SK; SK				2	2	100.0	Doubtful
-2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	YESQLSQIR	NH2-YESQLSQIR-COOH	323; 323	AR; AR	QS; QS				2	2	100.0	Doubtful
-3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	SHVVGAGLGGGSMGSMNQSMSLHGGR	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH	37; 37	RR; RR	AS; AS				2	2	100.0	Doubtful
-4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	EFDVEPLKEAYQAEIDEAK	NH2-EFDVEPLKEAYQAEIDEAK-COOH	128; 128	RR; RR	NL; NL				2	2	100.0	Doubtful
-5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	ISITTYEEEIEDLHATAR	NH2-ISITTYEEEIEDLHATAR-COOH	161; 161	LK; LK	IN; IN				2	2	100.0	Doubtful
-6	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH	442; 442	NR; NR	SE; SE				4	4	100.0	Doubtful
-7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	ASLGMAAGVAGGIATK	NH2-ASLGMAAGVAGGIATK-COOH	63; 63	GR; GR	DM; DM				2	2	100.0	Doubtful
-8	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	LISATSISPEHK	NH2-LISATSISPEHK-COOH	549; 542; 67	DR; DR; DR	ID; ID; ID				4	4	100.0	Doubtful
-9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH	403; 403	NK; NK	LS; LS				4	4	100.0	Doubtful
-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH	147; 147	AK; AK	IS; IS				4	4	100.0	Doubtful
-11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	SLQAENEQLR	NH2-SLQAENEQLR-COOH	110; 110	VR; VR	LK; LK				2	2	100.0	Doubtful
-12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	KGDIIATVDEWGPVNR	NH2-KGDIIATVDEWGPVNR-COOH	590; 583; 108	AK; AK; AK	NS; NS; NS				2	2	100.0	Doubtful
-13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	MEIITITNQLQR	NH2-MEIITITNQLQR-COOH	373; 373	MK; MK	SN; SN				2	2	100.0	Doubtful
-14	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 (Doubtful)	1	1	EIRDEYDNQLNLLSADLESK	NH2-EIRDEYDNQLNLLSADLESK-COOH	298; 298	MR; MR	YQ; YQ				2	2	100.0	Doubtful
-15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH	254; 254	QK; QK	SV; SV				4	4	100.0	Doubtful
-16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	INEDRIDELQDKVNK	NH2-INEDRIDELQDKVNK-COOH	179; 179	AR; AR	LI; LI				2	2	100.0	Doubtful
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptide_shaker_modifications_result1.output_peptides_nonvalidated
--- a/test-data/peptide_shaker_modifications_result1.output_peptides_nonvalidated	Thu Feb 20 05:51:38 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-	Protein(s)	Protein Group(s)	#Validated Protein Group(s)	Unique Database	Sequence	Modified Sequence	Position	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#Validated PSMs	#PSMs	Confidence [%]	Validation
-1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	SVISIGEVESEGQYVTLENTSSGR	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH	511; 504; 29	SK; SK; SK	SK; SK; SK				2	2	100.0	Doubtful
-2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	YESQLSQIR	NH2-YESQLSQIR-COOH	323; 323	AR; AR	QS; QS				2	2	100.0	Doubtful
-3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	SHVVGAGLGGGSMGSMNQSMSLHGGR	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH	37; 37	RR; RR	AS; AS				2	2	100.0	Doubtful
-4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	EFDVEPLKEAYQAEIDEAK	NH2-EFDVEPLKEAYQAEIDEAK-COOH	128; 128	RR; RR	NL; NL				2	2	100.0	Doubtful
-5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	ISITTYEEEIEDLHATAR	NH2-ISITTYEEEIEDLHATAR-COOH	161; 161	LK; LK	IN; IN				2	2	100.0	Doubtful
-6	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH	442; 442	NR; NR	SE; SE				4	4	100.0	Doubtful
-7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	ASLGMAAGVAGGIATK	NH2-ASLGMAAGVAGGIATK-COOH	63; 63	GR; GR	DM; DM				2	2	100.0	Doubtful
-8	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	LISATSISPEHK	NH2-LISATSISPEHK-COOH	549; 542; 67	DR; DR; DR	ID; ID; ID				4	4	100.0	Doubtful
-9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH	403; 403	NK; NK	LS; LS				4	4	100.0	Doubtful
-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH	147; 147	AK; AK	IS; IS				4	4	100.0	Doubtful
-11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	SLQAENEQLR	NH2-SLQAENEQLR-COOH	110; 110	VR; VR	LK; LK				2	2	100.0	Doubtful
-12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	KGDIIATVDEWGPVNR	NH2-KGDIIATVDEWGPVNR-COOH	590; 583; 108	AK; AK; AK	NS; NS; NS				2	2	100.0	Doubtful
-13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	MEIITITNQLQR	NH2-MEIITITNQLQR-COOH	373; 373	MK; MK	SN; SN				2	2	100.0	Doubtful
-14	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 (Doubtful)	1	1	EIRDEYDNQLNLLSADLESK	NH2-EIRDEYDNQLNLLSADLESK-COOH	298; 298	MR; MR	YQ; YQ				2	2	100.0	Doubtful
-15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH	254; 254	QK; QK	SV; SV				4	4	100.0	Doubtful
-16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	INEDRIDELQDKVNK	NH2-INEDRIDELQDKVNK-COOH	179; 179	AR; AR	LI; LI				2	2	100.0	Doubtful
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptide_shaker_modifications_result1.output_peptides_phosphorylation
--- a/test-data/peptide_shaker_modifications_result1.output_peptides_phosphorylation	Thu Feb 20 05:51:38 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-	Protein(s)	Protein Group(s)	#Validated Protein Group(s)	Unique Database	Sequence	Modified Sequence	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	Confident Phosphosites	#Confident Phosphosites	Ambiguous Phosphosites	#Ambiguous Phosphosites	#Validated PSMs	#PSMs	Confidence [%]	Validation
-1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	SVISIGEVESEGQYVTLENTSSGR	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH	SK; SK; SK	SK; SK; SK								2	2	100.0	Doubtful
-2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	YESQLSQIR	NH2-YESQLSQIR-COOH	AR; AR	QS; QS								2	2	100.0	Doubtful
-3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	SHVVGAGLGGGSMGSMNQSMSLHGGR	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH	RR; RR	AS; AS								2	2	100.0	Doubtful
-4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	EFDVEPLKEAYQAEIDEAK	NH2-EFDVEPLKEAYQAEIDEAK-COOH	RR; RR	NL; NL								2	2	100.0	Doubtful
-5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	ISITTYEEEIEDLHATAR	NH2-ISITTYEEEIEDLHATAR-COOH	LK; LK	IN; IN								2	2	100.0	Doubtful
-6	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH	NR; NR	SE; SE								4	4	100.0	Doubtful
-7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	ASLGMAAGVAGGIATK	NH2-ASLGMAAGVAGGIATK-COOH	GR; GR	DM; DM								2	2	100.0	Doubtful
-8	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	LISATSISPEHK	NH2-LISATSISPEHK-COOH	DR; DR; DR	ID; ID; ID								4	4	100.0	Doubtful
-9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH	NK; NK	LS; LS								4	4	100.0	Doubtful
-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH	AK; AK	IS; IS								4	4	100.0	Doubtful
-11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	SLQAENEQLR	NH2-SLQAENEQLR-COOH	VR; VR	LK; LK								2	2	100.0	Doubtful
-12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	KGDIIATVDEWGPVNR	NH2-KGDIIATVDEWGPVNR-COOH	AK; AK; AK	NS; NS; NS								2	2	100.0	Doubtful
-13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	MEIITITNQLQR	NH2-MEIITITNQLQR-COOH	MK; MK	SN; SN								2	2	100.0	Doubtful
-14	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 (Doubtful)	1	1	EIRDEYDNQLNLLSADLESK	NH2-EIRDEYDNQLNLLSADLESK-COOH	MR; MR	YQ; YQ								2	2	100.0	Doubtful
-15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH	QK; QK	SV; SV								4	4	100.0	Doubtful
-16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 (Doubtful)	1	1	INEDRIDELQDKVNK	NH2-INEDRIDELQDKVNK-COOH	AR; AR	LI; LI								2	2	100.0	Doubtful
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptide_shaker_modifications_result1.output_proteins
--- a/test-data/peptide_shaker_modifications_result1.output_proteins	Thu Feb 20 05:51:38 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-	Main Accession	Description	Gene Name	Chromosome	MW [kDa]	Possible Coverage [%]	Coverage [%]	Spectrum Counting	Confidently Localized Modification Sites	# Confidently Localized Modification Sites	Ambiguously Localized Modification Sites	#Ambiguously Localized Modification Sites	Protein Inference	Secondary Accessions	Protein Group	#Validated Peptides	#Peptides	#Unique	#Validated Unique	#Unique to Group	#Validated Unique to Group	#Validated PSMs	#PSMs	Confidence [%]	Validation
