| Previous changeset 48:64e3a8cc8ffb (2018-09-27) Next changeset 50:5814883aa217 (2018-11-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 |
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modified:
macros.xml peptide_shaker.xml searchgui.xml test-data/peptide_shaker_modifications_result1.cpsx test-data/peptide_shaker_modifications_result1.zip |
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added:
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 |
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removed:
test-data/peptide_shaker_certificate_result2.tabular test-data/peptide_shaker_certificate_result2.txt test-data/peptide_shaker_hierarchical_result2.tabular test-data/peptide_shaker_peptides_phoshorylation_result2.tabular test-data/peptide_shaker_peptides_result2.tabular test-data/peptide_shaker_peptides_result3.tabular test-data/peptide_shaker_proteins_phoshorylation_result2.tabular test-data/peptide_shaker_proteins_result2.tabular test-data/peptide_shaker_psm_phoshorylation_result2.tabular test-data/peptide_shaker_psm_result1.tabular test-data/peptide_shaker_psm_result2.tabular |
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| diff -r 64e3a8cc8ffb -r 58a3e6cb2598 macros.xml --- a/macros.xml Thu Sep 27 04:31:53 2018 -0400 +++ b/macros.xml Fri Oct 12 08:56:06 2018 -0400 |
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| @@ -2,12 +2,14 @@ <xml name="stdio"> <stdio> <exit_code range="1:" level="fatal" description="Job Failed" /> - <regex match="java.lang.OutOfMemoryError" level="fatal_oom" description="Java memory Exception"/> + <!-- <regex match="java.lang.OutOfMemoryError" level="fatal_oom" description="Java memory Exception"/> <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/> <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/> + <regex match="Native memory allocation (malloc) failed" level="fatal_oom" description="Java memory Exception"/>--> <regex match="java.*Exception" level="fatal" description="Java Exception"/> <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> - <regex match="CompomicsError" level="fatal" description="Compomics Error"/> + <regex match="PeptideShaker ran out of memory" level="fatal" description="JVM Error"/> + <regex match="CompomicsError" level="fatal" description="Compomics Error"/> </stdio> </xml> <token name="@GENERAL_PARAMETERS@"> @@ -52,7 +54,8 @@ </token> <token name="@SEARCHGUI_MAJOR_VERSION@">3</token> - <token name="@SEARCHGUI_VERSION@">3.3.3</token> + <token name="@SEARCHGUI_VERSION@">3.3.5</token> + <token name="@PEPTIDESHAKER_VERSION@">1.16.31</token> <xml name="general_options"> <section name="protein_digest_options" expanded="false" title="Protein Digestion Options"> |
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| diff -r 64e3a8cc8ffb -r 58a3e6cb2598 peptide_shaker.xml --- a/peptide_shaker.xml Thu Sep 27 04:31:53 2018 -0400 +++ b/peptide_shaker.xml Fri Oct 12 08:56:06 2018 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.26">\n+<tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@">\n <description>\n Perform protein identification using various search engines based on results from SearchGUI\n </description>\n@@ -6,11 +6,12 @@\n <import>macros.xml</import>\n </macros>\n <requirements>\n- <requirement type="package" version="1.16.26">peptide-shaker</requirement>\n+ <requirement type="package" version="@PEPTIDESHAKER_VERSION@">peptide-shaker</requirement>\n </requirements>\n <expand macro="stdio" />\n- <command>\n-<![CDATA[\n+\n+ <command><![CDATA[\n+ ## When supporting more advanced Galaxy versions: command use_shared_home="false"\n #from datetime import datetime\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@@ -18,16 +19,33 @@\n #set $bin_dir = "bin"\n \n \n- mkdir output_reports;\n- cwd=`pwd`;\n+ mkdir output_reports &&\n+ cwd=`pwd` &&\n+ export HOME=\\$cwd &&\n+\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+\t --exec_dir="\\$cwd/${bin_dir}"\n+ -temp_folder \\$cwd/PathSettingsCLI\n+ -log \\$cwd/peptideshaker.log &&\n+\n+ #if str($exporting_options.output_reports) != "None"\n+ #set $output_reports_list = set(str($exporting_options.output_reports).split(\',\'))\n+ #else\n+ #set $output_reports_list = set()\n+\t #end if\n+\n ######################\n ## PeptideShakerCLI ##\n ######################\n- (peptide-shaker eu.isas.peptideshaker.cmd.PeptideShakerCLI\n+ (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI\n --exec_dir="\\$cwd/${bin_dir}"\n+ -gui 0\n -temp_folder \\$cwd/PeptideShakerCLI\n -experiment \'$exp_str\'\n -sample \'$samp_str\'\n@@ -35,166 +53,123 @@\n -identification_files \\$cwd/searchgui_input.zip\n -id_params \\$cwd/SEARCHGUI_IdentificationParameters.par\n -out \\$cwd/peptideshaker_output.cpsx\n+\t #if $exporting_options.zip_conditional.zip_output_boolean == \'zip\':\n -zip \\$cwd/peptideshaker_output.zip\n- #set $cleaned_list = str($outputs).split(\',\')\n- #if \'cps\' in $cleaned_list:\n- #silent $cleaned_list.remove(\'cps\')\n- #end if\n- #if \'mzidentML\' in $cleaned_list:\n- #silent $cleaned_list.remove(\'mzidentML\')\n- #end if\n- #if \'zip\' in $cleaned_list:\n- #silent $cleaned_list.remove(\'zip\')\n- #end if\n- #if len($cleaned_list) > 0\n- ## Only numbers are left over. These corresponds to different reports.\n- -reports #echo \',\'.join($cleaned_list)#\n- #end if\n-\n+\t #end if\n -threads "\\${GALAXY_SLOTS:-12}"\n \n- ##Optional processing parameters:\n- #if $processing_options.processing_options_selector == "yes"\n- -protein_fdr "${processing_options.protein_fdr}"\n- -peptide_fdr "${processing_options.peptide_fdr}"\n- -psm_fdr "${processing_options.psm_fdr}"\n- -ptm_score "${processing_options.ptm_score.ptm_score_selector}"\n- #if $processing_options.ptm_score.ptm_score_selector == 1\n- -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"\n- #if str($processing_options.ptm_score.ptm_threshold) != \'\'\n- -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"\n- #end if\n'..b'rt_contents>\n- </output>\n- <output name="output_proteins">\n- <assert_contents>\n- <has_text text="Modification" />\n- <has_text text="cds.comp41779_c0_seq1" />\n- </assert_contents>\n- </output>\n- <output name="output_proteins_phosphorylation">\n- <assert_contents>\n- <has_text text="Phosphosite" />\n- <has_text text="cds.comp41779_c0_seq1" />\n- </assert_contents>\n- </output>\n+ <param name="mzidentml_creation" value="0"/>\n+ <param name="zip_output_boolean" value="separate"/>\n+ <param name="output_reports" value="0,1,2,3,4,5,6,7,8,9,10,11"/>\n+ <output name="output_certificate" file="peptide_shaker_modifications_result1.output_certificate" ftype="txt" lines_diff="6"/>\n+ <output name="output_hierarchical" file="peptide_shaker_modifications_result1.output_hierarchical" ftype="tabular"/>\n+ <output name="output_extended_psm" file="peptide_shaker_modifications_result1.output_extended_psm" ftype="tabular"/>\n+ <output name="output_psm" file="peptide_shaker_modifications_result1.output_psm" ftype="tabular"/>\n+ <output name="output_psm_phosphorylation" file="peptide_shaker_modifications_result1.output_psm_phosphorylation" ftype="tabular"/>\n+ <output