| Previous changeset 54:7fdd9119cc4f (2020-02-20) Next changeset 56:1beff3ddce58 (2021-01-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" |
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modified:
README.rst admin_scripts/build_mods_loc.py admin_scripts/build_species.py peptide_shaker.xml searchgui.xml test-data/searchgui_tinydb1.fasta test-data/searchgui_tinyspectra1.mgf |
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added:
fasta_cli.xml ident_params.xml macros_basic.xml test-data/Identification_Parameters_default.par test-data/Identification_Parameters_default_modifications.par test-data/Identification_Parameters_specific.par test-data/fastacli_searchgui_tinydb1.fasta test-data/fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta test-data/peptideshaker_reports_output_certificate.txt test-data/peptideshaker_reports_output_extendedpsm.tabular test-data/peptideshaker_reports_output_hierarchical.tabular test-data/peptideshaker_reports_output_peptides.tabular test-data/peptideshaker_reports_output_peptidesnonvalidated.tabular test-data/peptideshaker_reports_output_peptidesphosphorylation.tabular test-data/peptideshaker_reports_output_proteins.tabular test-data/peptideshaker_reports_output_proteinsnonvalidated.tabular test-data/peptideshaker_reports_output_proteinsphosphorylation.tabular test-data/peptideshaker_reports_output_psm.tabular test-data/peptideshaker_reports_output_psmnonvalidated.tabular test-data/peptideshaker_reports_output_psmphosphorylation.tabular test-data/searchgui_smallsearch_default_somesearchengines_modifications.zip test-data/searchgui_smallspectra.mgf test-data/searchgui_tiny_result_default_4engines.zip test-data/searchgui_tiny_result_default_4engines_modifications.zip |
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removed:
macros.xml test-data/peptide_shaker_modifications_result1.cpsx test-data/peptide_shaker_modifications_result1.output_certificate test-data/peptide_shaker_modifications_result1.output_extended_psm test-data/peptide_shaker_modifications_result1.output_hierarchical test-data/peptide_shaker_modifications_result1.output_peptides test-data/peptide_shaker_modifications_result1.output_peptides_nonvalidated test-data/peptide_shaker_modifications_result1.output_peptides_phosphorylation test-data/peptide_shaker_modifications_result1.output_proteins test-data/peptide_shaker_modifications_result1.output_proteins_nonvalidated test-data/peptide_shaker_modifications_result1.output_proteins_phosphorylation test-data/peptide_shaker_modifications_result1.output_psm test-data/peptide_shaker_modifications_result1.output_psm_nonvalidated test-data/peptide_shaker_modifications_result1.output_psm_phosphorylation test-data/peptide_shaker_modifications_result1.zip test-data/tiny_searchgui_modifications_result1.zip test-data/tiny_searchgui_modifications_result_amandaonly.zip test-data/tiny_searchgui_result1.zip test-data/tiny_searchgui_result_amandaonly.zip |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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"]: |
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| 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 |
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| @@ -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) |
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| 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 |
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| @@ -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<designation>.+)\.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> |
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| 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 |
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| b'@@ -0,0 +1,1904 @@\n+<tool id="ident_params" name="Identification Parameters" version="1.5.1">\n+ <description>\n+ Sets the identification parameters to be used in SearchGUI and PeptideShaker apps\n+ </description>\n+ <macros>\n+ <import>macros_basic.xml</import>\n+ <import>macros_modifications.xml</import>\n+ </macros>\n+ <requirements>\n+ \t<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>\n+ </requirements>\n+ <expand macro="stdio" />\n+ <command>\n+<![CDATA[\n+ #set $temp_stderr = "searchgui_stderr"\n+ #set $bin_dir = "bin"\n+\n+ mkdir output;\n+ cwd=`pwd`;\n+ export HOME=\\$cwd;\n+\n+\n+ echo "" > $temp_stderr &&\n+\n+ echo \'running Identification Parameters CLI\' &&\n+ #####################################################\n+ ## generate IdentificationParameters for SearchGUI ##\n+ #####################################################\n+ (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI\n+ --exec_dir="./bin/"\n+ -out \'./IdentificationParametersOutput.par\'\n+\n+ ## SPECTRUM MATCHING PARAMETERS\n+\n+ -frag_tol \'${spectrum_matching_options.fragment_tol}\'\n+ -frag_ppm \'${spectrum_matching_options.fragment_tol_units}\'\n+ -prec_tol \'${spectrum_matching_options.precursor_ion_tol}\'\n+ -prec_ppm \'${spectrum_matching_options.precursor_ion_tol_units}\'\n+\n+ #if $spectrum_matching_options.digestion.cleavage == \'default\':\n+ -mc $spectrum_matching_options.digestion.missed_cleavages\n+ #elif $spectrum_matching_options.digestion.cleavage == \'0\' and len($spectrum_matching_options.digestion.digests) > 0:\n+ #set $enzymes = []\n+ #set $missed_cleavages = []\n+ #set $specificities = []\n+ #for $i, $digest in enumerate($spectrum_matching_options.digestion.digests):\n+ #silent $enzymes.append(str($digest.enzyme))\n+ #silent $missed_cleavages.append(str($digest.missed_cleavages))\n+ #silent $specificities.append(str($digest.specificity))\n+ #end for\n+ -enzyme "#echo \',\'.join($enzymes)#"\n+ -mc "#echo \',\'.join($missed_cleavages)#"\n+ -specificity "#echo \',\'.join($specificities)#"\n+ #else:\n+ -digestion $spectrum_matching_options.digestion.cleavage\n+ #end if\n+\n+\n+ #set $fixed_mods_str = $spectrum_matching_options.fixed_modifications or \'\'\n+ #set $variable_mods_str = $spectrum_matching_options.variable_modifications or \'\'\n+ #if $fixed_mods_str\n+ -fixed_mods "$fixed_mods_str"\n+ #end if\n+ #if $variable_mods_str\n+ -variable_mods "$variable_mods_str"\n+ #end if\n+\n+\n+ -min_charge $spectrum_matching_options.min_charge\n+ -max_charge $spectrum_matching_options.max_charge\n+ -fi $spectrum_matching_options.forward_ion\n+ -ri $spectrum_matching_options.reverse_ion\n+ -min_isotope ${spectrum_matching_options.min_isotope}\n+ -max_isotope ${spectrum_matching_options.max_isotope}\n+ ## TODO: TO CHECK, these last two both are also present in the app in the import filters section.\n+\n+\n+ ## -- SEARCH ENGINES SPECIFIC PARAMETERS --\n+\n+ ## XTANDEM ADVANCED SETTINGS\n+\n+ #if $searchengines_options.xtandem.xtandem_advanced == "yes"\n+\n+ ## Spectrum import\n+ #if $searchengines_options.xtandem.xtandem_spectrum.xtandem_spectrum_selector == "yes"\n+ -xtandem_dynamic_range ${searchengines_options.xtandem.xtandem_spectrum.xtandem_dynamic_range}\n+ -xtandem_npeaks ${searchengines_options.xtandem.xtandem_spectrum.xtandem_npeaks}\n+ -xtandem_min_frag_mz ${searchengines_options.xtandem.xtand'..b'tide level" help="In percent (default 1% FDR: \'1\')" value="1" type="float">\n+ <validator type="in_range" min="0" max="100" />\n+ </param>\n+ <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: \'1\')" value="1" type="float">\n+ <validator type="in_range" min="0" max="100" />\n+ </param>\n+ </section>\n+\n+\n+ <!-- FRACTION ANALYSIS -->\n+\n+ <section name="fraction_analysis_options" expanded="false" title="Fraction Analysis">\n+ <param name="protein_fraction_mw_confidence" value="95.0" type="float"\n+ label="Minimum confidence required for a protein in the fraction MW plot (in percentage)"\n+ help="default 95%: \'95.0\'">\n+ <validator type="in_range" min="0" max="100" />\n+ </param>\n+ </section>\n+\n+\n+ <!-- DATABASE PROCESSING OPTIONS -->\n+\n+ <section name="database_processing_options" expanded="false" title="Database Processing Options">\n+ <conditional name="decoy_conditional">\n+ <param name="create_decoy_selector" type="select"\n+ label="Create a concatenated target/decoy database before running PeptideShaker"\n+ help="Selecting this option will help PeptideShaker calculate FDR values">\n+ <option value="yes" selected="True">Yes</option>\n+ <option value="no" >No</option>\n+ </param>\n+ <when value="no" />\n+ <when value="yes">\n+ <param name="decoy_tag" type="text" value="-REVERSED" label="The decoy flag">\n+ </param>\n+ <param name="decoy_type" type="select" label="Location of the decoy flag: prefix or suffix">\n+ <option value="0">Prefix</option>\n+ <option value="1" selected="True">Suffix</option>\n+ </param>\n+ </when>\n+ </conditional>\n+ <param name="decoy_file_tag" type="text" value="_concatenated_target_decoy" label="Target decoy suffix.">\n+ </param>\n+ </section>\n+\n+ </section>\n+\n+ </inputs>\n+ <outputs>\n+ <data name="Identification_Parameters_File" format="json" from_work_dir="IdentificationParametersOutput.par" label="${tool.name}: PAR file" />\n+ </outputs>\n+ <tests>\n+\n+ <!-- Test that default parameters generates a standard par file -->\n+ <test>\n+ <param name="xtandem_advanced" value="yes"/>\n+ <param name="xtandem_refine_selector" value="no"/>\n+ <output name="Identification_Parameters_File" file="Identification_Parameters_default.par" ftype="json" compare="sim_size" delta="1000" />\n+ </test>\n+ <!-- Test specific parameters with modifications -->\n+ <test>\n+ <param name="precursor_ion_tol" value="100"/>\n+ <param name="fixed_modifications" value="Carbamidomethylation of C"/>\n+ <param name="variable_modifications" value="Oxidation of M"/>\n+ <param name="min_charge" value="1"/>\n+ <param name="max_charge" value="3"/>\n+ <param name="xtandem_advanced" value="yes"/>\n+ <param name="xtandem_refine_selector" value="yes"/>\n+ <output name="Identification_Parameters_File" file="Identification_Parameters_specific.par" ftype="json" compare="sim_size" delta="1000" />\n+ </test>\n+\n+ </tests>\n+ <help>\n+**What it does**\n+\n+Creates a parameters file (.par) which can be used independently by SearchGUI or PeptideShaker apps.\n+\n+A FASTA file with decoy sequences generated by FastaCLI is recommended if SearchGUI and PeptideShaker are going to use the output of this tool.\n+\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| 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 |