-1	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91				69.96963713242043	100.0	3.25	4451.587393160344					Related Proteins	cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	1	1	1	1	1	1	2	2	100.0	Doubtful
-2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67				69.88215380565927	92.52	37.58	24162.449974467898					Related Proteins	cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	15	15	15	15	15	15	40	40	100.0	Doubtful
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptide_shaker_modifications_result1.output_proteins_nonvalidated
--- a/test-data/peptide_shaker_modifications_result1.output_proteins_nonvalidated	Thu Feb 20 05:51:38 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-	Main Accession	Description	Gene Name	Chromosome	MW [kDa]	Possible Coverage [%]	Coverage [%]	Spectrum Counting	Confidently Localized Modification Sites	# Confidently Localized Modification Sites	Ambiguously Localized Modification Sites	#Ambiguously Localized Modification Sites	Protein Inference	Secondary Accessions	Protein Group	#Validated Peptides	#Peptides	#Unique	#Validated Unique	#Unique to Group	#Validated Unique to Group	#Validated PSMs	#PSMs	Confidence [%]	Validation
-1	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91				69.96963713242043	100.0	3.25	4451.587393160344					Related Proteins	cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	1	1	1	1	1	1	2	2	100.0	Doubtful
-2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67				69.88215380565927	92.52	37.58	24162.449974467898					Related Proteins	cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	15	15	15	15	15	15	40	40	100.0	Doubtful
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptide_shaker_modifications_result1.output_proteins_phosphorylation
--- a/test-data/peptide_shaker_modifications_result1.output_proteins_phosphorylation	Thu Feb 20 05:51:38 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-	Main Accession	Description	Gene Name	Chromosome	MW [kDa]	Possible Coverage [%]	Coverage [%]	Spectrum Counting NSAF	Confident Phosphosites	#Confident Phosphosites	Ambiguous Phosphosites	#Ambiguous Phosphosites	Protein Inference	Secondary Accessions	Protein Group	#Validated Peptides	#Peptides	#Unique	#Validated Unique	#Unique to Group	#Validated Unique to Group	#Validated PSMs	#PSMs	Confidence [%]	Validation
-1	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91				69.96963713242043	100.0	3.25	0.0032520325203252032		0		0	Related Proteins	cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	1	1	1	1	1	1	2	2	100.0	Doubtful
-2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67				69.88215380565927	92.52	37.58	0.017651472642866785		0		0	Related Proteins	cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	15	15	15	15	15	15	40	40	100.0	Doubtful
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptide_shaker_modifications_result1.output_psm
--- a/test-data/peptide_shaker_modifications_result1.output_psm	Thu Feb 20 05:51:38 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-	Protein(s)	Sequence	AAs Before	AAs After	Position	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NK; NK	LS; LS	403; 403	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 1198, +MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560840995904	0	5.225020941769318				100.0	Doubtful
-2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	AK; AK	IS; IS	147; 147	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 207,  MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362356486903	0	-9.522902824571501				100.0	Doubtful
-3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	VR; VR	LK; LK	110; 110	NH2-SLQAENEQLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 39,  MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942144781802	0	2.063410823544894				100.0	Doubtful
-4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	RR; RR	NL; NL	128; 128	NH2-EFDVEPLKEAYQAEIDEAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 736,  MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583092202605	0	-1.1628605151025897				100.0	Doubtful
-5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	MK; MK	SN; SN	373; 373	NH2-MEIITITNQLQR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 636, +MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864490053003	0	-3.2324313291878943				100.0	Doubtful
-6	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	MR; MR	YQ; YQ	298; 298	NH2-EIRDEYDNQLNLLSADLESK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 748,  MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.14449845571	0	6.2066377342036665				100.0	Doubtful
-7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	AR; AR	QS; QS	323; 323	NH2-YESQLSQIR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 67, +MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669371011802	0	6.998127983906467				100.0	Doubtful
-8	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	MR; MR	YQ; YQ	298; 298	NH2-EIRDEYDNQLNLLSADLESK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 748, +MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.14449845571	0	6.2066377342036665				100.0	Doubtful
-9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	QK; QK	SV; SV	254; 254	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 875,  MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354589782603	0	2.711916908512312				100.0	Doubtful
-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	QK; QK	SV; SV	254; 254	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 871,  MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354589782603	0	1.7035983401739305				100.0	Doubtful
-11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	AK; AK; AK	NS; NS; NS	590; 583; 108	NH2-KGDIIATVDEWGPVNR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 582,  MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.91079757128	0	1.643983659206309				100.0	Doubtful
-12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	SK; SK; SK	SK; SK; SK	511; 504; 29	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 758,  MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.224205328391	0	2.5264056584343257				100.0	Doubtful
-13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	LK; LK	IN; IN	161; 161	NH2-ISITTYEEEIEDLHATAR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 752, +MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167787614505	0	6.6562738302421005				100.0	Doubtful
-14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	RR; RR	AS; AS	37; 37	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 220,  MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263804604496	0	2.939629370057349				100.0	Doubtful
-15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	QK; QK	SV; SV	254; 254	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 871, +MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354589782603	0	1.7035983401739305				100.0	Doubtful
-16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NR; NR	SE; SE	442; 442	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 591,  MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7729071161402	0	2.4535863107993414				100.0	Doubtful
-17	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	AK; AK	IS; IS	147; 147	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 207, +MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362356486903	0	-9.522902824571501				100.0	Doubtful
-18	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	QK; QK	SV; SV	254; 254	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 875, +MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354589782603	0	2.711916908512312				100.0	Doubtful
-19	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	GR; GR	DM; DM	63; 63	NH2-ASLGMAAGVAGGIATK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 357,  MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336851564503	0	-2.731669916283406				100.0	Doubtful