name="output_psm_nonvalidated" file="peptide_shaker_modifications_result1.output_psm_nonvalidated" ftype="tabular"/>\n+ <output name="output_peptides" file="peptide_shaker_modifications_result1.output_peptides" ftype="tabular"/>\n+ <output name="output_peptides_phosphorylation" file="peptide_shaker_modifications_result1.output_peptides_phosphorylation" ftype="tabular"/>\n+ <output name="output_peptides_nonvalidated" file="peptide_shaker_modifications_result1.output_peptides_nonvalidated" ftype="tabular"/>\n+ <output name="output_proteins" file="peptide_shaker_modifications_result1.output_proteins" ftype="tabular"/>\n+ <output name="output_proteins_phosphorylation" file="peptide_shaker_modifications_result1.output_proteins_phosphorylation" ftype="tabular"/>\n+ <output name="output_proteins_nonvalidated" file="peptide_shaker_modifications_result1.output_proteins_nonvalidated" ftype="tabular"/>\n </test>\n <test>\n <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>\n <param name="processing_options_selector" value="no"/>\n <param name="filtering_options_selector" value="no"/>\n- <param name="outputs" value="3,cps"/>\n+ <param name="mzidentml_creation" value="0"/>\n+ <param name="zip_output_boolean" value="separate"/>\n+ <param name="export_cps" value="1"/>\n+ <param name="output_reports" value="3"/>\n <output name="output_cps" file="peptide_shaker_modifications_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/>\n- <output name="output_psm">\n- <assert_contents>\n- <has_text text="cds.comp41779_c0_seq1" />\n- </assert_contents>\n- </output>\n+\t <output name="output_psm" file="peptide_shaker_modifications_result1.output_psm" ftype="tabular"/>\n </test>\n </tests>\n <help>\n **What it does**\n \n-Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI application and combines the results.\n+PeptideShaker is a search engine for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML.\n \n http://compomics.github.io/projects/peptide-shaker.html\n-http://compomics.github.io/projects/searchgui.html\n \n ----\n \n' |
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| diff -r 64e3a8cc8ffb -r 58a3e6cb2598 searchgui.xml --- a/searchgui.xml Thu Sep 27 04:31:53 2018 -0400 +++ b/searchgui.xml Fri Oct 12 08:56:06 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1"> +<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@"> <description> Perform protein identification using various search engines and prepare results for input to Peptide Shaker </description> @@ -23,6 +23,8 @@ cwd=`pwd`; export HOME=\$cwd; + echo "" > $temp_stderr && + ## echo the search engines to run (single quotes important because X!Tandem) echo '$search_engines_options.engines'; echo 'DB: ${input_database.element_identifier} sequences: ${input_database.metadata.sequences}'; @@ -43,7 +45,7 @@ #### Set paths #### ########################################### echo 'Setting paths' && - searchgui eu.isas.searchgui.cmd.PathSettingsCLI + searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI --exec_dir="\$cwd/${bin_dir}" -temp_folder \$cwd -log \$cwd/searchgui.log 2>> $temp_stderr && @@ -53,7 +55,7 @@ ########################################### #if $protein_database_options.create_decoy: echo 'Creating decoy database.' && - searchgui eu.isas.searchgui.cmd.FastaCLI + searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy 2>> $temp_stderr && @@ -66,7 +68,7 @@ ## generate IdentificationParameters for SearchGUI ## ##################################################### echo 'setting identification parameters' && - (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI + (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI --exec_dir="\$cwd/${bin_dir}" -out SEARCHGUI_IdentificationParameters.par @@ -435,9 +437,7 @@ (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr); - exit_code_for_galaxy=\$?; cat $temp_stderr 2>&1; - (exit \$exit_code_for_galaxy) ]]> </command> <inputs> @@ -1108,8 +1108,8 @@ <param name="min_charge" value="1"/> <param name="max_charge" value="3"/> <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> - <param name="xtandem.xtandem_advanced" value="yes"/> - <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/> + <param name="xtandem|xtandem_advanced" value="yes"/> + <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/> <output name="searchgui_results" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> </test> <!-- Test that search works with MSAmanda --> @@ -1124,7 +1124,6 @@ </test> <!-- Test that specifying non-default search engines works using modifications --> - <!-- <test> <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> @@ -1134,13 +1133,11 @@ <param name="min_charge" value="1"/> <param name="max_charge" value="3"/> <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> - <param name="xtandem.xtandem_advanced" value="yes"/> - <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/> - <output name="output" file="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> + <param name="xtandem|xtandem_advanced" value="yes"/> + <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/> + <output name="searchgui_results" file="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> </test> - --> <!-- Test that search works with MSAmanda - with modifications --> - <!-- <test> <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> @@ -1150,9 +1147,8 @@ <param name="min_charge" value="1"/> <param name="max_charge" value="3"/> <param name="engines" value="MS_Amanda"/> - <output name="output" file="tiny_searchgui_modifications_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> + <output name="searchgui_results" file="tiny_searchgui_modifications_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> </test> - --> </tests> <help> **What it does** |
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| diff -r 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_certificate_result2.tabular --- a/test-data/peptide_shaker_certificate_result2.tabular Thu Sep 27 04:31:53 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,68 +0,0 @@ -Project Details1: PeptideShaker Version: 0.37.4-beta -2: Date: Sat Feb 14 20:04:49 CET 2015 -3: Experiment: Galaxy_Experiment_2015021420041423940686 -4: Sample: Sample_2015021420041423940686 -5: Replicate Number: 1 -6: Identification Algorithms: X!Tandem and MS-GF+ -Database Search Parameters - -1: Precursor Accuracy Unit: ppm -2: Precursor Ion m/z Tolerance: 100.0 -3: Fragment Ion m/z Tolerance: 0.5 -4: Enzyme: Trypsin -5: Number of Missed Cleavages: Not implemented -6: Database: input_database.fasta -7: Forward Ion: b -8: Rewind Ion: y -9: Fixed Modifications: carbamidomethyl c -10: Variable Modifications: oxidation of m, acetylation of protein n-term, pyro-cmc, pyro-glu from n-term e, pyro-glu from n-term q -11: Refinement Variable Modifications: -12: 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: No -Validation Summary - -1: #Validated Proteins: 0.0 -2: Protein Total: 0.0 -3Protein FDR Limit: 1.0 % -4: Protein FNR Limit: 0.0 % -5: Protein Confidence Limit: -1.0 % -6: Protein PEP Limit: 101.0 % -7: Protein Confidence Accuracy: 0.0 % -8: #Validated Peptides: 0.0 -9: Peptide Total: 0.0 -10: Peptide FDR Limit: 1.0 % -11: Peptide FNR Limit: 0.0 % -12: Peptide Confidence Limit: -1.0 % -13: Peptide PEP Limit: 101.0 % -14: Peptide Confidence Accuracy: 0.0 % -15: #Validated PSM: 0.0 -16: PSM Total: 0.0 -17: PSM FDR Limit: 1.0 % -18: PSM FNR Limit: 0.0 % -19: PSM Confidence Limit: -1.0 % -20: PSM PEP Limit: 101.0 % -21: PSM Confidence Accuracy: 0.0 % -Postranslational Modification Scoring Settings - -1: A-score: No -2: Accounting for Neutral Losses: No -3: False Location Rate: 1.0 -Spectrum Counting Parameters - -1: Method: NSAF -2: Validated Matches Only: Yes -Annotation Settings - -1: Intensity Limit: 0.75 -2: Automatic Annotation: Yes -3: Selected Ions: b, y -4: Neutral Losses: NH3, H2O -5: Neutral Losses Sequence Dependence: Yes -6: Selected Charges: 1, 2 -7: Fragment Ion m/z Tolerance: 0.5 |
