| Previous changeset 20:2cafc729b2ae (2015-05-31) Next changeset 22:e3be595c0bf5 (2015-08-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c |
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modified:
README.rst peptide_shaker.xml repository_dependencies.xml searchgui.xml 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 test-data/peptide_shaker_result1.cps test-data/peptide_shaker_result1.zip test-data/tiny_searchgui_result1.zip tool_dependencies.xml |
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added:
test-data/peptide_shaker_certificate_result2.txt test-data/tiny_searchgui_result_amandaonly.zip |
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| diff -r 2cafc729b2ae -r dfaea053e32f README.rst --- a/README.rst Sun May 31 09:05:57 2015 -0400 +++ b/README.rst Tue Jun 16 23:43:39 2015 -0400 |
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| @@ -14,8 +14,8 @@ Includes tool wrappers for SearchGUI and PeptideShaker. The SearchGUI tool takes any number of mgf files and performs searches on these. It creates a large zip archive with all search results, the original database and spectra. This can then be fed to the PeptideShaker tool which merges the results and performs peptide and protein inference. -Configuration -------------- +General Requirements +-------------------- This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell: @@ -27,7 +27,20 @@ It is also possible to set this on a per tool basis using advanced features of the galaxy job config system. -Note: +MSAmanda on linux +----------------- + +Running MS Amanda on Linux requires that you have Mono installed. Mono 3.2.1 or newer is required. If you install via the toolshed Mono should be installed automatically, however if this does not work you can install it manually. + +On ubuntu Mono can be installed as follows + + sudo apt-get install mono-runtime + sudo apt-get install libmono-system-core4.0-cil + +For more help on installing Mono please see http://www.mono-project.com/download. + +Note +---- - PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server. @@ -75,4 +88,6 @@ * Cody Wang * Fred Sadler * John Chilton <jmchilton@gmail.com> +* Gerben Menschaert +* Elvis Ndah * Minnesota Supercomputing Institute, Univeristy of Minnesota |
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| diff -r 2cafc729b2ae -r dfaea053e32f peptide_shaker.xml --- a/peptide_shaker.xml Sun May 31 09:05:57 2015 -0400 +++ b/peptide_shaker.xml Tue Jun 16 23:43:39 2015 -0400 |
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| @@ -1,13 +1,13 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="0.38.0"> +<tool id="peptide_shaker" name="Peptide Shaker" version="0.40.0"> <description> Perform protein identification using various search engines based on results from SearchGUI </description> - <requirements> - <requirement type="package" version="0.38">peptide_shaker</requirement> - </requirements> <macros> <import>macros.xml</import> </macros> + <requirements> + <requirement type="package" version="0.40">peptide_shaker</requirement> + </requirements> <expand macro="stdio" /> <command> <![CDATA[ @@ -161,7 +161,7 @@ ]]> </command> <inputs> - <param name="searchgui_input" format="searchgui_zip" type="data" label="Compressed SearchGUI results" + <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results" help="SearchGUI Results from History"/> <conditional name="species_type"> @@ -545,7 +545,7 @@ </outputs> <tests> <test> - <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/> + <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> <param name="species_type_selector" value="no_species_type"/> <param name="processing_options_selector" value="no"/> <param name="filtering_options_selector" value="no"/> @@ -555,13 +555,13 @@ <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" /> </test> <test> - <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/> + <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> <param name="species_type_selector" value="no_species_type"/> <param name="processing_options_selector" value="no"/> <param name="filtering_options_selector" value="yes"/> <param name="min_peptide_length" value="1"/> <param name="outputs" value="0,1,2,3,4,5,6,7"/> - <output name="output_certificate" file="peptide_shaker_certificate_result2.tabular" ftype="tabular" lines_diff="4"/> + <output name="output_certificate" file="peptide_shaker_certificate_result2.txt" ftype="txt" lines_diff="6"/> <output name="output_hierarchical" file="peptide_shaker_hierarchical_result2.tabular" ftype="tabular" /> <output name="output_psm" file="peptide_shaker_psm_result2.tabular" ftype="tabular" /> <output name="output_psm_phosphorylation" file="peptide_shaker_psm_phoshorylation_result2.tabular" ftype="tabular" /> @@ -571,7 +571,7 @@ <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" /> </test> <test> - <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/> + <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> <param name="species_type_selector" value="Vertebrates"/> <param name="species" value="Human (Homo sapiens)"/> <param name="processing_options_selector" value="no"/> |
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| diff -r 2cafc729b2ae -r dfaea053e32f repository_dependencies.xml --- a/repository_dependencies.xml Sun May 31 09:05:57 2015 -0400 +++ b/repository_dependencies.xml Tue Jun 16 23:43:39 2015 -0400 |
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| @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="Required proteomics dependencies."> - <repository changeset_revision="d1ea609e57d4" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="300fc3aa6954" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories> |
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| diff -r 2cafc729b2ae -r dfaea053e32f searchgui.xml --- a/searchgui.xml Sun May 31 09:05:57 2015 -0400 +++ b/searchgui.xml Tue Jun 16 23:43:39 2015 -0400 |