-20	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NK; NK	LS; LS	403; 403	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 1197,  MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560840995904	0	5.228649666852938				100.0	Doubtful
-21	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	AK; AK; AK	NS; NS; NS	590; 583; 108	NH2-KGDIIATVDEWGPVNR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 582, +MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.91079757128	0	1.643983659206309				100.0	Doubtful
-22	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	AK; AK	IS; IS	147; 147	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 204, +MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362356486903	0	-6.678955564950069				100.0	Doubtful
-23	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NR; NR	SE; SE	442; 442	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 591, +MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7729071161402	0	2.4535863107993414				100.0	Doubtful
-24	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	AK; AK	IS; IS	147; 147	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 204,  MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362356486903	0	-6.678955564950069				100.0	Doubtful
-25	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NK; NK	LS; LS	403; 403	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 1198,  MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560840995904	0	5.225020941769318				100.0	Doubtful
-26	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	DR; DR; DR	ID; ID; ID	549; 542; 67	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 72,  MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928658902905	0	2.0041097707959827				100.0	Doubtful
-27	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	GR; GR	DM; DM	63; 63	NH2-ASLGMAAGVAGGIATK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 357, +MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336851564503	0	-2.731669916283406				100.0	Doubtful
-28	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	LK; LK	IN; IN	161; 161	NH2-ISITTYEEEIEDLHATAR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 752,  MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167787614505	0	6.6562738302421005				100.0	Doubtful
-29	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	DR; DR; DR	ID; ID; ID	549; 542; 67	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 75,  MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928658902905	0	1.481004205034201				100.0	Doubtful
-30	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	SK; SK; SK	SK; SK; SK	511; 504; 29	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 758, +MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.224205328391	0	2.5264056584343257				100.0	Doubtful
-31	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NK; NK	LS; LS	403; 403	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 1197, +MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560840995904	0	5.228649666852938				100.0	Doubtful
-32	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	DR; DR; DR	ID; ID; ID	549; 542; 67	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 72, +MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928658902905	0	2.0041097707959827				100.0	Doubtful
-33	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	RR; RR	AS; AS	37; 37	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 220, +MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263804604496	0	2.939629370057349				100.0	Doubtful
-34	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	DR; DR; DR	ID; ID; ID	549; 542; 67	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 75, +MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928658902905	0	1.481004205034201				100.0	Doubtful
-35	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	AR; AR	QS; QS	323; 323	NH2-YESQLSQIR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 67,  MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669371011802	0	6.998127983906467				100.0	Doubtful
-36	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	MK; MK	SN; SN	373; 373	NH2-MEIITITNQLQR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 636,  MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864490053003	0	-3.2324313291878943				100.0	Doubtful
-37	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	AR; AR	LI; LI	179; 179	NH2-INEDRIDELQDKVNK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 81, +MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326552146706	0	-1.7720894394949223				100.0	Doubtful
-38	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	RR; RR	NL; NL	128; 128	NH2-EFDVEPLKEAYQAEIDEAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 736, +MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583092202605	0	-1.1628605151025897				100.0	Doubtful
-39	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	VR; VR	LK; LK	110; 110	NH2-SLQAENEQLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 39, +MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942144781802	0	2.063410823544894				100.0	Doubtful
-40	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	AR; AR	LI; LI	179; 179	NH2-INEDRIDELQDKVNK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 81,  MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326552146706	0	-1.7720894394949223				100.0	Doubtful
-41	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NR; NR	SE; SE	442; 442	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 588,  MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7729071161402	0	3.113546101111509				100.0	Doubtful
-42	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NR; NR	SE; SE	442; 442	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 588, +MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7729071161402	0	3.113546101111509				100.0	Doubtful
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptide_shaker_modifications_result1.output_psm_nonvalidated
--- a/test-data/peptide_shaker_modifications_result1.output_psm_nonvalidated	Thu Feb 20 05:51:38 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-	Protein(s)	Sequence	AAs Before	AAs After	Position	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
-1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NK; NK	LS; LS	403; 403	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 1198, +MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560840995904	0	5.225020941769318				100.0	Doubtful
-2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	AK; AK	IS; IS	147; 147	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 207,  MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362356486903	0	-9.522902824571501				100.0	Doubtful
-3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	VR; VR	LK; LK	110; 110	NH2-SLQAENEQLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 39,  MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942144781802	0	2.063410823544894				100.0	Doubtful
-4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	RR; RR	NL; NL	128; 128	NH2-EFDVEPLKEAYQAEIDEAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 736,  MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583092202605	0	-1.1628605151025897				100.0	Doubtful
-5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	MK; MK	SN; SN	373; 373	NH2-MEIITITNQLQR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 636, +MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864490053003	0	-3.2324313291878943				100.0	Doubtful
-6	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	MR; MR	YQ; YQ	298; 298	NH2-EIRDEYDNQLNLLSADLESK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 748,  MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.14449845571	0	6.2066377342036665				100.0	Doubtful
-7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	AR; AR	QS; QS	323; 323	NH2-YESQLSQIR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 67, +MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669371011802	0	6.998127983906467				100.0	Doubtful