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| b'@@ -1,162 +0,0 @@\n-<macros>\n- <import>macros_modifications.xml</import>\n- <xml name="stdio">\n- <stdio>\n- <exit_code range="1:" level="fatal" description="Job Failed" />\n-\t <!--\t <regex match="java.lang.OutOfMemoryError" level="fatal_oom" description="Java memory Exception"/>\n-\t <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/>\n-\t <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/>\n-\t <regex match="Native memory allocation (malloc) failed" level="fatal_oom" description="Java memory Exception"/>-->\n-\t <regex match="java.*Exception" level="fatal" description="Java Exception"/>\n- <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>\n-\t <regex match="PeptideShaker ran out of memory" level="fatal" description="JVM Error"/>\n-\t <regex match="CompomicsError" level="fatal" description="Compomics Error"/>\n- </stdio>\n- </xml>\n-\n- <token name="@GENERAL_PARAMETERS@">\n- -frag_tol \'${precursor_options.fragment_tol}\'\n- -frag_ppm \'${precursor_options.fragment_tol_units}\'\n- -prec_tol \'${precursor_options.precursor_ion_tol}\'\n- -prec_ppm \'${precursor_options.precursor_ion_tol_units}\'\n-\n- -min_charge $precursor_options.min_charge\n- -max_charge $precursor_options.max_charge\n- -fi $precursor_options.forward_ion\n- -ri $precursor_options.reverse_ion\n- -min_isotope ${precursor_options.min_isotope}\n- -max_isotope ${precursor_options.max_isotope}\n- #if $protein_digest_options.digestion.cleavage == \'default\':\n- ## -enzyme "Trysin"\n- -mc $protein_digest_options.digestion.missed_cleavages\n- #elif $protein_digest_options.digestion.cleavage == \'0\' and len($protein_digest_options.digestion.digests) > 0:\n- #set $enzymes = []\n- #set $missed_cleavages = []\n- ## #set $specificities = []\n- #for $i, $digest in enumerate($protein_digest_options.digestion.digests):\n- #silent $enzymes.append(str($digest.enzyme))\n- #silent $missed_cleavages.append(str($digest.missed_cleavages))\n- ## #silent $specificities.append(str($digest.specificity))\n- #end for\n- -enzyme "#echo \',\'.join($enzymes)#"\n- -mc "#echo \',\'.join($missed_cleavages)#"\n- ## -specificity "#echo \',\'.join($specificities)#"\n- #else:\n- -digestion $protein_digest_options.digestion.cleavage\n- #end if\n-\n- #set $fixed_mods_str = $protein_modification_options.fixed_modifications or \'\'\n- #set $variable_mods_str = $protein_modification_options.variable_modifications or \'\'\n- #if $fixed_mods_str\n- -fixed_mods "$fixed_mods_str"\n- #end if\n- #if $variable_mods_str\n- -variable_mods "$variable_mods_str"\n- #end if\n-\n- </token>\n-\n- <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>\n- <token name="@SEARCHGUI_VERSION@">3.3.10</token>\n- <token name="@PEPTIDESHAKER_VERSION@">1.16.36</token>\n- <xml name="general_options">\n-\n- <section name="protein_digest_options" expanded="false" title="Protein Digestion Options">\n- <conditional name="digestion">\n- <param name="cleavage" type="select" label="Digestion">\n- <option value="0">Select Enzymes</option>\n- <option value="1">Unspecific Cleavage</option>\n- <option value="2">Whole Protein</option>\n- </param>\n- <when value="0">\n- <repeat name="digests" min="1" title="Enzymes">\n- <param name="enzyme" type="select" label="Enzyme"\n- help="Which enzyme was used '..b' <option value="3">Specific at the C-terminus only</option>\n- </param>\n- -->\n- </repeat>\n- </when>\n- <when value="1"/>\n- <when value="2"/>\n- </conditional>\n- </section>\n-\n- <section name="precursor_options" expanded="false" title="Precursor Options">\n- <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"\n- help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">\n- <option value="1">Parts per million (ppm)</option>\n- <option value="0">Daltons</option>\n- </param>\n- <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance"\n- help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>\n- <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units"\n- help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">\n- <option value="1">Parts per million (ppm)</option>\n- <option value="0" selected="true">Daltons</option>\n- </param>\n- <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance"\n- help="Provide error value for fragment ions, based on instrument used"/>\n- <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>\n- <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>\n- <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">\n- <option value="a">a</option>\n- <option value="b" selected="true">b</option>\n- <option value="c">c</option>\n- </param>\n- <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">\n- <option value="x">x</option>\n- <option value="y" selected="true">y</option>\n- <option value="z">z</option>\n- </param>\n- <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />\n- <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />\n- </section>\n-\n- <section name="protein_modification_options" expanded="false" title="Protein Modification Options">\n- <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"\n- help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">\n- <expand macro="modifications"/>\n- </param>\n- <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true"\n- help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> \n- <expand macro="modifications"/>\n- </param>\n- </section>\n-\n- </xml>\n-\n- <xml name="citations">\n- <citations>\n- <citation type="doi">10.1186/1471-2105-12-70</citation>\n- <citation type="doi">10.1002/pmic.201000595</citation>\n- <citation type="doi">doi:10.1038/nbt.3109</citation>\n- </citations>\n- </xml>\n-\n-</macros>\n' |
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| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| [ |
| b'@@ -1,12 +1,14 @@\n-<tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@.3">\n+<tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@+galaxy@PEPTIDESHAKER_VERSION_SUFFIX@">\n <description>\n Perform protein identification using various search engines based on results from SearchGUI\n </description>\n <macros>\n- <import>macros.xml</import>\n+ <import>macros_basic.xml</import>\n+ <import>macros_modifications.xml</import>\n </macros>\n <requirements>\n <requirement type="package" version="@PEPTIDESHAKER_VERSION@">peptide-shaker</requirement>\n+ <requirement type="package">unzip</requirement>\n </requirements>\n <expand macro="stdio" />\n \n@@ -17,7 +19,7 @@\n #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")\n #set $temp_stderr = "peptideshaker_stderr"\n #set $bin_dir = "bin"\n-\n+ #set $exporting_followup_boolean = False\n \n mkdir output_reports &&\n cwd=`pwd` &&\n@@ -26,67 +28,70 @@\n echo "" > $temp_stderr &&\n \n ln -s \'$searchgui_input\' searchgui_input.zip &&\n- jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&\n-\n \n- peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI\n- --exec_dir="\\$cwd/${bin_dir}"\n- -temp_folder \\$cwd/PathSettingsCLI\n- -log \\$cwd/peptideshaker.log &&\n+ ## OPTIONAL MAIN PARAMETERS\n+ ## If we have a specific Identification Parameters file to use, we will use it instead of the one provided in the search_gui file\n+ #if $optional_main_parameters.input_optional_identification_parameters:\n+ cp \'${optional_main_parameters.input_optional_identification_parameters}\' SEARCHGUI_IdentificationParameters.par &&\n+ #else:\n+ jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&\n+ #end if\n+ ## Optional Fasta file\n+ #if $optional_main_parameters.input_fasta_file:\n+ ## copy the input .fasta file to the working folder\n+ cp \'${optional_main_parameters.input_fasta_file}\' \'./input_fasta_file.fasta\' &&\n+ #end if\n+ ## Optional Spectrum files: if the user specified input spectra files, we use them\n+ ## NOTE: != None DOES NOT SEEM TO WORK ANYMORE ON MODERN GALAXIES\n+ #if str($optional_main_parameters.input_optional_spectrum_files) != \'None\' and str($optional_main_parameters.input_optional_spectrum_files) != \'\':\n+ mkdir peaklist_input_files &&\n+ #for $peak_list_file in $optional_main_parameters.input_optional_spectrum_files:\n+ #if $peak_list_file.is_of_type("mgf"):\n+ #set $input_name = $peak_list_file.element_identifier.split(\'/\')[-1].replace(".mgf", "") + ".mgf"\n+ #else if $peak_list_file.is_of_type("mzml"):\n+ #set $input_name = $peak_list_file.element_identifier.split(\'/\')[-1].replace(".mzml", "") + ".mzml"\n+ #end if\n+ ln -s -f \'${peak_list_file}\' \'peaklist_input_files/${input_name}\' &&\n+ #end for\n+ #end if\n \n- #if str($exporting_options.output_reports) != "None"\n+ #if str($exporting_options.output_reports) != "None" and str($exporting_options.output_reports) != ""\n #set $output_reports_list = set(str($exporting_options.output_reports).split(\',\'))\n #else\n #set $output_reports_list = set()\n- #end if\n+\t #end if\n \n ######################\n ## PeptideShakerCLI ##\n ######################\n (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI\n- --exec_dir="\\$cwd/${bin_dir}"\n -gui 0\n -temp_folder \\$cwd/PeptideShakerCLI\n- -experiment \'$exp_str\'\n- -sample \'$samp_str\'\n- -replicate 1\n+ -log \\$cwd/resources\n+ -reference'..b'e of the peptide.\n-* Confidence:\tConfidence in percent associated to the peptide.\n-* Decoy:\tIndicates whether the peptide is a decoy (1: yes, 0: no).\n-* Validation:\tIndicates the validation level of the protein group.\n-* Protein(s):\tProtein(s) to which the peptide can be attached.\n-* Sequence:\tSequence of the peptide.\n-* Modified Sequence:\tThe peptide sequence annotated with variable modifications.\n-* Variable Modifications:\tThe variable modifications.\n-* D-score:\tD-score for variable PTM localization.\n-* probabilistic PTM score:\tThe probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.\n-* Localization Confidence:\tThe confidence in variable PTM localization.\n-* Fixed Modifications:\tThe fixed modifications.\n-* Spectrum File:\tThe spectrum file.\n-* Spectrum Title:\tThe title of the spectrum.\n-* Spectrum Scan Number:\tThe spectrum scan number.\n-* RT:\tRetention time\n-* m/z:\tMeasured m/z\n-* Measured Charge:\tThe charge as given in the spectrum file.\n-* Identification Charge:\tThe charge as inferred by the search engine.\n-* Theoretical Mass:\tThe theoretical mass of the peptide.\n-* Isotope Number:\tThe isotope number targetted by the instrument.\n-* Precursor m/z Error:\tThe precursor m/z matching error.\n-* Score:\tScore of the retained peptide as a combination of the algorithm scores (used to rank PSMs).\n-* Confidence:\tConfidence in percent associated to the retained PSM.\n-* Decoy:\tIndicates whether the peptide is a decoy (1: yes, 0: no).\n-* Validation:\tIndicates the validation level of the protein group.\n-\n+========================================== =====================================================\n+ Column Description\n+========================================== =====================================================\n+Main Accession Main accession of the protein group.\n+Description\t Description of the protein designed by the main accession.\n+MW (kDa) Molecular Weight.\n+Possible Coverage (%) Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.\n+Coverage (%) Sequence coverage in percent of the protein designed by the main accession.\n+Spectrum Counting NSAF Normalized Spectrum Abundance Factor (NSAF)\n+Confidently Localized Modification Sites\t List of the sites where a variable modification was confidently localized.\n+# Confidently Localized Modification Sites\t Number of sites where a variable modification was confidently localized.\n+Ambiguously Localized Modification Sites\t List of the sites where ambiguously localized variable modification could possibly be located.\n+#Ambiguously Localized Modification Sites\t Number of ambiguously localized modifications.\n+Protein Inference\t Protein Inference status of the protein group.\n+Secondary Accessions Other accessions in the protein group (alphabetical order).\n+Protein Group The complete protein group (alphabetical order).\n+#Validated Peptides Number of validated peptides.\n+#Peptides Total number of peptides.\n+#Unique Total number of peptides unique to this protein group.\n+#Validated PSMs Number of validated PSMs\n+#PSMs Number of PSMs\n+Confidence Confidence in percent associated to the protein group.\n+Decoy Indicates whether the protein group is a decoy (1: yes, 0: no).\n+Validation Indicates the validation level of the protein group.\n+========================================== =====================================================\n \n ------\n \n' |