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| diff -r 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_certificate_result2.txt --- a/test-data/peptide_shaker_certificate_result2.txt Thu Sep 27 04:31:53 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,68 +0,0 @@ -Project Details1: PeptideShaker Version: 1.13.6 -2: Date: Fri Jan 13 11:06:50 CST 2017 -3: Experiment: Galaxy_Experiment_2017011311051484327131 -4: Sample: Sample_2017011311051484327131 -5: Replicate Number: 1 -6: Identification Algorithms: OMSSA, X!Tandem, MS-GF+, Comet and MyriMatch -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: Enzyme: Trypsin -6: Maximum Missed Cleavages: 2 -7: Database: input_database.fasta -8: Forward Ion: b -9: Rewind Ion: y -10: Fixed Modifications: Carbamidomethylation of C -11: Variable Modifications: Oxidation of M, Acetylation of protein N-term, Pyrolidone from E, Pyrolidone from Q, Pyrolidone from carbamidomethylated C -12: Refinement Variable Modifications: -13: 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: y, b -4: Neutral Losses: H2O, NH3, CH4OS -5: Neutral Losses Sequence Dependence: Yes -6: Fragment Ion m/z Tolerance: 0.5 |
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| diff -r 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_hierarchical_result2.tabular --- a/test-data/peptide_shaker_hierarchical_result2.tabular Thu Sep 27 04:31:53 2018 -0400 +++ /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.comp41779_c0_seq1\tm.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67\t69.88215380565927\t92.52\t37.58\t0.017651472642866785\t\t\t\t\tRelated Proteins\tcds.comp41779_c0_seq2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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-1.1\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tLHVEMESMIEELQMLMDAK\tNK; NK\tLS; LS\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-1.1.1\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tLHVEMESMIEELQMLMDAK\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+\t2276.05608409959\t0\t5.225020941968939\t0\t\t\t\t100.0\tDoubtful\n-1.1.2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tLHVEMESMIEELQMLMDAK\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+\t2276.05608409959\t0\t5.225020941968939\t0\t\t\t\t100.0\tDoubtful\n-1.1.3\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tLHVEMESMIEELQMLMDAK\tNH2-LHVEMESMIEELQMLMDAK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 1197, +MSn(759.6966), 115.6 min\t\t-1.0\t759.69661\t3+\t3+\t2276.05608409959\t0\t5.2286496671522364\t0\t\t\t\t100.0\tDoubtful\n-1.1.4\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tLHVEMESMIEELQMLMDAK\tNH2-LHVEMESMIEELQMLMDAK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 1197, MSn(759.6966), 115.6 min\t\t-1.0\t759.69661\t3+\t3+\t2276.05608409959\t0\t5.2286496671522364\t0\t\t\t\t100.0\tDoubtful\n-1.2\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tNLLLDANKENGELK\tAK; AK\tIS; IS\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-1.2.1\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tNLLLDANKENGELK\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+\t1569.8362356486905\t0\t-9.522902824571501\t0\t\t\t\t100.0\tDoubtful\n-1.2.2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tNLLLDANKENGELK\tNH2-NLLLDANKENGELK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 204, +MSn(524.2825), 35.5 min\t\t-1.0\t524.28252\t3+\t3+\t1569.8362356486905\t0\t-6.678955564950069\t0\t\t\t\t100.0\tDoubtful\n-1.2.3\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tNLLLDANKENGELK\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+\t1569.8362356486905\t0\t-9.522902824571501\t0\t\t\t\t100.0\tDoubtful\n-1.2.4\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tNLLLDANKENGELK\tNH2-NLLLDANKENGELK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 204, MSn(524.2825), 35.5 min\t\t-1.0\t524.28252\t3+\t3+\t1569.8362356486905\t0\t-6.678955564950069\t0\t\t\t\t100.0\tDoubtful\n-1.3\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2\tSLQAENEQLR\tVR; VR\tLK; LK\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\tIso'..b'\t-1.0\t590.64518\t3+\t3+\t1768.9107975712802\t0\t1.6439836590138295\t0\t\t\t\t100.0\tDoubtful\n-1.14\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2; cds.comp41779_c0_seq3\tSVISIGEVESEGQYVTLENTSSGR\tSK; SK; SK\tSK; SK; SK\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-1.14.1\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\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+\t2540.2242053283903\t0\t2.5264056585684305\t0\t\t\t\t100.0\tDoubtful\n-1.14.2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\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+\t2540.2242053283903\t0\t2.5264056585684305\t0\t\t\t\t100.0\tDoubtful\n-1.15\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2; cds.comp41779_c0_seq3\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-1.15.1\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\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\t1.4810042052113237\t0\t\t\t\t100.0\tDoubtful\n-1.15.2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\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-1.15.3\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\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\t1.4810042052113237\t0\t\t\t\t100.0\tDoubtful\n-1.15.4\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\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\tcds.comp52727_c0_seq1\tm.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91\t69.96963713242043\t100.0\t3.25\t0.0032520325203252032\t\t\t\t\tRelated Proteins\tcds.comp52727_c0_seq2\tcds.comp52727_c0_seq1, cds.comp52727_c0_seq2\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-2.1\tcds.comp52727_c0_seq1; cds.comp52727_c0_seq2\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-2.1.1\tcds.comp52727_c0_seq1, cds.comp52727_c0_seq2\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+\t2364.1444984557097\t0\t6.206637734347747\t0\t\t\t\t100.0\tDoubtful\n-2.1.2\tcds.comp52727_c0_seq1, cds.comp52727_c0_seq2\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+\t2364.1444984557097\t0\t6.206637734347747\t0\t\t\t\t100.0\tDoubtful\n' |
| b |
| diff -r 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_modifications_result1.cpsx |
| b |
| Binary file test-data/peptide_shaker_modifications_result1.cpsx has changed |