-8	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	MR; MR	YQ; YQ	298; 298	NH2-EIRDEYDNQLNLLSADLESK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 748, +MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.14449845571	0	6.2066377342036665				100.0	Doubtful
-9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	QK; QK	SV; SV	254; 254	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 875,  MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354589782603	0	2.711916908512312				100.0	Doubtful
-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	QK; QK	SV; SV	254; 254	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 871,  MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354589782603	0	1.7035983401739305				100.0	Doubtful
-11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	AK; AK; AK	NS; NS; NS	590; 583; 108	NH2-KGDIIATVDEWGPVNR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 582,  MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.91079757128	0	1.643983659206309				100.0	Doubtful
-12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	SK; SK; SK	SK; SK; SK	511; 504; 29	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 758,  MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.224205328391	0	2.5264056584343257				100.0	Doubtful
-13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	LK; LK	IN; IN	161; 161	NH2-ISITTYEEEIEDLHATAR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 752, +MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167787614505	0	6.6562738302421005				100.0	Doubtful
-14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	RR; RR	AS; AS	37; 37	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 220,  MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263804604496	0	2.939629370057349				100.0	Doubtful
-15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	QK; QK	SV; SV	254; 254	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 871, +MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354589782603	0	1.7035983401739305				100.0	Doubtful
-16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NR; NR	SE; SE	442; 442	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 591,  MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7729071161402	0	2.4535863107993414				100.0	Doubtful
-17	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	AK; AK	IS; IS	147; 147	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 207, +MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362356486903	0	-9.522902824571501				100.0	Doubtful
-18	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	QK; QK	SV; SV	254; 254	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 875, +MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354589782603	0	2.711916908512312				100.0	Doubtful
-19	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	GR; GR	DM; DM	63; 63	NH2-ASLGMAAGVAGGIATK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 357,  MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336851564503	0	-2.731669916283406				100.0	Doubtful
-20	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NK; NK	LS; LS	403; 403	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 1197,  MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560840995904	0	5.228649666852938				100.0	Doubtful
-21	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	AK; AK; AK	NS; NS; NS	590; 583; 108	NH2-KGDIIATVDEWGPVNR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 582, +MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.91079757128	0	1.643983659206309				100.0	Doubtful
-22	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	AK; AK	IS; IS	147; 147	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 204, +MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362356486903	0	-6.678955564950069				100.0	Doubtful
-23	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NR; NR	SE; SE	442; 442	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 591, +MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7729071161402	0	2.4535863107993414				100.0	Doubtful
-24	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	AK; AK	IS; IS	147; 147	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 204,  MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362356486903	0	-6.678955564950069				100.0	Doubtful
-25	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NK; NK	LS; LS	403; 403	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 1198,  MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560840995904	0	5.225020941769318				100.0	Doubtful
-26	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	DR; DR; DR	ID; ID; ID	549; 542; 67	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 72,  MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928658902905	0	2.0041097707959827				100.0	Doubtful
-27	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	GR; GR	DM; DM	63; 63	NH2-ASLGMAAGVAGGIATK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 357, +MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336851564503	0	-2.731669916283406				100.0	Doubtful
-28	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	LK; LK	IN; IN	161; 161	NH2-ISITTYEEEIEDLHATAR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 752,  MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167787614505	0	6.6562738302421005				100.0	Doubtful
-29	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	DR; DR; DR	ID; ID; ID	549; 542; 67	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 75,  MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928658902905	0	1.481004205034201				100.0	Doubtful
-30	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	SK; SK; SK	SK; SK; SK	511; 504; 29	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 758, +MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.224205328391	0	2.5264056584343257				100.0	Doubtful
-31	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NK; NK	LS; LS	403; 403	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 1197, +MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560840995904	0	5.228649666852938				100.0	Doubtful
-32	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	DR; DR; DR	ID; ID; ID	549; 542; 67	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 72, +MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928658902905	0	2.0041097707959827				100.0	Doubtful
-33	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	RR; RR	AS; AS	37; 37	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 220, +MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263804604496	0	2.939629370057349				100.0	Doubtful
-34	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	DR; DR; DR	ID; ID; ID	549; 542; 67	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 75, +MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928658902905	0	1.481004205034201				100.0	Doubtful
-35	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	AR; AR	QS; QS	323; 323	NH2-YESQLSQIR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 67,  MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669371011802	0	6.998127983906467				100.0	Doubtful
-36	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	MK; MK	SN; SN	373; 373	NH2-MEIITITNQLQR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 636,  MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864490053003	0	-3.2324313291878943				100.0	Doubtful
-37	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	AR; AR	LI; LI	179; 179	NH2-INEDRIDELQDKVNK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 81, +MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326552146706	0	-1.7720894394949223				100.0	Doubtful
-38	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	RR; RR	NL; NL	128; 128	NH2-EFDVEPLKEAYQAEIDEAK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 736, +MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583092202605	0	-1.1628605151025897				100.0	Doubtful
-39	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	VR; VR	LK; LK	110; 110	NH2-SLQAENEQLR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 39, +MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942144781802	0	2.063410823544894				100.0	Doubtful