| b |
| 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 |
| [ |
| b'@@ -1,9 +1,9 @@\n-<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1">\n+<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@+galaxy@SEARCHGUI_VERSION_SUFFIX@">\n <description>\n Perform protein identification using various search engines and prepare results for input to Peptide Shaker\n </description>\n <macros>\n- <import>macros.xml</import>\n+ <import>macros_basic.xml</import>\n </macros>\n <requirements>\n <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>\n@@ -13,6 +13,8 @@\n <command use_shared_home="false">\n <![CDATA[\n #from datetime import datetime\n+ #import json\n+ #import os\n #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")\n #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")\n #set $temp_stderr = "searchgui_stderr"\n@@ -27,313 +29,29 @@\n \n ## echo the search engines to run (single quotes important because X!Tandem)\n echo \'$search_engines_options.engines\';\n- echo \'DB: ${input_database.element_identifier} sequences: ${input_database.metadata.sequences}\';\n+ echo \'DB: ${input_fasta_file.element_identifier} sequences: ${input_fasta_file.metadata.sequences}\';\n \n ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present\n echo \'searchgui.version=@SEARCHGUI_VERSION@\' >> searchgui.properties;\n \n- #for $mgf in $peak_lists:\n- #set $input_name = $mgf.element_identifier.split(\'/\')[-1].replace(".mgf", "") + ".mgf"\n- ln -s -f \'${mgf}\' \'${input_name}\';\n- #set $encoded_id = $__app__.security.encode_id($mgf.id)\n- echo \'Spectrums:${mgf.element_identifier}(API:${encoded_id})\';\n- #end for\n- ##ln -s "${input_database}" input_database.fasta;\n- cp "${input_database}" input_database.fasta;\n-\n- ###########################################\n- #### Set paths ####\n- ###########################################\n- echo \'Setting paths\' &&\n- searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI\n- --exec_dir="\\$cwd/${bin_dir}"\n- -temp_folder \\$cwd\n- -log \\$cwd/searchgui.log 2>> $temp_stderr &&\n-\n- ###########################################\n- #### Creating decoy database ####\n- ###########################################\n- #if $protein_database_options.create_decoy:\n- echo \'Creating decoy database.\' &&\n- searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI\n- --exec_dir="\\$cwd/${bin_dir}"\n- -in input_database.fasta\n- -decoy 2>> $temp_stderr &&\n- rm input_database.fasta &&\n- cp input_database_concatenated_target_decoy.fasta input_database.fasta &&\n- ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;\n- #end if\n-\n- #####################################################\n- ## generate IdentificationParameters for SearchGUI ##\n- #####################################################\n- echo \'setting identification parameters\' &&\n- (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI\n- --exec_dir="\\$cwd/${bin_dir}"\n- -out SEARCHGUI_IdentificationParameters.par\n-\n- @GENERAL_PARAMETERS@\n-\n- -db input_database.fasta\n- $protein_database_options.use_gene_mapping\n- #if $protein_database_options.use_gene_mapping:\n- $protein_database_options.update_gene_mapping\n- #else:\n- -updateGeneMapping 0\n+ #for $peak_list_file in $peak_lists_files:\n+ #set $input_name = ""\n+ #if $peak_list_file.is_of_type("mgf"):\n'..b'tput>\n </test>\n \n- <!-- Test that specifying non-default search engines works using modifications -->\n+ <!-- Test that specifying non-default search engines with default parameters works using modifications -->\n <test>\n- <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>\n- <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>\n- <param name="precursor_ion_tol" value="100"/>\n- <param name="fixed_modifications" value="Carbamidomethylation of C"/>\n- <param name="variable_modifications" value="Oxidation of M"/>\n- <param name="min_charge" value="1"/>\n- <param name="max_charge" value="3"/>\n- <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>\n- <param name="xtandem|xtandem_advanced" value="yes"/>\n- <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/>\n- <output name="searchgui_results" file="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />\n+ <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>\n+ <param name="input_parameters_file" value="Identification_Parameters_default_modifications.par"/>\n+ <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />\n+ <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>\n+ <output name="searchgui_results" file="searchgui_tiny_result_default_4engines_modifications.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />\n </test>\n- <!-- Test that search works with MSAmanda - with modifications -->\n+\n+ <!--\n+ NOTE: Identification_Parameters_default_modifications.par adds:\n+ - "Carbamidomethylation of C" as fixed modification\n+ - "Oxidation of M" as variable modification\n+ -->\n+\n+ <!-- Test that search works with MSAmanda with default default parameters - with modifications -->\n <test>\n- <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>\n- <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>\n- <param name="precursor_ion_tol" value="100"/>\n- <param name="fixed_modifications" value="Carbamidomethylation of C"/>\n- <param name="variable_modifications" value="Oxidation of M"/>\n- <param name="min_charge" value="1"/>\n- <param name="max_charge" value="3"/>\n+ <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>\n+ <param name="input_parameters_file" value="Identification_Parameters_default_modifications.par"/>\n+ <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />\n <param name="engines" value="MS_Amanda"/>\n- <output name="searchgui_results" file="tiny_searchgui_modifications_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />\n+ <output name="searchgui_results" ftype="searchgui_archive">\n+ <assert_contents>\n+ <has_size value="118136" delta="30000"/>\n+ </assert_contents>\n+ </output>\n </test>\n+\n </tests>\n <help>\n **What it does**\n \n-Runs multiple search engines on any number of MGF peak lists using the SearchGUI.\n-Default: X! Tandem, OMSSA and MS-GF+ are executed.\n-Optional: MyriMatch, MS-Amanda, Comet and Tide can be executed.\n+Runs multiple search engines on any number of MGF peak lists using SearchGUI.\n+\n+Default: X! Tandem and MS-GF+ are executed.\n+\n+Optional: MyriMatch, MS-Amanda, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed.\n \n </help>\n <expand macro="citations" />\n' |
| b |
| 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 |
| [ |
| b'@@ -0,0 +1,662 @@\n+{\n+ "marshallableParameterType": "identification_parameters",\n+ "version": "5.0.1",\n+ "name": "IdentificationParametersOutput",\n+ "description": "Fragment Tolerance: 0.5 Da.\\n",\n+ "defaultDescription": true,\n+ "searchParameters": {\n+ "version": "5.0.1",\n+ "precursorAccuracyType": "PPM",\n+ "fragmentAccuracyType": "DA",\n+ "precursorTolerance": 10.0,\n+ "fragmentIonMZTolerance": 0.5,\n+ "modificationParameters": {\n+ "fixedModifications": [],\n+ "variableModifications": [],\n+ "refinementVariableModifications": [],\n+ "refinementFixedModifications": [],\n+ "colors": {},\n+ "backUp": {},\n+ "id": 0\n+ },\n+ "digestionParameters": {\n+ "cleavageParameter": "enzyme",\n+ "enzymes": [\n+ {\n+ "name": "Trypsin",\n+ "aminoAcidBefore": [\n+ "R",\n+ "K"\n+ ],\n+ "aminoAcidAfter": [],\n+ "restrictionBefore": [],\n+ "restrictionAfter": [\n+ "P"\n+ ],\n+ "cvTerm": {\n+ "ontology": "PSI-MS",\n+ "accession": "MS:1001251",\n+ "name": "Trypsin",\n+ "id": 0\n+ },\n+ "id": 0\n+ }\n+ ],\n+ "nMissedCleavages": {\n+ "Trypsin": 2\n+ },\n+ "specificity": {\n+ "Trypsin": "specific"\n+ },\n+ "id": 0\n+ },\n+ "forwardIons": [\n+ 1\n+ ],\n+ "rewindIons": [\n+ 4\n+ ],\n+ "minChargeSearched": 2,\n+ "maxChargeSearched": 4,\n+ "minIsotopicCorrection": 0,\n+ "maxIsotopicCorrection": 1,\n+ "refMass": 2000.0,\n+ "algorithmParameters": {\n+ "1": {\n+ "type": "com.compomics.util.parameters.identification.tool_specific.OmssaParameters",\n+ "data": {\n+ "maxEValue": 100.0,\n+ "hitListLength": 10,\n+ "minimalChargeForMultipleChargedFragments": 3,\n+ "minPeptideLength": 8,\n+ "maxPeptideLength": 30,\n+ "removePrecursor": false,\n+ "scalePrecursor": true,\n+ "estimateCharge": true,\n+ "selectedOutput": "OMX",\n+ "memoryMappedSequenceLibraries": false,\n+ "neutronThreshold": 1446.94,\n+ "lowIntensityCutOff": 0.0,\n+ "highIntensityCutOff": 0.2,\n+ "intensityCutOffIncrement": 5.0E-4,\n+ "singleChargeWindow": 27,\n+ "doubleChargeWindow": 14,\n+ "nPeaksInSingleChargeWindow": 2,\n+ "nPeaksIndoubleChargeWindow": 2,\n+ "maxHitsPerSpectrumPerCharge": 30,\n+ "nAnnotatedMostIntensePeaks": 6,\n+ "minAnnotatedPeaks": 2,\n+ "minPeaks": 4,\n+ "cleaveNtermMethionine": true,\n+ "maxMzLadders": 128,\n+ "maxFragmentCharge": 2,\n+ "fractionOfPeaksForChargeEstimation": 0.95,\n+ "determineChargePlusOneAlgorithmically": true,\n+ "searchPositiveIons": true,\n+ "minPrecPerSpectrum": 1,\n+ "searchForwardFragmentFirst": false,\n+ "searchRewindFragments": true,\n+ "maxFragmentPerSeries": 100,\n+ "useCorrelationCorrectionScore": true,\n+ "consecutiveIonProbability": 0.5,\n+ "iterativeSequenceEvalue": 0.0,\n+ "iterativeReplaceEvalue": 0.0,\n+ "iterativeSpectrumEvalue": 0.01,\n+ "noProlineRuleSeries": [],\n+ "ptmIndexes": {},\n+ "id": 0\n+ }\n+ },\n+ "33": {\n+ "type": "com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters",\n+ "data": {\n+ "minPeptideLength": 8,\n+ "maxPeptideLength": 30,\n+ "searchType": "Classic",\n+ "totalPartitions": 1,\n+ "dissociationType": "HCD",\n+ "maxModsForPeptide": 2,\n+ "initiatorMethionineBehavior": "Variable",\n+ "scoreCutoff": 5.0,\n+ "useDeltaScore": false,\n+ "fragmentationTerminus": "Both",\n+ "maxFragmentSize": 30000.0,\n+ "massDiffAcceptorType": "OneMM",\n+ "writeMzId": tru'..b'+ "aminoAcids": [\n+ "D",\n+ "E",\n+ "S",\n+ "T"\n+ ],\n+ "id": 0\n+ },\n+ {\n+ "composition": {\n+ "atomChain": [\n+ {\n+ "atomSymbol": "N",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ }\n+ ],\n+ "mass": -1.0,\n+ "id": 0\n+ },\n+ "name": "NH3",\n+ "fixed": false,\n+ "aminoAcids": [\n+ "K",\n+ "N",\n+ "Q",\n+ "R"\n+ ],\n+ "id": 0\n+ }\n+ ],\n+ "neutralLossesAuto": true,\n+ "reporterIons": true,\n+ "relatedIons": true,\n+ "fragmentIonAccuracy": 10.0,\n+ "fragmentIonPpm": false,\n+ "showForwardIonDeNovoTags": false,\n+ "showRewindIonDeNovoTags": false,\n+ "deNovoCharge": 1,\n+ "tiesResolution": "mostAccurateMz",\n+ "id": 0\n+ },\n+ "sequenceMatchingParameters": {\n+ "sequenceMatchingType": "indistiguishableAminoAcids",\n+ "limitX": 0.25,\n+ "enzymaticTagsOnly": false,\n+ "maxPtmsPerTagPeptide": 3,\n+ "minAminoAcidScore": 30,\n+ "minTagLength": 3,\n+ "id": 