| b |
| diff -r 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_modifications_result1.output_certificate --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_modifications_result1.output_certificate Fri Oct 12 08:56:06 2018 -0400 |
| [ |
| @@ -0,0 +1,79 @@ + +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 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_modifications_result1.output_extended_psm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_modifications_result1.output_extended_psm Fri Oct 12 08:56:06 2018 -0400 |
| [ |
| b'@@ -0,0 +1,43 @@\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 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_modifications_result1.output_hierarchical --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_modifications_result1.output_hierarchical Fri Oct 12 08:56:06 2018 -0400 |
| [ |
| b'@@ -0,0 +1,79 @@\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 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_modifications_result1.output_peptides --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_modifications_result1.output_peptides Fri Oct 12 08:56:06 2018 -0400 |
| [ |
| b'@@ -0,0 +1,17 @@\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 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_modifications_result1.output_peptides_nonvalidated --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_modifications_result1.output_peptides_nonvalidated Fri Oct 12 08:56:06 2018 -0400 |
| [ |
| b'@@ -0,0 +1,17 @@\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 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_modifications_result1.output_peptides_phosphorylation --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_modifications_result1.output_peptides_phosphorylation Fri Oct 12 08:56:06 2018 -0400 |
| [ |
| b'@@ -0,0 +1,17 @@\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 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_modifications_result1.output_proteins --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_modifications_result1.output_proteins Fri Oct 12 08:56:06 2018 -0400 |
| [ |
| @@ -0,0 +1,3 @@ + 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 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_modifications_result1.output_proteins_nonvalidated --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_modifications_result1.output_proteins_nonvalidated Fri Oct 12 08:56:06 2018 -0400 |
| [ |
| @@ -0,0 +1,3 @@ + 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 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_modifications_result1.output_proteins_phosphorylation --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_modifications_result1.output_proteins_phosphorylation Fri Oct 12 08:56:06 2018 -0400 |
| [ |
| @@ -0,0 +1,3 @@ + 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 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_modifications_result1.output_psm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_modifications_result1.output_psm Fri Oct 12 08:56:06 2018 -0400 |
| [ |
| b'@@ -0,0 +1,43 @@\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 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_modifications_result1.output_psm_nonvalidated --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_modifications_result1.output_psm_nonvalidated Fri Oct 12 08:56:06 2018 -0400 |
| [ |
| b'@@ -0,0 +1,43 @@\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 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_modifications_result1.output_psm_phosphorylation --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_modifications_result1.output_psm_phosphorylation Fri Oct 12 08:56:06 2018 -0400 |
| [ |
| b'@@ -0,0 +1,43 @@\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 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_modifications_result1.zip |
| b |
| Binary file test-data/peptide_shaker_modifications_result1.zip has changed |
| b |
| diff -r 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_peptides_phoshorylation_result2.tabular --- a/test-data/peptide_shaker_peptides_phoshorylation_result2.tabular Thu Sep 27 04:31:53 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,17 +0,0 @@ - Protein(s) Protein Group(s) #Validated Protein Group(s) Unique Database Sequence Modified Sequence AAs Before AAs After Variable Modifications Fixed Modifications Localization Confidence Confident Phosphosites #Confident Phosphosites Ambiguous Phosphosites #Ambiguous Phosphosites #Validated PSMs #PSMs Confidence [%] Validation -1 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2; cds.comp41779_c0_seq3 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 SVISIGEVESEGQYVTLENTSSGR NH2-SVISIGEVESEGQYVTLENTSSGR-COOH SK; SK; SK SK; SK; SK 2 2 100.0 Doubtful -2 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 YESQLSQIR NH2-YESQLSQIR-COOH AR; AR QS; QS 2 2 100.0 Doubtful -3 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 SHVVGAGLGGGSMGSMNQSMSLHGGR NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH RR; RR AS; AS 2 2 100.0 Doubtful -4 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 EFDVEPLKEAYQAEIDEAK NH2-EFDVEPLKEAYQAEIDEAK-COOH RR; RR NL; NL 2 2 100.0 Doubtful -5 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 ISITTYEEEIEDLHATAR NH2-ISITTYEEEIEDLHATAR-COOH LK; LK IN; IN 2 2 100.0 Doubtful -6 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH NR; NR SE; SE 4 4 100.0 Doubtful -7 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 ASLGMAAGVAGGIATK NH2-ASLGMAAGVAGGIATK-COOH GR; GR DM; DM 2 2 100.0 Doubtful -8 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2; cds.comp41779_c0_seq3 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 LISATSISPEHK NH2-LISATSISPEHK-COOH DR; DR; DR ID; ID; ID 4 4 100.0 Doubtful -9 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 LHVEMESMIEELQMLMDAK NH2-LHVEMESMIEELQMLMDAK-COOH NK; NK LS; LS 4 4 100.0 Doubtful -10 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH AK; AK IS; IS 4 4 100.0 Doubtful -11 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 SLQAENEQLR NH2-SLQAENEQLR-COOH VR; VR LK; LK 2 2 100.0 Doubtful -12 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2; cds.comp41779_c0_seq3 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 KGDIIATVDEWGPVNR NH2-KGDIIATVDEWGPVNR-COOH AK; AK; AK NS; NS; NS 2 2 100.0 Doubtful -13 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 MEIITITNQLQR NH2-MEIITITNQLQR-COOH MK; MK SN; SN 2 2 100.0 Doubtful -14 cds.comp52727_c0_seq1; cds.comp52727_c0_seq2 cds.comp52727_c0_seq1, cds.comp52727_c0_seq2 (Doubtful) 1 1 EIRDEYDNQLNLLSADLESK NH2-EIRDEYDNQLNLLSADLESK-COOH MR; MR YQ; YQ 2 2 100.0 Doubtful -15 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH QK; QK SV; SV 4 4 100.0 Doubtful -16 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 INEDRIDELQDKVNK NH2-INEDRIDELQDKVNK-COOH AR; AR LI; LI 2 2 100.0 Doubtful |
| b |