-40	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	AR; AR	LI; LI	179; 179	NH2-INEDRIDELQDKVNK-COOH			searchgui_tinyspectra1.mgf	 Cmpd 81,  MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326552146706	0	-1.7720894394949223				100.0	Doubtful
-41	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NR; NR	SE; SE	442; 442	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 588,  MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7729071161402	0	3.113546101111509				100.0	Doubtful
-42	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NR; NR	SE; SE	442; 442	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	 Cmpd 588, +MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7729071161402	0	3.113546101111509				100.0	Doubtful
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptide_shaker_modifications_result1.output_psm_phosphorylation
--- a/test-data/peptide_shaker_modifications_result1.output_psm_phosphorylation	Thu Feb 20 05:51:38 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-	Protein(s)	Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Localization Confidence	Probabilistic PTM score	D-score	Confident Phosphosites	#Confident Phosphosites	Ambiguous Phosphosites	#Ambiguous Phosphosites	Confidence [%]	Validation
-1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			searchgui_tinyspectra1.mgf	 Cmpd 1198, +MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560840995904	0	5.225020941769318								100.0	Doubtful
-2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			searchgui_tinyspectra1.mgf	 Cmpd 207,  MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362356486903	0	-9.522902824571501								100.0	Doubtful
-3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR			searchgui_tinyspectra1.mgf	 Cmpd 39,  MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942144781802	0	2.063410823544894								100.0	Doubtful
-4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK			searchgui_tinyspectra1.mgf	 Cmpd 736,  MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583092202605	0	-1.1628605151025897								100.0	Doubtful
-5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR			searchgui_tinyspectra1.mgf	 Cmpd 636, +MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864490053003	0	-3.2324313291878943								100.0	Doubtful
-6	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK			searchgui_tinyspectra1.mgf	 Cmpd 748,  MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.14449845571	0	6.2066377342036665								100.0	Doubtful
-7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR			searchgui_tinyspectra1.mgf	 Cmpd 67, +MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669371011802	0	6.998127983906467								100.0	Doubtful
-8	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK			searchgui_tinyspectra1.mgf	 Cmpd 748, +MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.14449845571	0	6.2066377342036665								100.0	Doubtful
-9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			searchgui_tinyspectra1.mgf	 Cmpd 875,  MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354589782603	0	2.711916908512312								100.0	Doubtful
-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			searchgui_tinyspectra1.mgf	 Cmpd 871,  MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354589782603	0	1.7035983401739305								100.0	Doubtful
-11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR			searchgui_tinyspectra1.mgf	 Cmpd 582,  MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.91079757128	0	1.643983659206309								100.0	Doubtful
-12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR			searchgui_tinyspectra1.mgf	 Cmpd 758,  MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.224205328391	0	2.5264056584343257								100.0	Doubtful
-13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR			searchgui_tinyspectra1.mgf	 Cmpd 752, +MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167787614505	0	6.6562738302421005								100.0	Doubtful
-14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR			searchgui_tinyspectra1.mgf	 Cmpd 220,  MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263804604496	0	2.939629370057349								100.0	Doubtful
-15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			searchgui_tinyspectra1.mgf	 Cmpd 871, +MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354589782603	0	1.7035983401739305								100.0	Doubtful
-16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			searchgui_tinyspectra1.mgf	 Cmpd 591,  MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7729071161402	0	2.4535863107993414								100.0	Doubtful
-17	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			searchgui_tinyspectra1.mgf	 Cmpd 207, +MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362356486903	0	-9.522902824571501								100.0	Doubtful
-18	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			searchgui_tinyspectra1.mgf	 Cmpd 875, +MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354589782603	0	2.711916908512312								100.0	Doubtful
-19	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK			searchgui_tinyspectra1.mgf	 Cmpd 357,  MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336851564503	0	-2.731669916283406								100.0	Doubtful
-20	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			searchgui_tinyspectra1.mgf	 Cmpd 1197,  MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560840995904	0	5.228649666852938								100.0	Doubtful
-21	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR			searchgui_tinyspectra1.mgf	 Cmpd 582, +MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.91079757128	0	1.643983659206309								100.0	Doubtful
-22	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			searchgui_tinyspectra1.mgf	 Cmpd 204, +MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362356486903	0	-6.678955564950069								100.0	Doubtful
-23	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			searchgui_tinyspectra1.mgf	 Cmpd 591, +MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7729071161402	0	2.4535863107993414								100.0	Doubtful
-24	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			searchgui_tinyspectra1.mgf	 Cmpd 204,  MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362356486903	0	-6.678955564950069								100.0	Doubtful
-25	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			searchgui_tinyspectra1.mgf	 Cmpd 1198,  MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560840995904	0	5.225020941769318								100.0	Doubtful
-26	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			searchgui_tinyspectra1.mgf	 Cmpd 72,  MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928658902905	0	2.0041097707959827								100.0	Doubtful
-27	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK			searchgui_tinyspectra1.mgf	 Cmpd 357, +MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336851564503	0	-2.731669916283406								100.0	Doubtful
-28	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR			searchgui_tinyspectra1.mgf	 Cmpd 752,  MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167787614505	0	6.6562738302421005								100.0	Doubtful
-29	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			searchgui_tinyspectra1.mgf	 Cmpd 75,  MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928658902905	0	1.481004205034201								100.0	Doubtful
-30	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR			searchgui_tinyspectra1.mgf	 Cmpd 758, +MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.224205328391	0	2.5264056584343257								100.0	Doubtful
-31	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			searchgui_tinyspectra1.mgf	 Cmpd 1197, +MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560840995904	0	5.228649666852938								100.0	Doubtful
-32	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			searchgui_tinyspectra1.mgf	 Cmpd 72, +MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928658902905	0	2.0041097707959827								100.0	Doubtful
-33	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR			searchgui_tinyspectra1.mgf	 Cmpd 220, +MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263804604496	0	2.939629370057349								100.0	Doubtful