0\n+ },\n+ "peptideVariantsParameters": {\n+ "variantType": "NO_VARIANT",\n+ "nVariants": 0,\n+ "nAaDeletions": 0,\n+ "nAaInsertions": 0,\n+ "nAaSubstitutions": 0,\n+ "nAaSwap": 0,\n+ "aaSubstitutionMatrix": {\n+ "name": "No Substitution",\n+ "description": "No substitution",\n+ "substitutions": {},\n+ "reverseMap": {},\n+ "id": 0\n+ },\n+ "fixedVariants": {},\n+ "id": 0\n+ },\n+ "geneParameters": {\n+ "autoUpdate": false,\n+ "useGeneMapping": false,\n+ "id": 0\n+ },\n+ "psmScoringParameters": {\n+ "spectrumMatchingScores": {\n+ "8": [\n+ 1\n+ ],\n+ "3": [\n+ 1\n+ ],\n+ "27": [\n+ 1\n+ ]\n+ },\n+ "defaultScores": [\n+ -1\n+ ],\n+ "minDecoysInBin": 10,\n+ "id": 0\n+ },\n+ "peptideAssumptionFilter": {\n+ "minPepLength": 8,\n+ "maxPepLength": 30,\n+ "maxMassDeviation": 10.0,\n+ "isPpm": true,\n+ "unknownModification": true,\n+ "minIsotopes": 0,\n+ "maxIsotopes": 1,\n+ "id": 0\n+ },\n+ "modificationLocalizationParameters": {\n+ "probabilisticScoreCalculation": true,\n+ "selectedProbabilisticScore": "PhosphoRS",\n+ "dScoreThreshold": 95.0,\n+ "probabilisticScoreThreshold": 95.0,\n+ "probabilisticScoreNeutralLosses": false,\n+ "sequenceMatchingParameters": {\n+ "sequenceMatchingType": "aminoAcid",\n+ "limitX": 0.25,\n+ "enzymaticTagsOnly": false,\n+ "maxPtmsPerTagPeptide": 3,\n+ "minAminoAcidScore": 30,\n+ "minTagLength": 3,\n+ "id": 0\n+ },\n+ "alignNonConfidentModifications": true,\n+ "id": 0\n+ },\n+ "proteinInferenceParameters": {\n+ "modificationRefinement": true,\n+ "simplifyProteinGroups": true,\n+ "simplifyGroupsEvidence": true,\n+ "simplifyGroupsConfidence": true,\n+ "simplifyGroupsEnzymaticity": true,\n+ "simplifyGroupsVariants": true,\n+ "confidenceThreshold": 0.05,\n+ "id": 0\n+ },\n+ "idValidationParameters": {\n+ "defaultProteinFDR": 1.0,\n+ "defaultPeptideFDR": 1.0,\n+ "defaultPsmFDR": 1.0,\n+ "validationQCPreferences": {\n+ "dbSize": false,\n+ "firstDecoy": true,\n+ "confidenceMargin": 1.0,\n+ "id": 0\n+ },\n+ "id": 0\n+ },\n+ "fractionParameters": {\n+ "proteinConfidenceMwPlots": 95.0,\n+ "fractionMolecularWeightRanges": {},\n+ "id": 0\n+ },\n+ "fastaParameters": {\n+ "targetDecoy": true,\n+ "decoyFlag": "-REVERSED",\n+ "decoySuffix": true,\n+ "targetDecoyFileNameTag": "_concatenated_target_decoy",\n+ "id": 0\n+ },\n+ "id": 0\n+}\n\\ No newline at end of file\n' |
| b |
| 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 |
| [ |
| b'@@ -0,0 +1,882 @@\n+{\n+ "marshallableParameterType": "identification_parameters",\n+ "version": "5.0.1",\n+ "name": "IdentificationParametersOutput",\n+ "description": "Fixed: Carbamidomethylation of C.\\nVariable: Oxidation of M.\\nFragment Tolerance: 0.5 Da.\\n",\n+ "defaultDescription": true,\n+ "searchParameters": {\n+ "version": "5.0.1",\n+ "precursorAccuracyType": "PPM",\n+ "fragmentAccuracyType": "DA",\n+ "precursorTolerance": 10.0,\n+ "fragmentIonMZTolerance": 0.5,\n+ "modificationParameters": {\n+ "fixedModifications": [\n+ "Carbamidomethylation of C"\n+ ],\n+ "variableModifications": [\n+ "Oxidation of M"\n+ ],\n+ "refinementVariableModifications": [],\n+ "refinementFixedModifications": [],\n+ "colors": {},\n+ "backUp": {\n+ "Carbamidomethylation of C": {\n+ "modificationType": "modaa",\n+ "name": "Carbamidomethylation of C",\n+ "shortName": "cmm",\n+ "neutralLosses": [],\n+ "reporterIons": [],\n+ "pattern": {\n+ "length": 0,\n+ "residueTargeted": {\n+ "0": [\n+ "C"\n+ ]\n+ },\n+ "id": 0\n+ },\n+ "atomChainAdded": {\n+ "atomChain": [\n+ {\n+ "atomSymbol": "C",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "C",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "N",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "O",\n+ "isotope": 0,\n+ "id": 0\n+ }\n+ ],\n+ "mass": -1.0,\n+ "id": 0\n+ },\n+ "atomChainRemoved": {\n+ "atomChain": [],\n+ "mass": -1.0,\n+ "id": 0\n+ },\n+ "unimodCvTerm": {\n+ "ontology": "UNIMOD",\n+ "accession": "UNIMOD:4",\n+ "name": "Carbamidomethyl",\n+ "id": 0\n+ },\n+ "psiModCvTerm": {\n+ "ontology": "MOD",\n+ "accession": "MOD:01060",\n+ "name": "S-carboxamidomethyl-L-cysteine",\n+ "id": 0\n+ },\n+ "category": "Common",\n+ "id": 0\n+ },\n+ "Oxidation of M": {\n+ "modificationType": "modaa",\n+ "name": "Oxidation of M",\n+ "shortName": "ox",\n+ "neutralLosses": [\n+ {\n+ "composition": {\n+ "atomChain": [\n+ {\n+ "atomSymbol": "C",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "O",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "S",\n+ '..b'isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "O",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "S",\n+ "isotope": 0,\n+ "id": 0\n+ }\n+ ],\n+ "mass": -1.0,\n+ "id": 0\n+ },\n+ "name": "CH4OS",\n+ "fixed": false,\n+ "id": 0\n+ }\n+ ],\n+ "neutralLossesAuto": true,\n+ "reporterIons": true,\n+ "relatedIons": true,\n+ "fragmentIonAccuracy": 10.0,\n+ "fragmentIonPpm": false,\n+ "showForwardIonDeNovoTags": false,\n+ "showRewindIonDeNovoTags": false,\n+ "deNovoCharge": 1,\n+ "tiesResolution": "mostAccurateMz",\n+ "id": 0\n+ },\n+ "sequenceMatchingParameters": {\n+ "sequenceMatchingType": "indistiguishableAminoAcids",\n+ "limitX": 0.25,\n+ "enzymaticTagsOnly": false,\n+ "maxPtmsPerTagPeptide": 3,\n+ "minAminoAcidScore": 30,\n+ "minTagLength": 3,\n+ "id": 0\n+ },\n+ "peptideVariantsParameters": {\n+ "variantType": "NO_VARIANT",\n+ "nVariants": 0,\n+ "nAaDeletions": 0,\n+ "nAaInsertions": 0,\n+ "nAaSubstitutions": 0,\n+ "nAaSwap": 0,\n+ "aaSubstitutionMatrix": {\n+ "name": "No Substitution",\n+ "description": "No substitution",\n+ "substitutions": {},\n+ "reverseMap": {},\n+ "id": 0\n+ },\n+ "fixedVariants": {},\n+ "id": 0\n+ },\n+ "geneParameters": {\n+ "autoUpdate": false,\n+ "useGeneMapping": false,\n+ "id": 0\n+ },\n+ "psmScoringParameters": {\n+ "spectrumMatchingScores": {\n+ "8": [\n+ 1\n+ ],\n+ "3": [\n+ 1\n+ ],\n+ "27": [\n+ 1\n+ ]\n+ },\n+ "defaultScores": [\n+ -1\n+ ],\n+ "minDecoysInBin": 10,\n+ "id": 0\n+ },\n+ "peptideAssumptionFilter": {\n+ "minPepLength": 8,\n+ "maxPepLength": 30,\n+ "maxMassDeviation": 10.0,\n+ "isPpm": true,\n+ "unknownModification": true,\n+ "minIsotopes": 0,\n+ "maxIsotopes": 1,\n+ "id": 0\n+ },\n+ "modificationLocalizationParameters": {\n+ "probabilisticScoreCalculation": true,\n+ "selectedProbabilisticScore": "PhosphoRS",\n+ "dScoreThreshold": 95.0,\n+ "probabilisticScoreThreshold": 95.0,\n+ "probabilisticScoreNeutralLosses": false,\n+ "sequenceMatchingParameters": {\n+ "sequenceMatchingType": "aminoAcid",\n+ "limitX": 0.25,\n+ "enzymaticTagsOnly": false,\n+ "maxPtmsPerTagPeptide": 3,\n+ "minAminoAcidScore": 30,\n+ "minTagLength": 3,\n+ "id": 0\n+ },\n+ "alignNonConfidentModifications": true,\n+ "id": 0\n+ },\n+ "proteinInferenceParameters": {\n+ "modificationRefinement": true,\n+ "simplifyProteinGroups": true,\n+ "simplifyGroupsEvidence": true,\n+ "simplifyGroupsConfidence": true,\n+ "simplifyGroupsEnzymaticity": true,\n+ "simplifyGroupsVariants": true,\n+ "confidenceThreshold": 0.05,\n+ "id": 0\n+ },\n+ "idValidationParameters": {\n+ "defaultProteinFDR": 1.0,\n+ "defaultPeptideFDR": 1.0,\n+ "defaultPsmFDR": 1.0,\n+ "validationQCPreferences": {\n+ "dbSize": false,\n+ "firstDecoy": true,\n+ "confidenceMargin": 1.0,\n+ "id": 0\n+ },\n+ "id": 0\n+ },\n+ "fractionParameters": {\n+ "proteinConfidenceMwPlots": 95.0,\n+ "fractionMolecularWeightRanges": {},\n+ "id": 0\n+ },\n+ "fastaParameters": {\n+ "targetDecoy": true,\n+ "decoyFlag": "-REVERSED",\n+ "decoySuffix": true,\n+ "targetDecoyFileNameTag": "_concatenated_target_decoy",\n+ "id": 0\n+ },\n+ "id": 0\n+}\n\\ No newline at end of file\n' |
| b |
| 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 |
| [ |
| b'@@ -0,0 +1,882 @@\n+{\n+ "marshallableParameterType": "identification_parameters",\n+ "version": "5.0.1",\n+ "name": "IdentificationParametersOutput",\n+ "description": "Fixed: Carbamidomethylation of C.\\nVariable: Oxidation of M.\\nPrecursor Tolerance: 100.0 ppm.\\nFragment Tolerance: 0.5 Da.\\nCharge: 1-3.\\n",\n+ "defaultDescription": true,\n+ "searchParameters": {\n+ "version": "5.0.1",\n+ "precursorAccuracyType": "PPM",\n+ "fragmentAccuracyType": "DA",\n+ "precursorTolerance": 100.0,\n+ "fragmentIonMZTolerance": 0.5,\n+ "modificationParameters": {\n+ "fixedModifications": [\n+ "Carbamidomethylation of C"\n+ ],\n+ "variableModifications": [\n+ "Oxidation of M"\n+ ],\n+ "refinementVariableModifications": [],\n+ "refinementFixedModifications": [],\n+ "colors": {},\n+ "backUp": {\n+ "Carbamidomethylation of C": {\n+ "modificationType": "modaa",\n+ "name": "Carbamidomethylation of C",\n+ "shortName": "cmm",\n+ "neutralLosses": [],\n+ "reporterIons": [],\n+ "pattern": {\n+ "length": 0,\n+ "residueTargeted": {\n+ "0": [\n+ "C"\n+ ]\n+ },\n+ "id": 0\n+ },\n+ "atomChainAdded": {\n+ "atomChain": [\n+ {\n+ "atomSymbol": "C",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "C",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "N",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "O",\n+ "isotope": 0,\n+ "id": 0\n+ }\n+ ],\n+ "mass": -1.0,\n+ "id": 0\n+ },\n+ "atomChainRemoved": {\n+ "atomChain": [],\n+ "mass": -1.0,\n+ "id": 0\n+ },\n+ "unimodCvTerm": {\n+ "ontology": "UNIMOD",\n+ "accession": "UNIMOD:4",\n+ "name": "Carbamidomethyl",\n+ "id": 0\n+ },\n+ "psiModCvTerm": {\n+ "ontology": "MOD",\n+ "accession": "MOD:01060",\n+ "name": "S-carboxamidomethyl-L-cysteine",\n+ "id": 0\n+ },\n+ "category": "Common",\n+ "id": 0\n+ },\n+ "Oxidation of M": {\n+ "modificationType": "modaa",\n+ "name": "Oxidation of M",\n+ "shortName": "ox",\n+ "neutralLosses": [\n+ {\n+ "composition": {\n+ "atomChain": [\n+ {\n+ "atomSymbol": "C",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "O",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ '..b'isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "H",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "O",\n+ "isotope": 0,\n+ "id": 0\n+ },\n+ {\n+ "atomSymbol": "S",\n+ "isotope": 0,\n+ "id": 0\n+ }\n+ ],\n+ "mass": -1.0,\n+ "id": 0\n+ },\n+ "name": "CH4OS",\n+ "fixed": false,\n+ "id": 0\n+ }\n+ ],\n+ "neutralLossesAuto": true,\n+ "reporterIons": true,\n+ "relatedIons": true,\n+ "fragmentIonAccuracy": 10.0,\n+ "fragmentIonPpm": false,\n+ "showForwardIonDeNovoTags": false,\n+ "showRewindIonDeNovoTags": false,\n+ "deNovoCharge": 1,\n+ "tiesResolution": "mostAccurateMz",\n+ "id": 0\n+ },\n+ "sequenceMatchingParameters": {\n+ "sequenceMatchingType": "indistiguishableAminoAcids",\n+ "limitX": 0.25,\n+ "enzymaticTagsOnly": false,\n+ "maxPtmsPerTagPeptide": 3,\n+ "minAminoAcidScore": 30,\n+ "minTagLength": 3,\n+ "id": 0\n+ },\n+ "peptideVariantsParameters": {\n+ "variantType": "NO_VARIANT",\n+ "nVariants": 0,\n+ "nAaDeletions": 0,\n+ "nAaInsertions": 0,\n+ "nAaSubstitutions": 0,\n+ "nAaSwap": 0,\n+ "aaSubstitutionMatrix": {\n+ "name": "No Substitution",\n+ "description": "No substitution",\n+ "substitutions": {},\n+ "reverseMap": {},\n+ "id": 0\n+ },\n+ "fixedVariants": {},\n+ "id": 0\n+ },\n+ "geneParameters": {\n+ "autoUpdate": false,\n+ "useGeneMapping": false,\n+ "id": 0\n+ },\n+ "psmScoringParameters": {\n+ "spectrumMatchingScores": {\n+ "8": [\n+ 1\n+ ],\n+ "3": [\n+ 1\n+ ],\n+ "27": [\n+ 1\n+ ]\n+ },\n+ "defaultScores": [\n+ -1\n+ ],\n+ "minDecoysInBin": 10,\n+ "id": 0\n+ },\n+ "peptideAssumptionFilter": {\n+ "minPepLength": 8,\n+ "maxPepLength": 