| diff -r 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_peptides_result2.tabular --- a/test-data/peptide_shaker_peptides_result2.tabular Thu Sep 27 04:31:53 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,17 +0,0 @@ - Protein(s) Protein Group(s) #Validated Protein Group(s) Unique Database Sequence Modified Sequence Position AAs Before AAs After Variable Modifications Fixed Modifications Localization Confidence #Validated PSMs #PSMs Confidence [%] Validation -1 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2; cds.comp41779_c0_seq3 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 SVISIGEVESEGQYVTLENTSSGR NH2-SVISIGEVESEGQYVTLENTSSGR-COOH 511; 504; 29 SK; SK; SK SK; SK; SK 2 2 100.0 Doubtful -2 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 YESQLSQIR NH2-YESQLSQIR-COOH 323; 323 AR; AR QS; QS 2 2 100.0 Doubtful -3 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 SHVVGAGLGGGSMGSMNQSMSLHGGR NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH 37; 37 RR; RR AS; AS 2 2 100.0 Doubtful -4 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 EFDVEPLKEAYQAEIDEAK NH2-EFDVEPLKEAYQAEIDEAK-COOH 128; 128 RR; RR NL; NL 2 2 100.0 Doubtful -5 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 ISITTYEEEIEDLHATAR NH2-ISITTYEEEIEDLHATAR-COOH 161; 161 LK; LK IN; IN 2 2 100.0 Doubtful -6 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH 442; 442 NR; NR SE; SE 4 4 100.0 Doubtful -7 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 ASLGMAAGVAGGIATK NH2-ASLGMAAGVAGGIATK-COOH 63; 63 GR; GR DM; DM 2 2 100.0 Doubtful -8 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2; cds.comp41779_c0_seq3 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 LISATSISPEHK NH2-LISATSISPEHK-COOH 549; 542; 67 DR; DR; DR ID; ID; ID 4 4 100.0 Doubtful -9 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 LHVEMESMIEELQMLMDAK NH2-LHVEMESMIEELQMLMDAK-COOH 403; 403 NK; NK LS; LS 4 4 100.0 Doubtful -10 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH 147; 147 AK; AK IS; IS 4 4 100.0 Doubtful -11 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 SLQAENEQLR NH2-SLQAENEQLR-COOH 110; 110 VR; VR LK; LK 2 2 100.0 Doubtful -12 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2; cds.comp41779_c0_seq3 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 KGDIIATVDEWGPVNR NH2-KGDIIATVDEWGPVNR-COOH 590; 583; 108 AK; AK; AK NS; NS; NS 2 2 100.0 Doubtful -13 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 MEIITITNQLQR NH2-MEIITITNQLQR-COOH 373; 373 MK; MK SN; SN 2 2 100.0 Doubtful -14 cds.comp52727_c0_seq1; cds.comp52727_c0_seq2 cds.comp52727_c0_seq1, cds.comp52727_c0_seq2 (Doubtful) 1 1 EIRDEYDNQLNLLSADLESK NH2-EIRDEYDNQLNLLSADLESK-COOH 298; 298 MR; MR YQ; YQ 2 2 100.0 Doubtful -15 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH 254; 254 QK; QK SV; SV 4 4 100.0 Doubtful -16 cds.comp41779_c0_seq1; cds.comp41779_c0_seq2 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 (Doubtful) 1 1 INEDRIDELQDKVNK NH2-INEDRIDELQDKVNK-COOH 179; 179 AR; AR LI; LI 2 2 100.0 Doubtful |
| b |
| diff -r 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_peptides_result3.tabular --- a/test-data/peptide_shaker_peptides_result3.tabular Thu Sep 27 04:31:53 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,17 +0,0 @@ - Protein(s) Sequence Modified Sequence AAs Before AAs After Variable Modifications Fixed Modifications Localization Confidence #Validated PSMs #PSMs Confidence Decoy Validation -1 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 NLLLDANKENGELK NH2-NLLLDANKENGELK-COOH AK; AK IS; IS 4 4 100.0 0 Doubtful -2 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISTGYITENIGGFR NH2-ISTGYITENIGGFR-COOH NR; NR SE; SE 4 4 100.0 0 Doubtful -3 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 EIRDEYDNQLNLLSADLESK NH2-EIRDEYDNQLNLLSADLESK-COOH MR; MR YQ; YQ 2 2 100.0 0 Doubtful -4 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 INEDRIDELQDKVNK NH2-INEDRIDELQDKVNK-COOH AR; AR LI; LI 2 2 100.0 0 Doubtful -5 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SHVVGAGLGGGSMGSMNQSMSLHGGR NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH RR; RR AS; AS 2 2 100.0 0 Doubtful -6 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 LISATSISPEHK NH2-LISATSISPEHK-COOH DR; DR; DR ID; ID; ID 4 4 100.0 0 Doubtful -7 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ISITTYEEEIEDLHATAR NH2-ISITTYEEEIEDLHATAR-COOH LK; LK IN; IN 2 2 100.0 0 Doubtful -8 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 VGNLEEELEFLR NH2-VGNLEEELEFLR-COOH QK; QK SV; SV 4 4 100.0 0 Doubtful -9 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 SVISIGEVESEGQYVTLENTSSGR NH2-SVISIGEVESEGQYVTLENTSSGR-COOH SK; SK; SK SK; SK; SK 2 2 100.0 0 Doubtful -10 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 SLQAENEQLR NH2-SLQAENEQLR-COOH VR; VR LK; LK 2 2 100.0 0 Doubtful -11 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 LHVEMESMIEELQMLMDAK NH2-LHVEMESMIEELQMLMDAK-COOH NK; NK LS; LS 4 4 100.0 0 Doubtful -12 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 KGDIIATVDEWGPVNR NH2-KGDIIATVDEWGPVNR-COOH AK; AK; AK NS; NS; NS 2 2 100.0 0 Doubtful -13 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 EFDVEPLKEAYQAEIDEAK NH2-EFDVEPLKEAYQAEIDEAK-COOH RR; RR NL; NL 2 2 100.0 0 Doubtful -14 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 ASLGMAAGVAGGIATK NH2-ASLGMAAGVAGGIATK-COOH GR; GR DM; DM 2 2 100.0 0 Doubtful -15 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 YESQLSQIR NH2-YESQLSQIR-COOH AR; AR QS; QS 2 2 100.0 0 Doubtful -16 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 MEIITITNQLQR NH2-MEIITITNQLQR-COOH MK; MK SN; SN 2 2 100.0 0 Doubtful |
| b |
| diff -r 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_proteins_phoshorylation_result2.tabular --- a/test-data/peptide_shaker_proteins_phoshorylation_result2.tabular Thu Sep 27 04:31:53 2018 -0400 +++ /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.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 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 15 15 15 15 15 15 40 40 100.0 Doubtful -2 cds.comp52727_c0_seq1 m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 69.96963713242043 100.0 3.25 0.0032520325203252032 0 0 Related Proteins cds.comp52727_c0_seq2 cds.comp52727_c0_seq1, cds.comp52727_c0_seq2 1 1 1 1 1 1 2 2 100.0 Doubtful |
| b |
| diff -r 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_proteins_result2.tabular --- a/test-data/peptide_shaker_proteins_result2.tabular Thu Sep 27 04:31:53 2018 -0400 +++ /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.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 cds.comp41779_c0_seq1, cds.comp41779_c0_seq2 15 15 15 15 15 15 40 40 100.0 Doubtful -2 cds.comp52727_c0_seq1 m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 69.96963713242043 100.0 3.25 4451.587393160344 Related Proteins cds.comp52727_c0_seq2 cds.comp52727_c0_seq1, cds.comp52727_c0_seq2 1 1 1 1 1 1 2 2 100.0 Doubtful |
| b |