-34	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			searchgui_tinyspectra1.mgf	 Cmpd 75, +MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928658902905	0	1.481004205034201								100.0	Doubtful
-35	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR			searchgui_tinyspectra1.mgf	 Cmpd 67,  MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669371011802	0	6.998127983906467								100.0	Doubtful
-36	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR			searchgui_tinyspectra1.mgf	 Cmpd 636,  MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864490053003	0	-3.2324313291878943								100.0	Doubtful
-37	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK			searchgui_tinyspectra1.mgf	 Cmpd 81, +MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326552146706	0	-1.7720894394949223								100.0	Doubtful
-38	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK			searchgui_tinyspectra1.mgf	 Cmpd 736, +MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583092202605	0	-1.1628605151025897								100.0	Doubtful
-39	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR			searchgui_tinyspectra1.mgf	 Cmpd 39, +MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942144781802	0	2.063410823544894								100.0	Doubtful
-40	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK			searchgui_tinyspectra1.mgf	 Cmpd 81,  MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326552146706	0	-1.7720894394949223								100.0	Doubtful
-41	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			searchgui_tinyspectra1.mgf	 Cmpd 588,  MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7729071161402	0	3.113546101111509								100.0	Doubtful
-42	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			searchgui_tinyspectra1.mgf	 Cmpd 588, +MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7729071161402	0	3.113546101111509								100.0	Doubtful
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptide_shaker_modifications_result1.zip
Binary file test-data/peptide_shaker_modifications_result1.zip has changed
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptideshaker_reports_output_certificate.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptideshaker_reports_output_certificate.txt	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,79 @@
+
+Project Details
+
+1: PeptideShaker Version: 2.0.2
+2: Date: Thu Nov 19 10:47:40 CET 2020
+3: Experiment: Galaxy_Experiment_2020111910471605779259
+4: Sample: Not implemented
+5: Replicate Number: Not implemented
+6: Identification Algorithms: OMSSA, X!Tandem and MS-GF+
+
+Database Search Parameters
+
+1: Precursor Tolerance Unit: ppm
+2: Precursor Ion m/z Tolerance: 10.0
+3: Fragment Ion Tolerance Unit: Da
+4: Fragment Ion m/z Tolerance: 0.5
+5: Cleavage: Enzyme
+6: Enzyme: Trypsin
+7: Missed Cleavages: 2
+8: Specificity: Specific
+9: Database: input_fasta_file.fasta
+10: Forward Ion: 1
+11: Rewind Ion: 4
+12: Fixed Modifications: 
+13: Variable Modifications: 
+14: Refinement Variable Modifications: 
+15: Refinement Fixed Modifications: 
+
+Input Filters
+
+1: Minimal Peptide Length: 8
+2: Maximal Peptide Length: 30
+3: Precursor m/z Tolerance: 10.0
+4: Precursor m/z Tolerance Unit: Yes
+5: Unrecognized Modifications Discarded: Yes
+
+Validation Summary
+
+1: Proteins: #Validated: 4.0
+2: Proteins: Total Possible TP: 4.0
+3: Proteins: FDR Limit [%]: 0.0
+4: Proteins: FNR Limit [%]: 0.0
+5: Proteins: Confidence Limit [%]: 100.0
+6: Proteins: PEP Limit [%]: 100.0
+7: Proteins: Confidence Accuracy [%]: 9.223372036854776E16
+8: Peptides: #Validated: 4.0
+9: Peptides: Total Possible TP: 4.0
+10: Peptides: FDR Limit [%]: 0.0
+11: Peptides: FNR Limit [%]: 0.0
+12: Peptides: Confidence Limit [%]: 100.0
+13: Peptides: PEP Limit [%]: 0.0
+14: Peptides: Confidence Accuracy [%]: 9.223372036854776E16
+15: PSMs: #Validated PSM: 6.0
+16: PSMs: Total Possible TP: 6.0
+17: PSMs: FDR Limit [%]: 0.0
+18: PSMs: 0.0
+19: PSMs: Confidence Limit [%]: 100.0
+20: PSMs: PEP Limit [%]: 0.0
+21: PSMs: Confidence Accuracy [%]: 9.223372036854776E16
+
+PTM Scoring Settings
+
+1: Probabilistic Score: PhosphoRS
+2: Accounting for Neutral Losses: No
+3: Threshold: 95.0
+
+Spectrum Counting Parameters
+
+1: Method: NSAF
+2: Validated Matches Only: Doubtful
+
+Annotation Settings
+
+1: Intensity Limit: 0.75
+2: Automatic Annotation: Yes
+3: Selected Ions: b, y
+4: Neutral Losses: H2O, NH3
+5: Neutral Losses Sequence Dependence: Yes
+6: Fragment Ion m/z Tolerance: 10.0
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptideshaker_reports_output_extendedpsm.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptideshaker_reports_output_extendedpsm.tabular	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,5 @@
+	Protein(s)	Sequence	AAs Before	AAs After	Position	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Validation
+1	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	LDRLISATSISPEHKIDFLFK	WK;WK;WK	DP;DP;DP	545;538;63	NH2-LDRLISATSISPEHKIDFLFK-COOH			searchgui_smallspectra	small.3.3. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=3"	0.6731	810.789428710938	2+, 3+, 4+	3	2429.33184573292	0	6.00693871414815	0				Confident
+2	cds.comp8310_c0_seq2	NLVAEESMNMLKNK	NR	FK	263	NH2-NLVAEESMNMLKNK-COOH			searchgui_smallspectra	small.17.17. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=17"	8.9853	811.408081054688	2+, 3+, 4+	2	1619.80111309327	1	-1.7626881884550694	0				Confident
+3	cds.comp41890_c0_seq1	PGGFAKVWANGMGDPNSGDLVWHNKSR	LK	LG	77	NH2-PGGFAKVWANGMGDPNSGDLVWHNKSR-COOH			searchgui_smallspectra	small.28.28. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=28"	16.3598	725.3583984375	2+, 3+, 4+	4	2896.38272917215	1	6.345261931182815	0				Confident
+4	cds.comp41890_c0_seq1_REVERSED	RYTSHEQLEGK	NK	VL	114	NH2-RYTSHEQLEGK-COOH			searchgui_smallspectra	small.46.46. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=46"	27.6339	674.841369628906	2+, 3+, 4+	2	1346.6578773639	1	5.1562724435666505	0				Confident
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptideshaker_reports_output_hierarchical.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptideshaker_reports_output_hierarchical.tabular	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,21 @@
+	Protein Inference	Main Accession	Description	Protein Group	Secondary Accessions	Validated Coverage [%]	Possible Coverage [%]	#Peptides	#Validated Peptides	#Unique Peptides	#PSMs	#Validated PSMs	Confidently Localized Modification Sites	#Confidently Localized Modification Sites	Ambiguously Localized Modification Sites	#Ambiguously Localized Modification Sites	Spectrum Counting NSAF	MW [kDa]	Confidence [%]	Validation	Decoy
+1	Single Protein	cds.comp8310_c0_seq2	m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16	cds.comp8310_c0_seq2		3.69	81.0	1	1	1	1	1					0.003257328990228013	45.26545451338222	100.0	Doubtful	0
+	Protein(s)	Sequence	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#PSMs	#Validated PSMs	Confidence [%]	Decoy	Validation
+1.1	cds.comp8310_c0_seq2	NLVAEESMNMLKNK	NR	FK				1	1	100.0	0	Confident
+	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
+1.1.1	cds.comp8310_c0_seq2	NLVAEESMNMLKNK	NH2-NLVAEESMNMLKNK-COOH			searchgui_smallspectra	small.17.17. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=17"	8.9853	811.408081054688	2+, 3+, 4+	2	1619.80111309327	1	-1.7626881884550694	0				100.0	Confident
+2	Single Protein	cds.comp41890_c0_seq1	m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20	cds.comp41890_c0_seq1		20.15	91.04	1	1	1	1	1					0.00819672131147541	14.802380493830709	100.0	Doubtful	0
+	Protein(s)	Sequence	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#PSMs	#Validated PSMs	Confidence [%]	Decoy	Validation
+2.1	cds.comp41890_c0_seq1	PGGFAKVWANGMGDPNSGDLVWHNKSR	LK	LG				1	1	100.0	0	Confident
+	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
+2.1.1	cds.comp41890_c0_seq1	PGGFAKVWANGMGDPNSGDLVWHNKSR	NH2-PGGFAKVWANGMGDPNSGDLVWHNKSR-COOH			searchgui_smallspectra	small.28.28. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=28"	16.3598	725.3583984375	2+, 3+, 4+	4	2896.38272917215	1	6.345261931182815	0				100.0	Confident