30,\n+ "maxMassDeviation": 10.0,\n+ "isPpm": true,\n+ "unknownModification": true,\n+ "minIsotopes": 0,\n+ "maxIsotopes": 1,\n+ "id": 0\n+ },\n+ "modificationLocalizationParameters": {\n+ "probabilisticScoreCalculation": true,\n+ "selectedProbabilisticScore": "PhosphoRS",\n+ "dScoreThreshold": 95.0,\n+ "probabilisticScoreThreshold": 95.0,\n+ "probabilisticScoreNeutralLosses": false,\n+ "sequenceMatchingParameters": {\n+ "sequenceMatchingType": "aminoAcid",\n+ "limitX": 0.25,\n+ "enzymaticTagsOnly": false,\n+ "maxPtmsPerTagPeptide": 3,\n+ "minAminoAcidScore": 30,\n+ "minTagLength": 3,\n+ "id": 0\n+ },\n+ "alignNonConfidentModifications": true,\n+ "id": 0\n+ },\n+ "proteinInferenceParameters": {\n+ "modificationRefinement": true,\n+ "simplifyProteinGroups": true,\n+ "simplifyGroupsEvidence": true,\n+ "simplifyGroupsConfidence": true,\n+ "simplifyGroupsEnzymaticity": true,\n+ "simplifyGroupsVariants": true,\n+ "confidenceThreshold": 0.05,\n+ "id": 0\n+ },\n+ "idValidationParameters": {\n+ "defaultProteinFDR": 1.0,\n+ "defaultPeptideFDR": 1.0,\n+ "defaultPsmFDR": 1.0,\n+ "validationQCPreferences": {\n+ "dbSize": false,\n+ "firstDecoy": true,\n+ "confidenceMargin": 1.0,\n+ "id": 0\n+ },\n+ "id": 0\n+ },\n+ "fractionParameters": {\n+ "proteinConfidenceMwPlots": 95.0,\n+ "fractionMolecularWeightRanges": {},\n+ "id": 0\n+ },\n+ "fastaParameters": {\n+ "targetDecoy": true,\n+ "decoyFlag": "-REVERSED",\n+ "decoySuffix": true,\n+ "targetDecoyFileNameTag": "_concatenated_target_decoy",\n+ "id": 0\n+ },\n+ "id": 0\n+}\n\\ No newline at end of file\n' |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| b'@@ -0,0 +1,48 @@\n+>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\n+LKSSFESSFSIKSRDVTFGNSMNITMVPPELEFFKDNRHKEKSEMQDLNTRLESYLSVGKDDSDANLKLMQELEEIKNGIKTETNNIKATFEAELGQLKNLLDDIDHDKNQVIVIGDNNDEMYKDLEQRIKNYNDMEMIHLSKIRQLDNLLSNYGLKMNQLQKKIGFLCEEKDRDIESINKLRADIDVAKNDLSNEILLRTDAQNRCQSLEEDIEFTKEVHQRELSNMIALADYDPVSQSMDWWNDEFARCIKEIQDEYEDRLNNIQYDMDSHYNSKIQDVETTILQSSAKSEMLDQCSMLENSNAEIEDQTSELEKKNAMLKEQNDLLNRGIREIQSQFETLITEKQSEMLEIRKHFEQSLADLQAIVDDNLSLQMEIMSYKKLLECEELRVGIYPESNANENQGDQGQRQNEQITEPITETIPKRKKPERKISYQRSSKGPLTISECKSDGSYILIENMDQYDGQNLGGWRLVQNVDGMEEYDYTFSRYYLGPGESVKIWAENAGPKGVNDLVWDDLKCLGIGEKVITSLMNQKGKEKSSYTQKAIYKV\n+>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\n+VKYIAKQTYSSKEKGKQNMLSTIVKEGIGLCKLDDWVLDNVGKPGANEAWIKVSEGPGLYYRSFTYDYEEMGDVNQVLRWGGLNQGDYQDMNEILIYSGDSKCESITLPGKSSRQYSIKREPKKRKPITETIPETIQENQRQGQDGQNENANSEPYIGVRLEECELLKKYSMIEMQLSLNDDVIAQLDALSQEFHKRIELMESQKETILTEFQSQIERIGRNLLDNQEKLMANKKELESTQDEIEANSNELMSCQDLMESKASSQLITTEVDQIKSNYHSDMDYQINNLRDEYEDQIEKICRAFEDNWWDMSQSVPDYDALAIMNSLERQHVEKTFEIDEELSQCRNQADTRLLIENSLDNKAVDIDARLKNISEIDRDKEECLFGIKKQLQNMKLGYNSLLNDLQRIKSLHIMEMDNYNKIRQELDKYMEDNNDGIVIVQNKDHDIDDLLNKLQGLEAEFTAKINNTETKIGNKIEELEQMLKLNADSDDKGVSLYSELRTNLDQMESKEKHRNDKFFELEPPVMTINMSNGFTVDRSKISFSSEFSSKL\n+>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\n+DDNYDSLQYSFPKSDHQRKTTYQRSAKGPITITRVQPDGSYIEIENTNIAVNEDISGWKMVQCTDDKIYEYIFDDHVLNGGTCVKIWANGLSGKEENDLVWIDRTCLTTGSVVTTTLMDYNGNEKATFTQ\n+>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\n+QTFTAKENGNYDMLTTTVVSGTTLCTRDIWVLDNEEKGSLGNAWIKVCTGGNLVHDDFIYEYIKDDTCQVMKWGSIDENVAINTNEIEIYSGDPQVRTITIPGKASRQYTTKRQHDSKPFSYQLSDYNDD\n+>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\n+KELEDINEDNLGRLRRQDEDVSNYEAQNASLRRKCDNLQADKDRDRNNVEKLKGEVTSLRNDLMMETVSRIDSQNKCQTLREELEFLKDIHSQELKELSPTLGKDPFAKSKEWWSSEFSNCIREIQEEYDNRLDSIKTDMDNYYTLKVQEIQTGAAR\n+>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\n+RAAGTQIEQVKLTYYNDMDTKISDLRNDYEEQIERICNSFESSWWEKSKAFPDKGLTPSLEKLEQSHIDKLFELEERLTQCKNQSDIRSVTEMMLDNRLSTVEGKLKEVNNRDRDKDAQLNDCKRRLSANQAEYNSVDEDQRRLRGLNDENIDELEK\n+>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\n+METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT\n+>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\n+TVVKTSLNAKLADKEDYLSFVSNRNVPGWEDVTAIIDGKKAMKQYNKAWIKISQEGELVVPDKFLFDIKHEPSISTASILRDLKWGKMNVSTKSRGSSTNELTVYQGESEVEGISIVSKSSRQITLRGTLTSTSASDGALGSGSGSGSGGGGGGGGGGSGFELINALNDGAESRFGGINETIYGTSIRNEEGELLKRYAAIELELSLKADMLMQLEEIMSEMEVHLKNVETTRLDKENELDENSRQLQNTITIIEMKMRELQSELEKIRMDKQVSVMGTSKESKTHVAAVPEAHASQRIQSLQSEYRASMEDSIDALRQDYEERLEKMCNSMENNWAASVNTGTDDEKSLMAKYEKIEADTVSRLFELEEELNGVKQQLFIRQQTEDKLDARTAQLQTNVENYKARWHAVQKELEDLKKHLMSCEAE'..b'LMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF\n+>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\n+FVVKITLTAKEVGNEDYLTIISNRNVQGWDAVSSIIDDPKIEPDKEFNKAWVRINQQADLSTDRNIIYEFSLEQLSNTRIFERKIKWGKLNQLRKMRTTSTNDLTVYRGTNDVEAISIVGKSSRQMTVRGSEGMSSSAEFSAGSRELINALADETQGRYGGVMQTMSGISLRNEEVELLKRYAAIELELSLKADMLLQLEKIVGELETNLKQVESVRLTKENDLEATTSDLESTLLHVQSKLKDIQSQLDMMHSDKDTIQSRLRRNEESAQASEANGKTAGLRIENLQVQYKSELDASLLNLQNDYEDRIERMCKSLENNWYERMQPVNDEKMLMAKYEKIEADTVSRLFNLEEELAQARTSEALRQCTEEQLDIRLGQLQTDVHAYKAKWDALQKELEQVKRKLMENDAIRRAIDDNLTDINNQLQDNVDNSHRLQARLDELEDELTNIRVKLNGNDNNADDLLKKAENIEIQYMQKLPEPDFDKKSKNLADRLAKNEAELFRAQEIFNALRENLDQLEKKEGERKLKMSAVGKHSINGLVGAQLHGGLGLGSSMSSRSRQMTSMATGPSLSVRNIVINKSQTFPKYNVSQRSTTVTQRTEVGQKEM\n+>generic|cds.comp55448_c0_seq1|m.24261 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 96.04 EValue:0.0\n+MRRIKKKITLDVRVTELIDQLERQQKELEESRTYHQIDQEQIARQNQQLADLEGEISMLRRSIESLEKEKMRQSNILAKMNDELEKLRMDLNNETINHLDAENRRQTLEEELEFQKDVHAQELKELAALAYRDTTAENREFWRNELAQAIRDIQQEYDAKCDQMRGDIEAYYNLKVQEFRTGATKQNMEVTRNKEENTKLRSNMNEVRNRLADLEARNAQLERTNQDLLRDLEEKDRQNELESCQYKEEITKLRGEMESILKELQDLMDIKLSLELEIAAYRKLLEGEESRVGMKQIVEQVVGARPNEAEVLSSILTRSEGGYEATGDSQISMKMMRGELAAKTTYQRTSKGPVSIKEADSQGQFIALETKKEENITGWKIVRKVDDNMVYSYEIPNVVLKTGTVIKIWSKSHQAQARGDDIVSRENDTWGTGSNVVTILQNEKGEEKANYTQNTVYQ\n+>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\n+QYVTNQTYNAKEEGKENQLITVVNSGTGWTDNERSVIDDGRAQAQHSKSWIKIVTGTKLVVNPIEYSYVMNDDVKRVIKWGTINEEKKTELAIFQGQSDAEKISVPGKSTRQYTTKAALEGRMMKMSIQSDGTAEYGGESRTLISSLVEAENPRAGVVQEVIQKMGVRSEEGELLKRYAAIELELSLKIDMLDQLEKLISEMEGRLKTIEEKYQCSELENQRDKEELDRLLDQNTRELQANRAELDALRNRVENMNSRLKTNEEKNRTVEMNQKTAGTRFEQVKLNYYAEIDGRMQDCKADYEQQIDRIAQALENRWFERNEATTDRYALAALEKLEQAHVDKQFELEEELTQRRNEADLHNITENNLDMRLKELEDNMKALINSQRMKEKELSEISRRLMSIEGELDALQQNQRAIQEQDIQHYTRSEELEKQQRELQDILETVRVDLTIKKKIRRM\n+>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\n+MSGGFSYSAKIHPRTGYVSRTSQSPYRSSMGSNAAFTRSYEFNYGATAMPGAYANISSTGVNHVKANREREKQDMRDLNERFANYIEKVRFLEAQNKKLAGELEELKSKWGKETSAIKEMYETELEEARKLIDATNKEKNYLGRESN\n+>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\n+NSERGLYNKEKNTADILKRAEELETEYMEKIASTEKGWKSKLEELEGALKKNQAELFRVKEIYNAFRENLDRMDQKERERNAKVHNVGTSSINAYAGPMATAGYNFEYSRTFAANSGMSSRYPSQSTRSVYGTRPHIKASYSFGGSM\n+>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\n+FKDTCIRDKTDMKGLNERLSEFIEVARYNAILAKKLEKTIKRFHSQEIPEDVERIYEATIKKLRKLLVVFENERDNERAKNLKLQTECAKLKESLEDLKAKEIENRDRLISKFKILEDLQSKAIRIEKNIEIVAEENVLKNNKIEKLKKHFENLKSKITSERRNRSTHKESYDEVKEDFGIFKELKNQQLSSVRFPKYKDSIKYLRKQWSNEFSKCIKELQNEYESRVSSVKEELESNYCTKTEEIQNYVLKSNYESDFLKNRNLVAEESMNMLKNKFKEAKKENVLLNHEKEELEIEFNKSKNEYDHLAEEKNNEILNFKEYAEKILIQLTEILEINNHLQFEIEYYKTVITSGETKIDFDFDGLDDECMTSINSELP\n+>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\n+PLESNISTMCEDDLGDFDFDIKTEGSTIVTKYYEIEFQLHNNIELIETLQILIKEAYEKFNLIENNKEEALHDYENKSKNFEIELEEKEHNLLVNEKKAEKFKNKLMNMSEEAVLNRNKLFDSEYNSKLVYNQIEETKTCYNSELEEKVSSVRSEYENQLEKICKSFENSWQKRLYKISDKYKPFRVSSLQQNKLEKFIGFDEKVEDYSEKHTSRNRRESTIKSKLNEFHKKLKEIKNNKLVNEEAVIEINKEIRIAKSQLDELIKFKSILRDRNEIEKAKLDELSEKLKACETQLKLNKARENDRENEFVVLLKRLKKITAEYIREVDEPIEQSHFRKITKELKKALIANYRAVEIFESLRENLGKMDTKDRICTDKF\n' |
| b |
| diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptide_shaker_modifications_result1.cpsx |
| b |
| Binary file test-data/peptide_shaker_modifications_result1.cpsx has changed |
| b |
| 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 |
| b |
| 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 |
| [ |
| b'@@ -1,43 +0,0 @@\n-\tProtein(s)\tSequence\tAAs Before\tAAs After\tPosition\tModified Sequence\tVariable Modifications\tFixed Modifications\tSpectrum File\tSpectrum Title\tSpectrum Scan Number\tRT\tm/z\tMeasured Charge\tIdentification Charge\tTheoretical Mass\tIsotope Number\tPrecursor m/z Error [ppm]\tDecoy\tLocalization Confidence\tProbabilistic PTM score\tD-score\tConfidence [%]\tValidation\n-1\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tLHVEMESMIEELQMLMDAK\tNK; NK\tLS; LS\t403; 403\tNH2-LHVEMESMIEELQMLMDAK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 1198, +MSn(1139.0413), 115.6 min\t\t-1.0\t1139.04127\t2+\t2+\t2276.0560840995904\t0\t5.225020941769318\t0\t\t\t\t100.0\tDoubtful\n-2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tNLLLDANKENGELK\tAK; AK\tIS; IS\t147; 147\tNH2-NLLLDANKENGELK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 207, MSn(785.9179), 35.7 min\t\t-1.0\t785.91791\t2+\t2+\t1569.8362356486903\t0\t-9.522902824571501\t0\t\t\t\t100.0\tDoubtful\n-3\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tSLQAENEQLR\tVR; VR\tLK; LK\t110; 110\tNH2-SLQAENEQLR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 39, MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942144781802\t0\t2.063410823544894\t0\t\t\t\t100.0\tDoubtful\n-4\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tEFDVEPLKEAYQAEIDEAK\tRR; RR\tNL; NL\t128; 128\tNH2-EFDVEPLKEAYQAEIDEAK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 736, MSn(742.0258), 75.1 min\t\t-1.0\t742.02585\t3+\t3+\t2223.0583092202605\t0\t-1.1628605151025897\t0\t\t\t\t100.0\tDoubtful\n-5\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tMEIITITNQLQR\tMK; MK\tSN; SN\t373; 373\tNH2-MEIITITNQLQR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 636, +MSn(730.3981), 66.9 min\t\t-1.0\t730.39814\t2+\t2+\t1458.7864490053003\t0\t-3.2324313291878943\t0\t\t\t\t100.0\tDoubtful\n-6\tcds.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\tEIRDEYDNQLNLLSADLESK\tMR; MR\tYQ; YQ\t298; 298\tNH2-EIRDEYDNQLNLLSADLESK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 748, MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.14449845571\t0\t6.2066377342036665\t0\t\t\t\t100.0\tDoubtful\n-7\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tYESQLSQIR\tAR; AR\tQS; QS\t323; 323\tNH2-YESQLSQIR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 67, +MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669371011802\t0\t6.998127983906467\t0\t\t\t\t100.0\tDoubtful\n-8\tcds.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'..b'PEHK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 75, +MSn(641.8547), 26.7 min\t\t-1.0\t641.85466\t2+\t2+\t1281.6928658902905\t0\t1.481004205034201\t0\t\t\t\t100.0\tDoubtful\n-35\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tYESQLSQIR\tAR; AR\tQS; QS\t323; 323\tNH2-YESQLSQIR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 67, MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669371011802\t0\t6.998127983906467\t0\t\t\t\t100.0\tDoubtful\n-36\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tMEIITITNQLQR\tMK; MK\tSN; SN\t373; 373\tNH2-MEIITITNQLQR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 636, MSn(730.3981), 66.9 min\t\t-1.0\t730.39814\t2+\t2+\t1458.7864490053003\t0\t-3.2324313291878943\t0\t\t\t\t100.0\tDoubtful\n-37\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tINEDRIDELQDKVNK\tAR; AR\tLI; LI\t179; 179\tNH2-INEDRIDELQDKVNK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 81, +MSn(610.3171), 27.0 min\t\t-1.0\t610.31708\t3+\t3+\t1827.9326552146706\t0\t-1.7720894394949223\t0\t\t\t\t100.0\tDoubtful\n-38\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tEFDVEPLKEAYQAEIDEAK\tRR; RR\tNL; NL\t128; 128\tNH2-EFDVEPLKEAYQAEIDEAK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 736, +MSn(742.0258), 75.1 min\t\t-1.0\t742.02585\t3+\t3+\t2223.0583092202605\t0\t-1.1628605151025897\t0\t\t\t\t100.0\tDoubtful\n-39\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tSLQAENEQLR\tVR; VR\tLK; LK\t110; 110\tNH2-SLQAENEQLR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 39, +MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942144781802\t0\t2.063410823544894\t0\t\t\t\t100.0\tDoubtful\n-40\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tINEDRIDELQDKVNK\tAR; AR\tLI; LI\t179; 179\tNH2-INEDRIDELQDKVNK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 81, MSn(610.3171), 27.0 min\t\t-1.0\t610.31708\t3+\t3+\t1827.9326552146706\t0\t-1.7720894394949223\t0\t\t\t\t100.0\tDoubtful\n-41\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISTGYITENIGGFR\tNR; NR\tSE; SE\t442; 442\tNH2-ISTGYITENIGGFR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 588, MSn(764.3961), 63.5 min\t\t-1.0\t764.39611\t2+\t2+\t1526.7729071161402\t0\t3.113546101111509\t0\t\t\t\t100.0\tDoubtful\n-42\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISTGYITENIGGFR\tNR; NR\tSE; SE\t442; 442\tNH2-ISTGYITENIGGFR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 588, +MSn(764.3961), 63.5 min\t\t-1.0\t764.39611\t2+\t2+\t1526.7729071161402\t0\t3.113546101111509\t0\t\t\t\t100.0\tDoubtful\n' |