| diff -r 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_psm_phoshorylation_result2.tabular --- a/test-data/peptide_shaker_psm_phoshorylation_result2.tabular Thu Sep 27 04:31:53 2018 -0400 +++ /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, cds.comp41779_c0_seq2\tLHVEMESMIEELQMLMDAK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 1198, +MSn(1139.0413), 115.6 min\t\t-1.0\t1139.04127\t2+\t2+\t2276.05608409959\t0\t5.225020941968939\t\t\t\t\t\t\t\t100.0\tDoubtful\n-2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tNLLLDANKENGELK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 207, MSn(785.9179), 35.7 min\t\t-1.0\t785.91791\t2+\t2+\t1569.8362356486905\t0\t-9.522902824571501\t\t\t\t\t\t\t\t100.0\tDoubtful\n-3\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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-3.232431329032245\t\t\t\t\t\t\t\t100.0\tDoubtful\n-4\tcds.comp52727_c0_seq1, cds.comp52727_c0_seq2\tEIRDEYDNQLNLLSADLESK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 748, +MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.1444984557097\t0\t6.206637734347747\t\t\t\t\t\t\t\t100.0\tDoubtful\n-5\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tLHVEMESMIEELQMLMDAK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 1198, MSn(1139.0413), 115.6 min\t\t-1.0\t1139.04127\t2+\t2+\t2276.05608409959\t0\t5.225020941968939\t\t\t\t\t\t\t\t100.0\tDoubtful\n-6\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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-3.232431329032245\t\t\t\t\t\t\t\t100.0\tDoubtful\n-7\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tNLLLDANKENGELK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 207, +MSn(785.9179), 35.7 min\t\t-1.0\t785.91791\t2+\t2+\t1569.8362356486905\t0\t-9.522902824571501\t\t\t\t\t\t\t\t100.0\tDoubtful\n-8\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tSHVVGAGLGGGSMGSMNQSMSLHGGR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 220, MSn(824.3852), 36.3 min\t\t-1.0\t824.38516\t3+\t3+\t2470.1263804604496\t0\t2.939629370057349\t\t\t\t\t\t\t\t100.0\tDoubtful\n-9\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tEFDVEPLKEAYQAEIDEAK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 736, MSn(742.0258), 75.1 min\t\t-1.0\t742.02585\t3+\t3+\t2223.05830922026\t0\t-1.1628605149493787\t\t\t\t\t\t\t\t100.0\tDoubtful\n-10\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tINEDRIDELQDKVNK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 81, MSn(610.3171), 27.0 min\t\t-1.0\t610.31708\t3+\t3+\t1827.9326552146704\t0\t-1.7720894394949223\t\t\t\t\t\t\t\t100.0\tDoubtful\n-11\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tVGNLEEELEFLR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 875, +MSn(483.2538), 89.2 min\t\t-1.0\t483.25374\t3+\t3+\t1446.7354589782603\t0\t2.711916908512312\t\t\t\t\t\t\t\t100.0\tDoubtful\n-12\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tEFDVEPLKEAYQAEIDEAK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 736, +MSn(742.0258), 75.1 min\t\t-1.0\t742.02585\t3+\t3+\t2223.05830922026\t0\t-1.1628605149493787\t\t\t\t\t\t\t\t100.0\tDoubtful\n-13\tcds.comp52727_c0_seq1, cds.comp52727_c0_seq2\tEIRDEYDNQLNLLSADLESK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 748, MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.1444984557097\t0\t6.206637734347747\t\t\t\t\t\t\t\t100.0\tDoubtful\n-14\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tASLGMAAGVAGGIATK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 357, MSn(687.8723), 46.6 min\t\t-1.0\t687.87224\t2+\t2+\t1373.7336851564505\t0\t-2.731669916283406\t\t\t\t\t\t\t\t100.0\tDoubtful\n-15\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tVGNLEEELEFLR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 875, MSn(483.2538), 89.2 min\t\t-1.0\t483.25374\t3+\t3+\t1446.7354589782603\t0\t2.711916908512312\t\t\t\t\t\t\t\t100.0\tDoubtful\n-16\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tINEDRIDELQDKVNK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 81, +MSn(610.3171), 27.0 min\t\t-1.0\t610.31708\t3+\t3+\t1827.9326552146704\t0\t-1.7720894394949223\t\t\t\t\t\t\t\t100.0\tDoubtful\n-17\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tLHVEMESMIEELQMLMDAK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 1197, MSn(759.6966), 115.6 min\t\t-1.0\t759.69661\t3+'..b'2\t0\t1.6439836590138295\t\t\t\t\t\t\t\t100.0\tDoubtful\n-25\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tSVISIGEVESEGQYVTLENTSSGR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 758, +MSn(847.7508), 76.8 min\t\t-1.0\t847.75082\t3+\t3+\t2540.2242053283903\t0\t2.5264056585684305\t\t\t\t\t\t\t\t100.0\tDoubtful\n-26\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\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\t1.4810042052113237\t\t\t\t\t\t\t\t100.0\tDoubtful\n-27\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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\t6.998127984108653\t\t\t\t\t\t\t\t100.0\tDoubtful\n-28\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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\t2.0634108237361883\t\t\t\t\t\t\t\t100.0\tDoubtful\n-29\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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\t6.998127984108653\t\t\t\t\t\t\t\t100.0\tDoubtful\n-30\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tVGNLEEELEFLR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 871, +MSn(724.3762), 88.9 min\t\t-1.0\t724.37624\t2+\t2+\t1446.7354589782603\t0\t1.7035983403308754\t\t\t\t\t\t\t\t100.0\tDoubtful\n-31\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tKGDIIATVDEWGPVNR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 582, +MSn(590.6452), 63.2 min\t\t-1.0\t590.64518\t3+\t3+\t1768.9107975712802\t0\t1.6439836590138295\t\t\t\t\t\t\t\t100.0\tDoubtful\n-32\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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\t3.1135461012602375\t\t\t\t\t\t\t\t100.0\tDoubtful\n-33\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tSVISIGEVESEGQYVTLENTSSGR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 758, MSn(847.7508), 76.8 min\t\t-1.0\t847.75082\t3+\t3+\t2540.2242053283903\t0\t2.5264056585684305\t\t\t\t\t\t\t\t100.0\tDoubtful\n-34\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISITTYEEEIEDLHATAR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 752, +MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167787614505\t0\t6.6562738302421005\t\t\t\t\t\t\t\t100.0\tDoubtful\n-35\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISTGYITENIGGFR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 591, MSn(509.9328), 63.7 min\t\t-1.0\t509.93283\t3+\t3+\t1526.7729071161402\t0\t2.4535863107993414\t\t\t\t\t\t\t\t100.0\tDoubtful\n-36\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tLHVEMESMIEELQMLMDAK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 1197, +MSn(759.6966), 115.6 min\t\t-1.0\t759.69661\t3+\t3+\t2276.05608409959\t0\t5.2286496671522364\t\t\t\t\t\t\t\t100.0\tDoubtful\n-37\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISITTYEEEIEDLHATAR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 752, MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167787614505\t0\t6.6562738302421005\t\t\t\t\t\t\t\t100.0\tDoubtful\n-38\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tASLGMAAGVAGGIATK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 357, +MSn(687.8723), 46.6 min\t\t-1.0\t687.87224\t2+\t2+\t1373.7336851564505\t0\t-2.731669916283406\t\t\t\t\t\t\t\t100.0\tDoubtful\n-39\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tNLLLDANKENGELK\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 204, +MSn(524.2825), 35.5 min\t\t-1.0\t524.28252\t3+\t3+\t1569.8362356486905\t0\t-6.678955564950069\t\t\t\t\t\t\t\t100.0\tDoubtful\n-40\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tLISATSISPEHK\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\t\t\t\t\t\t\t\t100.0\tDoubtful\n-41\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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\t2.0634108237361883\t\t\t\t\t\t\t\t100.0\tDoubtful\n-42\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISTGYITENIGGFR\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 591, +MSn(509.9328), 63.7 min\t\t-1.0\t509.93283\t3+\t3+\t1526.7729071161402\t0\t2.4535863107993414\t\t\t\t\t\t\t\t100.0\tDoubtful\n' |