+3	Related Proteins	cds.comp41779_c0_seq1	m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	3.34	78.82	1	1	1	1	1					0.00202020202020202	69.88215380565931	100.0	Doubtful	0
+	Protein(s)	Sequence	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#PSMs	#Validated PSMs	Confidence [%]	Decoy	Validation
+3.1	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	LDRLISATSISPEHKIDFLFK	WK;WK;WK	DP;DP;DP				1	1	100.0	0	Confident
+	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
+3.1.1	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	LDRLISATSISPEHKIDFLFK	NH2-LDRLISATSISPEHKIDFLFK-COOH			searchgui_smallspectra	small.3.3. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=3"	0.6731	810.789428710938	2+, 3+, 4+	3	2429.33184573292	0	6.00693871414815	0				100.0	Confident
+4	Single Protein	cds.comp41890_c0_seq1_REVERSED	m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20-REVERSED	cds.comp41890_c0_seq1_REVERSED		8.21	90.3	1	1	1	1	1					0.008264462809917356	14.802380493830709	100.0	Doubtful	0
+	Protein(s)	Sequence	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#PSMs	#Validated PSMs	Confidence [%]	Decoy	Validation
+4.1	cds.comp41890_c0_seq1_REVERSED	RYTSHEQLEGK	NK	VL				1	1	100.0	0	Confident
+	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
+4.1.1	cds.comp41890_c0_seq1_REVERSED	RYTSHEQLEGK	NH2-RYTSHEQLEGK-COOH			searchgui_smallspectra	small.46.46. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=46"	27.6339	674.841369628906	2+, 3+, 4+	2	1346.6578773639	1	5.1562724435666505	0				100.0	Confident
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptideshaker_reports_output_peptides.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptideshaker_reports_output_peptides.tabular	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,5 @@
+	Protein(s)	Protein Group(s)	#Validated Protein Group(s)	Unique Protein Group	Sequence	Modified Sequence	Position	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#PSMs	#Validated PSMs	Confidence [%]	Validation
+1	cds.comp41890_c0_seq1	cds.comp41890_c0_seq1 (Doubtful)	1	1	PGGFAKVWANGMGDPNSGDLVWHNKSR	NH2-PGGFAKVWANGMGDPNSGDLVWHNKSR-COOH	cds.comp41890_c0_seq1 (78)	LK	LG				1	1	100.0	Confident
+2	cds.comp8310_c0_seq2	cds.comp8310_c0_seq2 (Doubtful)	1	1	NLVAEESMNMLKNK	NH2-NLVAEESMNMLKNK-COOH	cds.comp8310_c0_seq2 (264)	NR	FK				1	1	100.0	Confident
+3	cds.comp41890_c0_seq1_REVERSED	cds.comp41890_c0_seq1_REVERSED (Doubtful)	1	1	RYTSHEQLEGK	NH2-RYTSHEQLEGK-COOH	cds.comp41890_c0_seq1_REVERSED (115)	NK	VL				1	1	100.0	Confident
+4	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3 (Doubtful)	1	1	LDRLISATSISPEHKIDFLFK	NH2-LDRLISATSISPEHKIDFLFK-COOH	cds.comp41779_c0_seq1 (546);cds.comp41779_c0_seq2 (539);cds.comp41779_c0_seq3 (64)	WK;WK;WK	DP;DP;DP				1	1	100.0	Confident
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptideshaker_reports_output_peptidesnonvalidated.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptideshaker_reports_output_peptidesnonvalidated.tabular	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,5 @@
+	Protein(s)	Protein Group(s)	#Validated Protein Group(s)	Unique Protein Group	Sequence	Modified Sequence	Position	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#PSMs	#Validated PSMs	Confidence [%]	Validation
+1	cds.comp41890_c0_seq1	cds.comp41890_c0_seq1 (Doubtful)	1	1	PGGFAKVWANGMGDPNSGDLVWHNKSR	NH2-PGGFAKVWANGMGDPNSGDLVWHNKSR-COOH	cds.comp41890_c0_seq1 (78)	LK	LG				1	1	100.0	Confident
+2	cds.comp8310_c0_seq2	cds.comp8310_c0_seq2 (Doubtful)	1	1	NLVAEESMNMLKNK	NH2-NLVAEESMNMLKNK-COOH	cds.comp8310_c0_seq2 (264)	NR	FK				1	1	100.0	Confident
+3	cds.comp41890_c0_seq1_REVERSED	cds.comp41890_c0_seq1_REVERSED (Doubtful)	1	1	RYTSHEQLEGK	NH2-RYTSHEQLEGK-COOH	cds.comp41890_c0_seq1_REVERSED (115)	NK	VL				1	1	100.0	Confident
+4	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3 (Doubtful)	1	1	LDRLISATSISPEHKIDFLFK	NH2-LDRLISATSISPEHKIDFLFK-COOH	cds.comp41779_c0_seq1 (546);cds.comp41779_c0_seq2 (539);cds.comp41779_c0_seq3 (64)	WK;WK;WK	DP;DP;DP				1	1	100.0	Confident
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptideshaker_reports_output_peptidesphosphorylation.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptideshaker_reports_output_peptidesphosphorylation.tabular	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,5 @@
+	Protein(s)	Protein Group(s)	#Validated Protein Group(s)	Unique Protein Group	Sequence	Modified Sequence	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	Confident Phosphosites	#Confident Phosphosites	Ambiguous Phosphosites	#Ambiguous Phosphosites	#PSMs	#Validated PSMs	Confidence [%]	Validation
+1	cds.comp41890_c0_seq1	cds.comp41890_c0_seq1 (Doubtful)	1	1	PGGFAKVWANGMGDPNSGDLVWHNKSR	NH2-PGGFAKVWANGMGDPNSGDLVWHNKSR-COOH	LK	LG								1	1	100.0	Confident
+2	cds.comp8310_c0_seq2	cds.comp8310_c0_seq2 (Doubtful)	1	1	NLVAEESMNMLKNK	NH2-NLVAEESMNMLKNK-COOH	NR	FK								1	1	100.0	Confident
+3	cds.comp41890_c0_seq1_REVERSED	cds.comp41890_c0_seq1_REVERSED (Doubtful)	1	1	RYTSHEQLEGK	NH2-RYTSHEQLEGK-COOH	NK	VL								1	1	100.0	Confident
+4	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3 (Doubtful)	1	1	LDRLISATSISPEHKIDFLFK	NH2-LDRLISATSISPEHKIDFLFK-COOH	WK;WK;WK	DP;DP;DP								1	1	100.0	Confident
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptideshaker_reports_output_proteins.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptideshaker_reports_output_proteins.tabular	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,5 @@
+	Protein Inference	Main Accession	Description	Protein Group	Secondary Accessions	Chromosome	Gene Name	Taxonomy	Validated Coverage [%]	All Coverage [%]	Possible Coverage [%]	#Peptides	#Validated Peptides	#Unique Peptides	#Validated Unique Peptides	#PSMs	#Validated PSMs	Confidently Localized Modification Sites	#Confidently Localized Modification Sites	Ambiguously Localized Modification Sites	#Ambiguously Localized Modification Sites	Spectrum Counting	MW [kDa]	Confidence [%]	Validation
+1	Single Protein	cds.comp8310_c0_seq2	m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16	cds.comp8310_c0_seq2					3.69	3.69	81.0	1	1	1	1	1	1					12239.035185720222	45.26545451338222	100.0	Doubtful
+2	Single Protein	cds.comp41890_c0_seq1	m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20	cds.comp41890_c0_seq1					20.15	20.15	91.04	1	1	1	1	1	1					30798.227885377935	14.802380493830709	100.0	Doubtful
+3	Related Proteins	cds.comp41779_c0_seq1	m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	cds.comp41779_c0_seq2,cds.comp41779_c0_seq3				3.34	3.34	78.82	1	1	1	1	1	1					7590.674347507289	69.88215380565931	100.0	Doubtful
+4	Single Protein	cds.comp41890_c0_seq1_REVERSED	m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20-REVERSED	cds.comp41890_c0_seq1_REVERSED					8.21	8.21	90.3	1	1	1	1	1	1					31052.758694348	14.802380493830709	100.0	Doubtful
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptideshaker_reports_output_proteinsnonvalidated.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptideshaker_reports_output_proteinsnonvalidated.tabular	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,5 @@
+	Protein Inference	Main Accession	Description	Protein Group	Secondary Accessions	Chromosome	Gene Name	Taxonomy	Validated Coverage [%]	All Coverage [%]	Possible Coverage [%]	#Peptides	#Validated Peptides	#Unique Peptides	#Validated Unique Peptides	#PSMs	#Validated PSMs	Confidently Localized Modification Sites	#Confidently Localized Modification Sites	Ambiguously Localized Modification Sites	#Ambiguously Localized Modification Sites	Spectrum Counting	MW [kDa]	Confidence [%]	Validation
+1	Single Protein	cds.comp8310_c0_seq2	m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16	cds.comp8310_c0_seq2					3.69	3.69	81.0	1	1	1	1	1	1					12239.035185720222	45.26545451338222	100.0	Doubtful
+2	Single Protein	cds.comp41890_c0_seq1	m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20	cds.comp41890_c0_seq1					20.15	20.15	91.04	1	1	1	1	1	1					30798.227885377935	14.802380493830709	100.0	Doubtful
+3	Related Proteins	cds.comp41779_c0_seq1	m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	cds.comp41779_c0_seq2,cds.comp41779_c0_seq3				3.34	3.34	78.82	1	1	1	1	1	1					7590.674347507289	69.88215380565931	100.0	Doubtful