| b |
| 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 |
| [ |
| b'@@ -1,79 +0,0 @@\n-\tMain Accession\tDescription\tMW [kDa]\tPossible Coverage [%]\tCoverage [%]\tSpectrum Counting NSAF\tConfidently Localized Modification Sites\t# Confidently Localized Modification Sites\tAmbiguously Localized Modification Sites\t#Ambiguously Localized Modification Sites\tProtein Inference\tSecondary Accessions\tProtein Group\t#Validated Peptides\t#Peptides\t#Unique\t#Validated PSMs\t#PSMs\tConfidence [%]\tDecoy\tValidation\n-1\tcds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91\t\t69.96963713242043\t100.0\t3.25\t0.0032520325203252032\t\t\t\t\tRelated Proteins\tcds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92\tcds.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\t1\t1\t1\t2\t2\t100.0\t0\tDoubtful\n-\tProtein(s)\tSequence\tAAs Before\tAAs After\tVariable Modifications\tFixed Modifications\tLocalization Confidence\t#Validated PSMs\t#PSMs\tConfidence [%]\tDecoy\tValidation\n-1.1\tcds.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\tEIRDEYDNQLNLLSADLESK\tMR; MR\tYQ; YQ\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-\tProtein(s)\tSequence\tModified Sequence\tVariable Modifications\tFixed Modifications\tSpectrum File\tSpectrum Title\tSpectrum Scan Number\tRT\tm/z\tMeasured Charge\tIdentification Charge\tTheoretical Mass\tIsotope Number\tPrecursor m/z Error [ppm]\tDecoy\tLocalization Confidence\tProbabilistic PTM score\tD-score\tConfidence [%]\tValidation\n-1.1.1\tcds.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\tEIRDEYDNQLNLLSADLESK\tNH2-EIRDEYDNQLNLLSADLESK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 748, +MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.14449845571\t0\t6.2066377342036665\t0\t\t\t\t100.0\tDoubtful\n-1.1.2\tcds.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\tEIRDEYDNQLNLLSADLESK\tNH2-EIRDEYDNQLNLLSADLESK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 748, MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.14449845571\t0\t6.2066377342036665\t0\t\t\t\t100.0\tDoubtful\n-2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67\t\t69.88215380565927\t92.52\t37.58\t0.017651472642866785\t\t\t\t\tRelated Proteins\tcds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\t15\t15\t15\t40\t40\t100.0\t0\tDoubtful\n-\tProtein(s)\tSequence\tAAs Before\tAAs After\tVariable Modifications\tFixed Modifications\tLocalization Confidence\t#Validated PSMs\t#PSMs\tConfidence [%]\tDecoy\tValidation\n-2.1\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tLHVEMESMIEELQMLMDAK\tNK; NK\tLS; LS\t\t\t\t4\t4\t100.0\t0\tDoubtful\n-\tProtein(s)\tSequence\tM'..b'Value:4.0e-10\tSVISIGEVESEGQYVTLENTSSGR\tNH2-SVISIGEVESEGQYVTLENTSSGR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 758, +MSn(847.7508), 76.8 min\t\t-1.0\t847.75082\t3+\t3+\t2540.224205328391\t0\t2.5264056584343257\t0\t\t\t\t100.0\tDoubtful\n-2.14.2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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\tSVISIGEVESEGQYVTLENTSSGR\tNH2-SVISIGEVESEGQYVTLENTSSGR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 758, MSn(847.7508), 76.8 min\t\t-1.0\t847.75082\t3+\t3+\t2540.224205328391\t0\t2.5264056584343257\t0\t\t\t\t100.0\tDoubtful\n-2.15\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; 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\tLISATSISPEHK\tDR; DR; DR\tID; ID; ID\t\t\t\t4\t4\t100.0\t0\tDoubtful\n-\tProtein(s)\tSequence\tModified Sequence\tVariable Modifications\tFixed Modifications\tSpectrum File\tSpectrum Title\tSpectrum Scan Number\tRT\tm/z\tMeasured Charge\tIdentification Charge\tTheoretical Mass\tIsotope Number\tPrecursor m/z Error [ppm]\tDecoy\tLocalization Confidence\tProbabilistic PTM score\tD-score\tConfidence [%]\tValidation\n-2.15.1\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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\tLISATSISPEHK\tNH2-LISATSISPEHK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 75, +MSn(641.8547), 26.7 min\t\t-1.0\t641.85466\t2+\t2+\t1281.6928658902905\t0\t1.481004205034201\t0\t\t\t\t100.0\tDoubtful\n-2.15.2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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\tLISATSISPEHK\tNH2-LISATSISPEHK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 72, +MSn(428.2391), 26.6 min\t\t-1.0\t428.23909\t3+\t3+\t1281.6928658902905\t0\t2.0041097707959827\t0\t\t\t\t100.0\tDoubtful\n-2.15.3\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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\tLISATSISPEHK\tNH2-LISATSISPEHK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 75, MSn(641.8547), 26.7 min\t\t-1.0\t641.85466\t2+\t2+\t1281.6928658902905\t0\t1.481004205034201\t0\t\t\t\t100.0\tDoubtful\n-2.15.4\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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\tLISATSISPEHK\tNH2-LISATSISPEHK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 72, MSn(428.2391), 26.6 min\t\t-1.0\t428.23909\t3+\t3+\t1281.6928658902905\t0\t2.0041097707959827\t0\t\t\t\t100.0\tDoubtful\n' |
| b |
| 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 |
| [ |
| b'@@ -1,17 +0,0 @@\n-\tProtein(s)\tProtein Group(s)\t#Validated Protein Group(s)\tUnique Database\tSequence\tModified Sequence\tPosition\tAAs Before\tAAs After\tVariable Modifications\tFixed Modifications\tLocalization Confidence\t#Validated PSMs\t#PSMs\tConfidence [%]\tValidation\n-1\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; 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\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tSVISIGEVESEGQYVTLENTSSGR\tNH2-SVISIGEVESEGQYVTLENTSSGR-COOH\t511; 504; 29\tSK; SK; SK\tSK; SK; SK\t\t\t\t2\t2\t100.0\tDoubtful\n-2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tYESQLSQIR\tNH2-YESQLSQIR-COOH\t323; 323\tAR; AR\tQS; QS\t\t\t\t2\t2\t100.0\tDoubtful\n-3\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tSHVVGAGLGGGSMGSMNQSMSLHGGR\tNH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH\t37; 37\tRR; RR\tAS; AS\t\t\t\t2\t2\t100.0\tDoubtful\n-4\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tEFDVEPLKEAYQAEIDEAK\tNH2-EFDVEPLKEAYQAEIDEAK-COOH\t128; 128\tRR; RR\tNL; NL\t\t\t\t2\t2\t100.0\tDoubtful\n-5\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tISITTYEEEIEDLHATAR\tNH2-ISITTYEEEIEDLHATAR-COOH\t161; 161\tLK; LK\tIN; IN\t\t\t\t2\t2\t100.0\tDoubtful\n-6\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament pro'..b'\n-11\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tSLQAENEQLR\tNH2-SLQAENEQLR-COOH\t110; 110\tVR; VR\tLK; LK\t\t\t\t2\t2\t100.0\tDoubtful\n-12\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; 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\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tKGDIIATVDEWGPVNR\tNH2-KGDIIATVDEWGPVNR-COOH\t590; 583; 108\tAK; AK; AK\tNS; NS; NS\t\t\t\t2\t2\t100.0\tDoubtful\n-13\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tMEIITITNQLQR\tNH2-MEIITITNQLQR-COOH\t373; 373\tMK; MK\tSN; SN\t\t\t\t2\t2\t100.0\tDoubtful\n-14\tcds.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\tcds.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)\t1\t1\tEIRDEYDNQLNLLSADLESK\tNH2-EIRDEYDNQLNLLSADLESK-COOH\t298; 298\tMR; MR\tYQ; YQ\t\t\t\t2\t2\t100.0\tDoubtful\n-15\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tVGNLEEELEFLR\tNH2-VGNLEEELEFLR-COOH\t254; 254\tQK; QK\tSV; SV\t\t\t\t4\t4\t100.0\tDoubtful\n-16\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tINEDRIDELQDKVNK\tNH2-INEDRIDELQDKVNK-COOH\t179; 179\tAR; AR\tLI; LI\t\t\t\t2\t2\t100.0\tDoubtful\n' |
| b |
| 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 |
| [ |
| b'@@ -1,17 +0,0 @@\n-\tProtein(s)\tProtein Group(s)\t#Validated Protein Group(s)\tUnique Database\tSequence\tModified Sequence\tPosition\tAAs Before\tAAs After\tVariable Modifications\tFixed Modifications\tLocalization Confidence\t#Validated PSMs\t#PSMs\tConfidence [%]\tValidation\n-1\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; 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\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tSVISIGEVESEGQYVTLENTSSGR\tNH2-SVISIGEVESEGQYVTLENTSSGR-COOH\t511; 504; 29\tSK; SK; SK\tSK; SK; SK\t\t\t\t2\t2\t100.0\tDoubtful\n-2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tYESQLSQIR\tNH2-YESQLSQIR-COOH\t323; 323\tAR; AR\tQS; QS\t\t\t\t2\t2\t100.0\tDoubtful\n-3\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tSHVVGAGLGGGSMGSMNQSMSLHGGR\tNH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH\t37; 37\tRR; RR\tAS; AS\t\t\t\t2\t2\t100.0\tDoubtful\n-4\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tEFDVEPLKEAYQAEIDEAK\tNH2-EFDVEPLKEAYQAEIDEAK-COOH\t128; 128\tRR; RR\tNL; NL\t\t\t\t2\t2\t100.0\tDoubtful\n-5\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tISITTYEEEIEDLHATAR\tNH2-ISITTYEEEIEDLHATAR-COOH\t161; 161\tLK; LK\tIN; IN\t\t\t\t2\t2\t100.0\tDoubtful\n-6\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament pro'..b'\n-11\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tSLQAENEQLR\tNH2-SLQAENEQLR-COOH\t110; 110\tVR; VR\tLK; LK\t\t\t\t2\t2\t100.0\tDoubtful\n-12\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; 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\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tKGDIIATVDEWGPVNR\tNH2-KGDIIATVDEWGPVNR-COOH\t590; 583; 108\tAK; AK; AK\tNS; NS; NS\t\t\t\t2\t2\t100.0\tDoubtful\n-13\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tMEIITITNQLQR\tNH2-MEIITITNQLQR-COOH\t373; 373\tMK; MK\tSN; SN\t\t\t\t2\t2\t100.0\tDoubtful\n-14\tcds.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\tcds.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)\t1\t1\tEIRDEYDNQLNLLSADLESK\tNH2-EIRDEYDNQLNLLSADLESK-COOH\t298; 298\tMR; MR\tYQ; YQ\t\t\t\t2\t2\t100.0\tDoubtful\n-15\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tVGNLEEELEFLR\tNH2-VGNLEEELEFLR-COOH\t254; 254\tQK; QK\tSV; SV\t\t\t\t4\t4\t100.0\tDoubtful\n-16\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tINEDRIDELQDKVNK\tNH2-INEDRIDELQDKVNK-COOH\t179; 179\tAR; AR\tLI; LI\t\t\t\t2\t2\t100.0\tDoubtful\n' |