| b |
| diff -r 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_psm_result1.tabular --- a/test-data/peptide_shaker_psm_result1.tabular Thu Sep 27 04:31:53 2018 -0400 +++ /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, cds.comp41779_c0_seq2\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+\t2276.05608409959\t0\t5.225020941968939\t\t\t\t100.0\tDoubtful\n-2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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+\t1569.8362356486905\t0\t-9.522902824571501\t\t\t\t100.0\tDoubtful\n-3\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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-3.232431329032245\t\t\t\t100.0\tDoubtful\n-4\tcds.comp52727_c0_seq1, cds.comp52727_c0_seq2\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+\t2364.1444984557097\t0\t6.206637734347747\t\t\t\t100.0\tDoubtful\n-5\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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+\t2276.05608409959\t0\t5.225020941968939\t\t\t\t100.0\tDoubtful\n-6\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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-3.232431329032245\t\t\t\t100.0\tDoubtful\n-7\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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+\t1569.8362356486905\t0\t-9.522902824571501\t\t\t\t100.0\tDoubtful\n-8\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tSHVVGAGLGGGSMGSMNQSMSLHGGR\tRR; RR\tAS; AS\t37; 37\tNH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 220, MSn(824.3852), 36.3 min\t\t-1.0\t824.38516\t3+\t3+\t2470.1263804604496\t0\t2.939629370057349\t\t\t\t100.0\tDoubtful\n-9\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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+\t2223.05830922026\t0\t-1.1628605149493787\t\t\t\t100.0\tDoubtful\n-10\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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+\t1827.9326552146704\t0\t-1.7720894394949223\t\t\t\t100.0\tDoubtful\n-11\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tVGNLEEELEFLR\tQK; QK\tSV; SV\t254; 254\tNH2-VGNLEEELEFLR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 875, +MSn(483.2538), 89.2 min\t\t-1.0\t483.25374\t3+\t3+\t1446.7354589782603\t0\t2.711916908512312\t\t\t\t100.0\tDoubtful\n-12\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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+\t2223.05830922026\t0\t-1.1628605149493787\t\t\t\t100.0\tDoubtful\n-13\tcds.comp52727_c0_seq1, cds.comp52727_c0_seq2\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+\t2364.1444984557097\t0\t6.206637734347747\t\t\t\t100.0\tDoubtful\n-14\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tASLGMAAGVAGGIATK\tGR; GR\tDM; DM\t63; 63\tNH2-ASLGMAAGVAGGIATK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 357, MSn(687.8723), 46.6 min\t\t-1.0\t687.87224\t2+\t2+\t1373.7336851564505\t0\t-2.731669916283406\t\t\t\t'..b'2\t0\t6.998127984108653\t\t\t\t100.0\tDoubtful\n-28\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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\t2.0634108237361883\t\t\t\t100.0\tDoubtful\n-29\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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\t6.998127984108653\t\t\t\t100.0\tDoubtful\n-30\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tVGNLEEELEFLR\tQK; QK\tSV; SV\t254; 254\tNH2-VGNLEEELEFLR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 871, +MSn(724.3762), 88.9 min\t\t-1.0\t724.37624\t2+\t2+\t1446.7354589782603\t0\t1.7035983403308754\t\t\t\t100.0\tDoubtful\n-31\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tKGDIIATVDEWGPVNR\tAK; AK; AK\tNS; NS; NS\t590; 583; 108\tNH2-KGDIIATVDEWGPVNR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 582, +MSn(590.6452), 63.2 min\t\t-1.0\t590.64518\t3+\t3+\t1768.9107975712802\t0\t1.6439836590138295\t\t\t\t100.0\tDoubtful\n-32\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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\t3.1135461012602375\t\t\t\t100.0\tDoubtful\n-33\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tSVISIGEVESEGQYVTLENTSSGR\tSK; SK; SK\tSK; SK; SK\t511; 504; 29\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+\t2540.2242053283903\t0\t2.5264056585684305\t\t\t\t100.0\tDoubtful\n-34\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISITTYEEEIEDLHATAR\tLK; LK\tIN; IN\t161; 161\tNH2-ISITTYEEEIEDLHATAR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 752, +MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167787614505\t0\t6.6562738302421005\t\t\t\t100.0\tDoubtful\n-35\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISTGYITENIGGFR\tNR; NR\tSE; SE\t442; 442\tNH2-ISTGYITENIGGFR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 591, MSn(509.9328), 63.7 min\t\t-1.0\t509.93283\t3+\t3+\t1526.7729071161402\t0\t2.4535863107993414\t\t\t\t100.0\tDoubtful\n-36\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tLHVEMESMIEELQMLMDAK\tNK; NK\tLS; LS\t403; 403\tNH2-LHVEMESMIEELQMLMDAK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 1197, +MSn(759.6966), 115.6 min\t\t-1.0\t759.69661\t3+\t3+\t2276.05608409959\t0\t5.2286496671522364\t\t\t\t100.0\tDoubtful\n-37\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISITTYEEEIEDLHATAR\tLK; LK\tIN; IN\t161; 161\tNH2-ISITTYEEEIEDLHATAR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 752, MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167787614505\t0\t6.6562738302421005\t\t\t\t100.0\tDoubtful\n-38\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tASLGMAAGVAGGIATK\tGR; GR\tDM; DM\t63; 63\tNH2-ASLGMAAGVAGGIATK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 357, +MSn(687.8723), 46.6 min\t\t-1.0\t687.87224\t2+\t2+\t1373.7336851564505\t0\t-2.731669916283406\t\t\t\t100.0\tDoubtful\n-39\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tNLLLDANKENGELK\tAK; AK\tIS; IS\t147; 147\tNH2-NLLLDANKENGELK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 204, +MSn(524.2825), 35.5 min\t\t-1.0\t524.28252\t3+\t3+\t1569.8362356486905\t0\t-6.678955564950069\t\t\t\t100.0\tDoubtful\n-40\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tLISATSISPEHK\tDR; DR; DR\tID; ID; ID\t549; 542; 67\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\t\t\t\t100.0\tDoubtful\n-41\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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\t2.0634108237361883\t\t\t\t100.0\tDoubtful\n-42\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISTGYITENIGGFR\tNR; NR\tSE; SE\t442; 442\tNH2-ISTGYITENIGGFR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 591, +MSn(509.9328), 63.7 min\t\t-1.0\t509.93283\t3+\t3+\t1526.7729071161402\t0\t2.4535863107993414\t\t\t\t100.0\tDoubtful\n' |