+4	Single Protein	cds.comp41890_c0_seq1_REVERSED	m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20-REVERSED	cds.comp41890_c0_seq1_REVERSED					8.21	8.21	90.3	1	1	1	1	1	1					31052.758694348	14.802380493830709	100.0	Doubtful
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptideshaker_reports_output_proteinsphosphorylation.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptideshaker_reports_output_proteinsphosphorylation.tabular	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,5 @@
+	Protein Inference	Main Accession	Description	Protein Group	Secondary Accessions	Chromosome	Gene Name	Taxonomy	Validated Coverage [%]	All Coverage [%]	Possible Coverage [%]	#Peptides	#Validated Peptides	#Unique Peptides	#Validated Unique Peptides	#PSMs	#Validated PSMs	Confident Phosphosites	#Confident Phosphosites	Ambiguous Phosphosites	#Ambiguous Phosphosites	Spectrum Counting NSAF	MW [kDa]	Confidence [%]	Validation
+1	Single Protein	cds.comp8310_c0_seq2	m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16	cds.comp8310_c0_seq2					3.69	3.69	81.0	1	1	1	1	1	1		0		0	0.003257328990228013	45.26545451338222	100.0	Doubtful
+2	Single Protein	cds.comp41890_c0_seq1	m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20	cds.comp41890_c0_seq1					20.15	20.15	91.04	1	1	1	1	1	1		0		0	0.00819672131147541	14.802380493830709	100.0	Doubtful
+3	Related Proteins	cds.comp41779_c0_seq1	m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	cds.comp41779_c0_seq2,cds.comp41779_c0_seq3				3.34	3.34	78.82	1	1	1	1	1	1		0		0	0.00202020202020202	69.88215380565931	100.0	Doubtful
+4	Single Protein	cds.comp41890_c0_seq1_REVERSED	m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20-REVERSED	cds.comp41890_c0_seq1_REVERSED					8.21	8.21	90.3	1	1	1	1	1	1		0		0	0.008264462809917356	14.802380493830709	100.0	Doubtful
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptideshaker_reports_output_psm.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptideshaker_reports_output_psm.tabular	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,5 @@
+	Protein(s)	Sequence	AAs Before	AAs After	Position	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
+1	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	LDRLISATSISPEHKIDFLFK	WK;WK;WK	DP;DP;DP	545;538;63	NH2-LDRLISATSISPEHKIDFLFK-COOH			searchgui_smallspectra	small.3.3. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=3"		0.6731	810.789428710938	2+, 3+, 4+	3	2429.33184573292	0	6.00693871414815				100.0	Confident
+2	cds.comp8310_c0_seq2	NLVAEESMNMLKNK	NR	FK	263	NH2-NLVAEESMNMLKNK-COOH			searchgui_smallspectra	small.17.17. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=17"		8.9853	811.408081054688	2+, 3+, 4+	2	1619.80111309327	1	-1.7626881884550694				100.0	Confident
+3	cds.comp41890_c0_seq1	PGGFAKVWANGMGDPNSGDLVWHNKSR	LK	LG	77	NH2-PGGFAKVWANGMGDPNSGDLVWHNKSR-COOH			searchgui_smallspectra	small.28.28. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=28"		16.3598	725.3583984375	2+, 3+, 4+	4	2896.38272917215	1	6.345261931182815				100.0	Confident
+4	cds.comp41890_c0_seq1_REVERSED	RYTSHEQLEGK	NK	VL	114	NH2-RYTSHEQLEGK-COOH			searchgui_smallspectra	small.46.46. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=46"		27.6339	674.841369628906	2+, 3+, 4+	2	1346.6578773639	1	5.1562724435666505				100.0	Confident
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptideshaker_reports_output_psmnonvalidated.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptideshaker_reports_output_psmnonvalidated.tabular	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,5 @@
+	Protein(s)	Sequence	AAs Before	AAs After	Position	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
+1	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	LDRLISATSISPEHKIDFLFK	WK;WK;WK	DP;DP;DP	545;538;63	NH2-LDRLISATSISPEHKIDFLFK-COOH			searchgui_smallspectra	small.3.3. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=3"		0.6731	810.789428710938	2+, 3+, 4+	3	2429.33184573292	0	6.00693871414815				100.0	Confident
+2	cds.comp8310_c0_seq2	NLVAEESMNMLKNK	NR	FK	263	NH2-NLVAEESMNMLKNK-COOH			searchgui_smallspectra	small.17.17. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=17"		8.9853	811.408081054688	2+, 3+, 4+	2	1619.80111309327	1	-1.7626881884550694				100.0	Confident
+3	cds.comp41890_c0_seq1	PGGFAKVWANGMGDPNSGDLVWHNKSR	LK	LG	77	NH2-PGGFAKVWANGMGDPNSGDLVWHNKSR-COOH			searchgui_smallspectra	small.28.28. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=28"		16.3598	725.3583984375	2+, 3+, 4+	4	2896.38272917215	1	6.345261931182815				100.0	Confident
+4	cds.comp41890_c0_seq1_REVERSED	RYTSHEQLEGK	NK	VL	114	NH2-RYTSHEQLEGK-COOH			searchgui_smallspectra	small.46.46. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=46"		27.6339	674.841369628906	2+, 3+, 4+	2	1346.6578773639	1	5.1562724435666505				100.0	Confident
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptideshaker_reports_output_psmphosphorylation.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptideshaker_reports_output_psmphosphorylation.tabular	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,5 @@
+	Protein(s)	Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Localization Confidence	Probabilistic PTM score	D-score	Confident Phosphosites	#Confident Phosphosites	Ambiguous Phosphosites	#Ambiguous Phosphosites	Confidence [%]	Validation
+1	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	LDRLISATSISPEHKIDFLFK			searchgui_smallspectra	small.3.3. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=3"	0.6731	810.789428710938	2+, 3+, 4+	3	2429.33184573292	0	6.00693871414815					0		0	100.0	Confident
+2	cds.comp8310_c0_seq2	NLVAEESMNMLKNK			searchgui_smallspectra	small.17.17. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=17"	8.9853	811.408081054688	2+, 3+, 4+	2	1619.80111309327	1	-1.7626881884550694					0		0	100.0	Confident
+3	cds.comp41890_c0_seq1	PGGFAKVWANGMGDPNSGDLVWHNKSR			searchgui_smallspectra	small.28.28. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=28"	16.3598	725.3583984375	2+, 3+, 4+	4	2896.38272917215	1	6.345261931182815					0		0	100.0	Confident
+4	cds.comp41890_c0_seq1_REVERSED	RYTSHEQLEGK			searchgui_smallspectra	small.46.46. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=46"	27.6339	674.841369628906	2+, 3+, 4+	2	1346.6578773639	1	5.1562724435666505					0		0	100.0	Confident
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/searchgui_smallsearch_default_somesearchengines_modifications.zip
Binary file test-data/searchgui_smallsearch_default_somesearchengines_modifications.zip has changed
diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/searchgui_smallspectra.mgf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/searchgui_smallspectra.mgf	Fri Jan 15 14:06:27 2021 +0000
@@ -0,0 +1,25548 @@
+BEGIN IONS
+TITLE=small.3.3. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=3"
+RTINSECONDS=0.6731
+PEPMASS=810.789428710938 183838.71875
+CHARGE=2+ and 3+ and 4+
+231.3888397 26.5451126099
+233.3398285 20.4479541779
+239.3961487 17.9991588593
+240.3084717 44.7395210266
+245.1689453 283.3832702637
+246.1925354 75.7845687866
+247.8092346 23.2885246277
+251.197052 628.9126586914
+252.3562469 41.6676368713
+259.3575439 51.3414955139
+262.2673035 341.8115539551
+264.271759 19.0200614929
+266.2132263 111.3928222656
+272.3408508 27.5777511597
+273.1651001 46.4653587341
+276.2359009 66.1921005249
+277.3269958 36.7716407776
+279.2734375 151.997756958
+280.2745056 30.4819164276
+281.2428894 20.6155757904
+286.1730042 26.2698879242
+290.194519 1193.4537353516
+291.2459717 152.4249267578
+294.2355957 413.9957275391
+295.1256409 17.1910572052
+299.1573792 54.0453262329
+305.8824768 33.266960144
+308.1987305 4068.3127441406
+309.2765503 735.5776367188
+315.3105774 44.0675201416
+316.2329102 87.3488922119
+319.4229736 68.6050643921
+324.0772705 20.8427391052
+326.1818848 118.679145813
+328.2772522 72.1243438721
+330.1789551 24.7702865601
+332.6609497 31.4776382446
+336.117981 115.9179992676
+337.3536072 167.551864624
+338.2251587 16.7139282227
+339.2226562 23.1128787994
+345.9707947 65.1955108643
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