| b |
| 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 |
| [ |
| b'@@ -1,17 +0,0 @@\n-\tProtein(s)\tProtein Group(s)\t#Validated Protein Group(s)\tUnique Database\tSequence\tModified Sequence\tAAs Before\tAAs After\tVariable Modifications\tFixed Modifications\tLocalization Confidence\tConfident Phosphosites\t#Confident Phosphosites\tAmbiguous Phosphosites\t#Ambiguous Phosphosites\t#Validated PSMs\t#PSMs\tConfidence [%]\tValidation\n-1\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; 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\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tSVISIGEVESEGQYVTLENTSSGR\tNH2-SVISIGEVESEGQYVTLENTSSGR-COOH\tSK; SK; SK\tSK; SK; SK\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n-2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tYESQLSQIR\tNH2-YESQLSQIR-COOH\tAR; AR\tQS; QS\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n-3\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tSHVVGAGLGGGSMGSMNQSMSLHGGR\tNH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH\tRR; RR\tAS; AS\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n-4\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tEFDVEPLKEAYQAEIDEAK\tNH2-EFDVEPLKEAYQAEIDEAK-COOH\tRR; RR\tNL; NL\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n-5\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tISITTYEEEIEDLHATAR\tNH2-ISITTYEEEIEDLHATAR-COOH\tLK; LK\tIN; IN\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n-6\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp4'..b'AK\tIS; IS\t\t\t\t\t\t\t\t4\t4\t100.0\tDoubtful\n-11\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tSLQAENEQLR\tNH2-SLQAENEQLR-COOH\tVR; VR\tLK; LK\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n-12\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; 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\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tKGDIIATVDEWGPVNR\tNH2-KGDIIATVDEWGPVNR-COOH\tAK; AK; AK\tNS; NS; NS\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n-13\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tMEIITITNQLQR\tNH2-MEIITITNQLQR-COOH\tMK; MK\tSN; SN\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n-14\tcds.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\tcds.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)\t1\t1\tEIRDEYDNQLNLLSADLESK\tNH2-EIRDEYDNQLNLLSADLESK-COOH\tMR; MR\tYQ; YQ\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n-15\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tVGNLEEELEFLR\tNH2-VGNLEEELEFLR-COOH\tQK; QK\tSV; SV\t\t\t\t\t\t\t\t4\t4\t100.0\tDoubtful\n-16\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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)\t1\t1\tINEDRIDELQDKVNK\tNH2-INEDRIDELQDKVNK-COOH\tAR; AR\tLI; LI\t\t\t\t\t\t\t\t2\t2\t100.0\tDoubtful\n' |
| b |
| 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 |
| b |
| 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 |
| b |
| 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 |
| b |
| 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 |
| [ |
| b'@@ -1,43 +0,0 @@\n-\tProtein(s)\tSequence\tAAs Before\tAAs After\tPosition\tModified Sequence\tVariable Modifications\tFixed Modifications\tSpectrum File\tSpectrum Title\tSpectrum Scan Number\tRT\tm/z\tMeasured Charge\tIdentification Charge\tTheoretical Mass\tIsotope Number\tPrecursor m/z Error [ppm]\tLocalization Confidence\tProbabilistic PTM score\tD-score\tConfidence [%]\tValidation\n-1\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tLHVEMESMIEELQMLMDAK\tNK; NK\tLS; LS\t403; 403\tNH2-LHVEMESMIEELQMLMDAK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 1198, +MSn(1139.0413), 115.6 min\t\t-1.0\t1139.04127\t2+\t2+\t2276.0560840995904\t0\t5.225020941769318\t\t\t\t100.0\tDoubtful\n-2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tNLLLDANKENGELK\tAK; AK\tIS; IS\t147; 147\tNH2-NLLLDANKENGELK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 207, MSn(785.9179), 35.7 min\t\t-1.0\t785.91791\t2+\t2+\t1569.8362356486903\t0\t-9.522902824571501\t\t\t\t100.0\tDoubtful\n-3\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tSLQAENEQLR\tVR; VR\tLK; LK\t110; 110\tNH2-SLQAENEQLR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 39, MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942144781802\t0\t2.063410823544894\t\t\t\t100.0\tDoubtful\n-4\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tEFDVEPLKEAYQAEIDEAK\tRR; RR\tNL; NL\t128; 128\tNH2-EFDVEPLKEAYQAEIDEAK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 736, MSn(742.0258), 75.1 min\t\t-1.0\t742.02585\t3+\t3+\t2223.0583092202605\t0\t-1.1628605151025897\t\t\t\t100.0\tDoubtful\n-5\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tMEIITITNQLQR\tMK; MK\tSN; SN\t373; 373\tNH2-MEIITITNQLQR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 636, +MSn(730.3981), 66.9 min\t\t-1.0\t730.39814\t2+\t2+\t1458.7864490053003\t0\t-3.2324313291878943\t\t\t\t100.0\tDoubtful\n-6\tcds.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\tEIRDEYDNQLNLLSADLESK\tMR; MR\tYQ; YQ\t298; 298\tNH2-EIRDEYDNQLNLLSADLESK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 748, MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.14449845571\t0\t6.2066377342036665\t\t\t\t100.0\tDoubtful\n-7\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tYESQLSQIR\tAR; AR\tQS; QS\t323; 323\tNH2-YESQLSQIR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 67, +MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669371011802\t0\t6.998127983906467\t\t\t\t100.0\tDoubtful\n-8\tcds.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-9'..b'2; 67\tNH2-LISATSISPEHK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 75, +MSn(641.8547), 26.7 min\t\t-1.0\t641.85466\t2+\t2+\t1281.6928658902905\t0\t1.481004205034201\t\t\t\t100.0\tDoubtful\n-35\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tYESQLSQIR\tAR; AR\tQS; QS\t323; 323\tNH2-YESQLSQIR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 67, MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669371011802\t0\t6.998127983906467\t\t\t\t100.0\tDoubtful\n-36\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tMEIITITNQLQR\tMK; MK\tSN; SN\t373; 373\tNH2-MEIITITNQLQR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 636, MSn(730.3981), 66.9 min\t\t-1.0\t730.39814\t2+\t2+\t1458.7864490053003\t0\t-3.2324313291878943\t\t\t\t100.0\tDoubtful\n-37\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tINEDRIDELQDKVNK\tAR; AR\tLI; LI\t179; 179\tNH2-INEDRIDELQDKVNK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 81, +MSn(610.3171), 27.0 min\t\t-1.0\t610.31708\t3+\t3+\t1827.9326552146706\t0\t-1.7720894394949223\t\t\t\t100.0\tDoubtful\n-38\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tEFDVEPLKEAYQAEIDEAK\tRR; RR\tNL; NL\t128; 128\tNH2-EFDVEPLKEAYQAEIDEAK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 736, +MSn(742.0258), 75.1 min\t\t-1.0\t742.02585\t3+\t3+\t2223.0583092202605\t0\t-1.1628605151025897\t\t\t\t100.0\tDoubtful\n-39\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tSLQAENEQLR\tVR; VR\tLK; LK\t110; 110\tNH2-SLQAENEQLR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 39, +MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942144781802\t0\t2.063410823544894\t\t\t\t100.0\tDoubtful\n-40\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tINEDRIDELQDKVNK\tAR; AR\tLI; LI\t179; 179\tNH2-INEDRIDELQDKVNK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 81, MSn(610.3171), 27.0 min\t\t-1.0\t610.31708\t3+\t3+\t1827.9326552146706\t0\t-1.7720894394949223\t\t\t\t100.0\tDoubtful\n-41\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISTGYITENIGGFR\tNR; NR\tSE; SE\t442; 442\tNH2-ISTGYITENIGGFR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 588, MSn(764.3961), 63.5 min\t\t-1.0\t764.39611\t2+\t2+\t1526.7729071161402\t0\t3.113546101111509\t\t\t\t100.0\tDoubtful\n-42\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISTGYITENIGGFR\tNR; NR\tSE; SE\t442; 442\tNH2-ISTGYITENIGGFR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 588, +MSn(764.3961), 63.5 min\t\t-1.0\t764.39611\t2+\t2+\t1526.7729071161402\t0\t3.113546101111509\t\t\t\t100.0\tDoubtful\n' |
| b |
| 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 |
| [ |
| b'@@ -1,43 +0,0 @@\n-\tProtein(s)\tSequence\tAAs Before\tAAs After\tPosition\tModified Sequence\tVariable Modifications\tFixed Modifications\tSpectrum File\tSpectrum Title\tSpectrum Scan Number\tRT\tm/z\tMeasured Charge\tIdentification Charge\tTheoretical Mass\tIsotope Number\tPrecursor m/z Error [ppm]\tLocalization Confidence\tProbabilistic PTM score\tD-score\tConfidence [%]\tValidation\n-1\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tLHVEMESMIEELQMLMDAK\tNK; NK\tLS; LS\t403; 403\tNH2-LHVEMESMIEELQMLMDAK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 1198, +MSn(1139.0413), 115.6 min\t\t-1.0\t1139.04127\t2+\t2+\t2276.0560840995904\t0\t5.225020941769318\t\t\t\t100.0\tDoubtful\n-2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tNLLLDANKENGELK\tAK; AK\tIS; IS\t147; 147\tNH2-NLLLDANKENGELK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 207, MSn(785.9179), 35.7 min\t\t-1.0\t785.91791\t2+\t2+\t1569.8362356486903\t0\t-9.522902824571501\t\t\t\t100.0\tDoubtful\n-3\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tSLQAENEQLR\tVR; VR\tLK; LK\t110; 110\tNH2-SLQAENEQLR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 39, MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942144781802\t0\t2.063410823544894\t\t\t\t100.0\tDoubtful\n-4\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tEFDVEPLKEAYQAEIDEAK\tRR; RR\tNL; NL\t128; 128\tNH2-EFDVEPLKEAYQAEIDEAK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 736, MSn(742.0258), 75.1 min\t\t-1.0\t742.02585\t3+\t3+\t2223.0583092202605\t0\t-1.1628605151025897\t\t\t\t100.0\tDoubtful\n-5\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tMEIITITNQLQR\tMK; MK\tSN; SN\t373; 373\tNH2-MEIITITNQLQR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 636, +MSn(730.3981), 66.9 min\t\t-1.0\t730.39814\t2+\t2+\t1458.7864490053003\t0\t-3.2324313291878943\t\t\t\t100.0\tDoubtful\n-6\tcds.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\tEIRDEYDNQLNLLSADLESK\tMR; MR\tYQ; YQ\t298; 298\tNH2-EIRDEYDNQLNLLSADLESK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 748, MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.14449845571\t0\t6.2066377342036665\t\t\t\t100.0\tDoubtful\n-7\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tYESQLSQIR\tAR; AR\tQS; QS\t323; 323\tNH2-YESQLSQIR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 67, +MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669371011802\t0\t6.998127983906467\t\t\t\t100.0\tDoubtful\n-8\tcds.