| b |
| diff -r 64e3a8cc8ffb -r 58a3e6cb2598 test-data/peptide_shaker_psm_result2.tabular --- a/test-data/peptide_shaker_psm_result2.tabular Thu Sep 27 04:31:53 2018 -0400 +++ /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, cds.comp41779_c0_seq2\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+\t2276.05608409959\t0\t5.225020941968939\t\t\t\t100.0\tDoubtful\n-2\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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+\t1569.8362356486905\t0\t-9.522902824571501\t\t\t\t100.0\tDoubtful\n-3\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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-3.232431329032245\t\t\t\t100.0\tDoubtful\n-4\tcds.comp52727_c0_seq1, cds.comp52727_c0_seq2\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+\t2364.1444984557097\t0\t6.206637734347747\t\t\t\t100.0\tDoubtful\n-5\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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+\t2276.05608409959\t0\t5.225020941968939\t\t\t\t100.0\tDoubtful\n-6\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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-3.232431329032245\t\t\t\t100.0\tDoubtful\n-7\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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+\t1569.8362356486905\t0\t-9.522902824571501\t\t\t\t100.0\tDoubtful\n-8\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tSHVVGAGLGGGSMGSMNQSMSLHGGR\tRR; RR\tAS; AS\t37; 37\tNH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 220, MSn(824.3852), 36.3 min\t\t-1.0\t824.38516\t3+\t3+\t2470.1263804604496\t0\t2.939629370057349\t\t\t\t100.0\tDoubtful\n-9\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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+\t2223.05830922026\t0\t-1.1628605149493787\t\t\t\t100.0\tDoubtful\n-10\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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+\t1827.9326552146704\t0\t-1.7720894394949223\t\t\t\t100.0\tDoubtful\n-11\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tVGNLEEELEFLR\tQK; QK\tSV; SV\t254; 254\tNH2-VGNLEEELEFLR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 875, +MSn(483.2538), 89.2 min\t\t-1.0\t483.25374\t3+\t3+\t1446.7354589782603\t0\t2.711916908512312\t\t\t\t100.0\tDoubtful\n-12\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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+\t2223.05830922026\t0\t-1.1628605149493787\t\t\t\t100.0\tDoubtful\n-13\tcds.comp52727_c0_seq1, cds.comp52727_c0_seq2\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+\t2364.1444984557097\t0\t6.206637734347747\t\t\t\t100.0\tDoubtful\n-14\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tASLGMAAGVAGGIATK\tGR; GR\tDM; DM\t63; 63\tNH2-ASLGMAAGVAGGIATK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 357, MSn(687.8723), 46.6 min\t\t-1.0\t687.87224\t2+\t2+\t1373.7336851564505\t0\t-2.731669916283406\t\t\t\t'..b'2\t0\t6.998127984108653\t\t\t\t100.0\tDoubtful\n-28\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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\t2.0634108237361883\t\t\t\t100.0\tDoubtful\n-29\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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\t6.998127984108653\t\t\t\t100.0\tDoubtful\n-30\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tVGNLEEELEFLR\tQK; QK\tSV; SV\t254; 254\tNH2-VGNLEEELEFLR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 871, +MSn(724.3762), 88.9 min\t\t-1.0\t724.37624\t2+\t2+\t1446.7354589782603\t0\t1.7035983403308754\t\t\t\t100.0\tDoubtful\n-31\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tKGDIIATVDEWGPVNR\tAK; AK; AK\tNS; NS; NS\t590; 583; 108\tNH2-KGDIIATVDEWGPVNR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 582, +MSn(590.6452), 63.2 min\t\t-1.0\t590.64518\t3+\t3+\t1768.9107975712802\t0\t1.6439836590138295\t\t\t\t100.0\tDoubtful\n-32\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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\t3.1135461012602375\t\t\t\t100.0\tDoubtful\n-33\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tSVISIGEVESEGQYVTLENTSSGR\tSK; SK; SK\tSK; SK; SK\t511; 504; 29\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+\t2540.2242053283903\t0\t2.5264056585684305\t\t\t\t100.0\tDoubtful\n-34\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISITTYEEEIEDLHATAR\tLK; LK\tIN; IN\t161; 161\tNH2-ISITTYEEEIEDLHATAR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 752, +MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167787614505\t0\t6.6562738302421005\t\t\t\t100.0\tDoubtful\n-35\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISTGYITENIGGFR\tNR; NR\tSE; SE\t442; 442\tNH2-ISTGYITENIGGFR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 591, MSn(509.9328), 63.7 min\t\t-1.0\t509.93283\t3+\t3+\t1526.7729071161402\t0\t2.4535863107993414\t\t\t\t100.0\tDoubtful\n-36\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tLHVEMESMIEELQMLMDAK\tNK; NK\tLS; LS\t403; 403\tNH2-LHVEMESMIEELQMLMDAK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 1197, +MSn(759.6966), 115.6 min\t\t-1.0\t759.69661\t3+\t3+\t2276.05608409959\t0\t5.2286496671522364\t\t\t\t100.0\tDoubtful\n-37\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISITTYEEEIEDLHATAR\tLK; LK\tIN; IN\t161; 161\tNH2-ISITTYEEEIEDLHATAR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 752, MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167787614505\t0\t6.6562738302421005\t\t\t\t100.0\tDoubtful\n-38\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tASLGMAAGVAGGIATK\tGR; GR\tDM; DM\t63; 63\tNH2-ASLGMAAGVAGGIATK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 357, +MSn(687.8723), 46.6 min\t\t-1.0\t687.87224\t2+\t2+\t1373.7336851564505\t0\t-2.731669916283406\t\t\t\t100.0\tDoubtful\n-39\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tNLLLDANKENGELK\tAK; AK\tIS; IS\t147; 147\tNH2-NLLLDANKENGELK-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 204, +MSn(524.2825), 35.5 min\t\t-1.0\t524.28252\t3+\t3+\t1569.8362356486905\t0\t-6.678955564950069\t\t\t\t100.0\tDoubtful\n-40\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2, cds.comp41779_c0_seq3\tLISATSISPEHK\tDR; DR; DR\tID; ID; ID\t549; 542; 67\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\t\t\t\t100.0\tDoubtful\n-41\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\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\t2.0634108237361883\t\t\t\t100.0\tDoubtful\n-42\tcds.comp41779_c0_seq1, cds.comp41779_c0_seq2\tISTGYITENIGGFR\tNR; NR\tSE; SE\t442; 442\tNH2-ISTGYITENIGGFR-COOH\t\t\tsearchgui_tinyspectra1.mgf\t Cmpd 591, +MSn(509.9328), 63.7 min\t\t-1.0\t509.93283\t3+\t3+\t1526.7729071161402\t0\t2.4535863107993414\t\t\t\t100.0\tDoubtful\n' |