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-9'..b'2; 67\tNH2-LISATSISPEHK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 75, +MSn(641.8547), 26.7 min\t\t-1.0\t641.85466\t2+\t2+\t1281.6928658902905\t0\t1.481004205034201\t\t\t\t100.0\tDoubtful\n-35\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tYESQLSQIR\tAR; AR\tQS; QS\t323; 323\tNH2-YESQLSQIR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 67, MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669371011802\t0\t6.998127983906467\t\t\t\t100.0\tDoubtful\n-36\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tMEIITITNQLQR\tMK; MK\tSN; SN\t373; 373\tNH2-MEIITITNQLQR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 636, MSn(730.3981), 66.9 min\t\t-1.0\t730.39814\t2+\t2+\t1458.7864490053003\t0\t-3.2324313291878943\t\t\t\t100.0\tDoubtful\n-37\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tINEDRIDELQDKVNK\tAR; AR\tLI; LI\t179; 179\tNH2-INEDRIDELQDKVNK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 81, +MSn(610.3171), 27.0 min\t\t-1.0\t610.31708\t3+\t3+\t1827.9326552146706\t0\t-1.7720894394949223\t\t\t\t100.0\tDoubtful\n-38\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tEFDVEPLKEAYQAEIDEAK\tRR; RR\tNL; NL\t128; 128\tNH2-EFDVEPLKEAYQAEIDEAK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 736, +MSn(742.0258), 75.1 min\t\t-1.0\t742.02585\t3+\t3+\t2223.0583092202605\t0\t-1.1628605151025897\t\t\t\t100.0\tDoubtful\n-39\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tSLQAENEQLR\tVR; VR\tLK; LK\t110; 110\tNH2-SLQAENEQLR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 39, +MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942144781802\t0\t2.063410823544894\t\t\t\t100.0\tDoubtful\n-40\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tINEDRIDELQDKVNK\tAR; AR\tLI; LI\t179; 179\tNH2-INEDRIDELQDKVNK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 81, MSn(610.3171), 27.0 min\t\t-1.0\t610.31708\t3+\t3+\t1827.9326552146706\t0\t-1.7720894394949223\t\t\t\t100.0\tDoubtful\n-41\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISTGYITENIGGFR\tNR; NR\tSE; SE\t442; 442\tNH2-ISTGYITENIGGFR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 588, MSn(764.3961), 63.5 min\t\t-1.0\t764.39611\t2+\t2+\t1526.7729071161402\t0\t3.113546101111509\t\t\t\t100.0\tDoubtful\n-42\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISTGYITENIGGFR\tNR; NR\tSE; SE\t442; 442\tNH2-ISTGYITENIGGFR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 588, +MSn(764.3961), 63.5 min\t\t-1.0\t764.39611\t2+\t2+\t1526.7729071161402\t0\t3.113546101111509\t\t\t\t100.0\tDoubtful\n' |
| b |
| 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 |
| [ |
| b'@@ -1,43 +0,0 @@\n-\tProtein(s)\tSequence\tVariable Modifications\tFixed Modifications\tSpectrum File\tSpectrum Title\tSpectrum Scan Number\tRT\tm/z\tMeasured Charge\tIdentification Charge\tTheoretical Mass\tIsotope Number\tPrecursor m/z Error [ppm]\tLocalization Confidence\tProbabilistic PTM score\tD-score\tConfident Phosphosites\t#Confident Phosphosites\tAmbiguous Phosphosites\t#Ambiguous Phosphosites\tConfidence [%]\tValidation\n-1\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tLHVEMESMIEELQMLMDAK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 1198, +MSn(1139.0413), 115.6 min\t\t-1.0\t1139.04127\t2+\t2+\t2276.0560840995904\t0\t5.225020941769318\t\t\t\t\t\t\t\t100.0\tDoubtful\n-2\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tNLLLDANKENGELK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 207, MSn(785.9179), 35.7 min\t\t-1.0\t785.91791\t2+\t2+\t1569.8362356486903\t0\t-9.522902824571501\t\t\t\t\t\t\t\t100.0\tDoubtful\n-3\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tSLQAENEQLR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 39, MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942144781802\t0\t2.063410823544894\t\t\t\t\t\t\t\t100.0\tDoubtful\n-4\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tEFDVEPLKEAYQAEIDEAK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 736, MSn(742.0258), 75.1 min\t\t-1.0\t742.02585\t3+\t3+\t2223.0583092202605\t0\t-1.1628605151025897\t\t\t\t\t\t\t\t100.0\tDoubtful\n-5\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tMEIITITNQLQR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 636, +MSn(730.3981), 66.9 min\t\t-1.0\t730.39814\t2+\t2+\t1458.7864490053003\t0\t-3.2324313291878943\t\t\t\t\t\t\t\t100.0\tDoubtful\n-6\tcds.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\tEIRDEYDNQLNLLSADLESK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 748, MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.14449845571\t0\t6.2066377342036665\t\t\t\t\t\t\t\t100.0\tDoubtful\n-7\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tYESQLSQIR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 67, +MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669371011802\t0\t6.998127983906467\t\t\t\t\t\t\t\t100.0\tDoubtful\n-8\tcds.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\tEIRDEYDNQLNLLSADLESK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 748, +MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.14449845571\t0\t6.2066377342036665\t\t\t\t\t\t\t\t100.0\tDoubtful\n-9\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:000'..b'rofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, 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\tLISATSISPEHK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 75, +MSn(641.8547), 26.7 min\t\t-1.0\t641.85466\t2+\t2+\t1281.6928658902905\t0\t1.481004205034201\t\t\t\t\t\t\t\t100.0\tDoubtful\n-35\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tYESQLSQIR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 67, MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669371011802\t0\t6.998127983906467\t\t\t\t\t\t\t\t100.0\tDoubtful\n-36\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tMEIITITNQLQR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 636, MSn(730.3981), 66.9 min\t\t-1.0\t730.39814\t2+\t2+\t1458.7864490053003\t0\t-3.2324313291878943\t\t\t\t\t\t\t\t100.0\tDoubtful\n-37\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tINEDRIDELQDKVNK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 81, +MSn(610.3171), 27.0 min\t\t-1.0\t610.31708\t3+\t3+\t1827.9326552146706\t0\t-1.7720894394949223\t\t\t\t\t\t\t\t100.0\tDoubtful\n-38\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tEFDVEPLKEAYQAEIDEAK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 736, +MSn(742.0258), 75.1 min\t\t-1.0\t742.02585\t3+\t3+\t2223.0583092202605\t0\t-1.1628605151025897\t\t\t\t\t\t\t\t100.0\tDoubtful\n-39\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tSLQAENEQLR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 39, +MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942144781802\t0\t2.063410823544894\t\t\t\t\t\t\t\t100.0\tDoubtful\n-40\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tINEDRIDELQDKVNK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 81, MSn(610.3171), 27.0 min\t\t-1.0\t610.31708\t3+\t3+\t1827.9326552146706\t0\t-1.7720894394949223\t\t\t\t\t\t\t\t100.0\tDoubtful\n-41\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISTGYITENIGGFR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 588, MSn(764.3961), 63.5 min\t\t-1.0\t764.39611\t2+\t2+\t1526.7729071161402\t0\t3.113546101111509\t\t\t\t\t\t\t\t100.0\tDoubtful\n-42\tcds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67\tISTGYITENIGGFR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 588, +MSn(764.3961), 63.5 min\t\t-1.0\t764.39611\t2+\t2+\t1526.7729071161402\t0\t3.113546101111509\t\t\t\t\t\t\t\t100.0\tDoubtful\n' |
| b |
| diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/peptide_shaker_modifications_result1.zip |
| b |
| Binary file test-data/peptide_shaker_modifications_result1.zip has changed |
| b |
| 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 |
| b |
| 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 |
| b |
| 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 |
| b |
| 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 |
| b |
| 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 |
| b |
| 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 |
| b |
| 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 |
| b |
| 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 |
| b |
| 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 |
| b |
| 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 |
| b |
| 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 |
| b |
| 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 |
| b |
| diff -r 7fdd9119cc4f -r bb0130ff73ce test-data/searchgui_smallsearch_default_somesearchengines_modifications.zip |
| b |
| Binary file test-data/searchgui_smallsearch_default_somesearchengines_modifications.zip has changed |
| b |
| 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 |
| b |
| b'@@ -0,0 +1,25548 @@\n+BEGIN IONS\n+TITLE=small.3.3. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=3"\n+RTINSECONDS=0.6731\n+PEPMASS=810.789428710938 183838.71875\n+CHARGE=2+ and 3+ and 4+\n+231.3888397 26.5451126099\n+233.3398285 20.4479541779\n+239.3961487 17.9991588593\n+240.3084717 44.7395210266\n+245.1689453 283.3832702637\n+246.1925354 75.7845687866\n+247.8092346 23.2885246277\n+251.197052 628.9126586914\n+252.3562469 41.6676368713\n+259.3575439 51.3414955139\n+262.2673035 341.8115539551\n+264.271759 19.0200614929\n+266.2132263 111.3928222656\n+272.3408508 27.5777511597\n+273.1651001 46.4653587341\n+276.2359009 66.1921005249\n+277.3269958 36.7716407776\n+279.2734375 151.997756958\n+280.2745056 30.4819164276\n+281.2428894 20.6155757904\n+286.1730042 26.2698879242\n+290.194519 1193.4537353516\n+291.2459717 152.4249267578\n+294.2355957 413.9957275391\n+295.1256409 17.1910572052\n+299.1573792 54.0453262329\n+305.8824768 33.266960144\n+308.1987305 4068.3127441406\n+309.2765503 735.5776367188\n+315.3105774 44.0675201416\n+316.2329102 87.3488922119\n+319.4229736 68.6050643921\n+324.0772705 20.8427391052\n+326.1818848 118.679145813\n+328.2772522 72.1243438721\n+330.1789551 24.7702865601\n+332.6609497 31.4776382446\n+336.117981 115.9179992676\n+337.3536072 167.551864624\n+338.2251587 16.7139282227\n+339.2226562 23.1128787994\n+345.9707947 65.1955108643\n+347.5861206 54.7535209656\n+361.4074097 27.8001232147\n+362.967041 113.9151000977\n+364.2114868 1090.4406738281\n+365.3210449 373.6746826172\n+366.1662598 33.3494911194\n+368.3313599 158.1134490967\n+371.2240601 33.2658576965\n+376.3760376 51.6286468506\n+377.3157349 24.8427410126\n+378.6485596 85.5033416748\n+379.335907 483.3477783203\n+380.5695496 92.3005218506\n+381.4432373 72.2191772461\n+382.2927246 203.6508483887\n+383.3612061 73.57371521\n+384.3339233 14.9419174194\n+389.2349854 17.1471920013\n+390.1678467 33.9905509949\n+391.1951294 23.2546920776\n+393.521637 106.212928772\n+396.4468384 965.7248535156\n+397.2388916 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1.2564569712\n+1364.838013 2.7277929783\n+1365.635498 1.7941657305\n+1369.533325 2.7822601795\n+1429.61853 2.346054554\n+1446.664429 2.0156695843\n+1483.107544 5.2070007324\n+1547.776733 1.2610274553\n+1723.519287 1.640920639\n+1724.323975 1.2519712448\n+1724.991333 5.1561379433\n+1743.361206 3.1923613548\n+END IONS\n' |
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