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| b'@@ -1,13 +1,14 @@\n-<tool id="search_gui" name="Search GUI" version="1.27.0">\n+<tool id="search_gui" name="Search GUI" version="1.28.0">\n <description>\n Perform protein identification using various search engines and prepare results for input to Peptide Shaker\n </description>\n- <requirements>\n- <requirement type="package" version="1.27">searchgui</requirement>\n- </requirements>\n <macros>\n <import>macros.xml</import>\n </macros>\n+ <requirements>\n+ <requirement type="package" version="1.28">searchgui</requirement>\n+ <environment_variable name="LC_ALL" action="set_to">C</environment_variable> \n+ </requirements>\n <expand macro="stdio" />\n <command>\n <![CDATA[\n@@ -34,7 +35,7 @@\n java -cp \\$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy &&\n rm input_database.fasta &&\n cp input_database_concatenated_target_decoy.fasta input_database.fasta &&\n- ##ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;\n+ ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;\n #end if\n \n #####################################################\n@@ -48,43 +49,196 @@\n \n -db input_database.fasta\n \n- #if $advanced.advanced_type_selector == "advanced":\n+ #if $xtandem.xtandem_advanced == "yes"\n+\n+ -xtandem_npeaks ${xtandem.xtandem_npeaks}\n+ -xtandem_min_peaks ${xtandem.xtandem_min_peaks}\n+ -xtandem_min_frag_mz ${xtandem.xtandem_min_frag_mz}\n+ -xtandem_min_prec_mass ${xtandem.xtandem_min_prec_mass}\n+ -xtandem_noise_suppr ${xtandem.xtandem_noise_suppr}\n+ -xtandem_dynamic_range ${xtandem.xtandem_dynamic_range}\n+ -xtandem_quick_acetyl ${xtandem.xtandem_quick_acetyl} \n+ -xtandem_quick_pyro ${xtandem.xtandem_quick_pyro} \n+ -xtandem_stp_bias ${xtandem.xtandem_stp_bias} \n+ -xtandem_evalue ${xtandem.xtandem_evalue} \n+ -xtandem_output_proteins ${xtandem.xtandem_output_proteins} \n+ -xtandem_output_sequences ${xtandem.xtandem_output_sequences} \n+ -xtandem_output_spectra ${xtandem.xtandem_output_spectra}\n+ ## -xtandem_skyline_path ${xtandem.xtandem_skyline_path}\n+\n+ #if $xtandem.xtandem_refine.xtandem_refine_selector == "yes"\n+ -xtandem_refine 1\n+ -xtandem_refine_unc ${xtandem.xtandem_refine.xtandem_refine_unc}\n+ -xtandem_refine_semi ${xtandem.xtandem_refine.xtandem_refine_semi}\n+ -xtandem_refine_p_mut ${xtandem.xtandem_refine.xtandem_refine_p_mut}\n+ -xtandem_refine_snaps ${xtandem.xtandem_refine.xtandem_refine_snaps}\n+ -xtandem_refine_spec_synt ${xtandem.xtandem_refine.xtandem_refine_spec_synt}\n+ -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_pot}\n+ -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_evalue}\n+ \n+ #end if\n+ #end if\n \n- #if $advanced.xtandem.xtandem_selector == "yes"\n+ #if $omssa.omssa_advanced == "yes"\n+ -omssa_hitlist_length ${omssa.hitlist_length}\n+ -omssa_remove_prec ${omssa.remove_precursor}\n+ -omssa_scale_prec ${omssa.scale_precursor}\n+ -omssa_estimate_charge ${omssa.estimate_charge}\n+\n+ -omssa_memory ${omssa.omssa_memory}\n+ -omssa_isotopes ${omssa.omssa_isotopes} \n+ -omssa_neutron ${omssa.omssa_neutron} \n+ -omssa_low_intensity "${omssa.omssa_low_intensity}" \n+ -omssa_high_intensity ${omssa.omssa_high_intensity} \n+ -omssa_intensity_incr ${omssa.omssa_intensity_incr} \n+ -o'..b'aks are represented (0 or 1 values are allowed)" /> \n </when>\n </conditional>\n-\n- <conditional name="ms_amanda">\n- <param name="ms_amanda_selector" type="select" label="Run MS Amanda search">\n- <option value="yes">Search with MS Amanda</option>\n- <option value="no" selected="True">No MS Amanda search</option>\n- </param>\n- <when value="no" />\n- <when value="yes">\n- </when>\n- </conditional>\n-\n- <conditional name="tide">\n- <param name="tide_selector" type="select" label="Run Tide search">\n- <option value="yes">Search with Tide</option>\n- <option value="no" selected="True">No Comet search</option>\n- </param>\n- <when value="no" />\n- <when value="yes">\n- </when>\n- </conditional>\n-\n </when>\n </conditional>\n </inputs>\n <outputs>\n- <data name="searchgui_results" format="searchgui_zip" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />\n+ <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />\n </outputs>\n <tests>\n+\n+ <!-- Test that specifying non-default search engines works -->\n <test>\n <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>\n <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>\n@@ -344,21 +883,35 @@\n <param name="variable_modifications" value="oxidation of m"/>\n <param name="min_charge" value="1"/>\n <param name="max_charge" value="3"/>\n- <param name="advanced_type_selector" value="advanced"/>\n- <param name="xtandem_selector" value="yes"/>\n- <param name="xtandem_selector.xtandem_refine_selector" value="yes"/>\n- <param name="omssa_selector" value="no"/>\n- <param name="msgf_selector" value="yes"/>\n- <param name="ms_amanda_selector" value="no"/>\n- <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_zip" compare="sim_size" delta="600" /> \n+ <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>\n+ <param name="xtandem.xtandem_advanced" value="yes"/>\n+ <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>\n+\n+ <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="600" /> \n </test>\n+\n+ <!-- Test that search works with MSAmanda -->\n+ <test>\n+ <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>\n+ <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>\n+ <param name="precursor_ion_tol" value="100"/>\n+ <param name="fixed_modifications" value="carbamidomethyl c"/>\n+ <param name="variable_modifications" value="oxidation of m"/>\n+ <param name="min_charge" value="1"/>\n+ <param name="max_charge" value="3"/>\n+ <param name="engines" value="MS_Amanda"/>\n+\n+ <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="600" /> \n+ </test>\n+\n+\n </tests>\n <help>\n **What it does**\n \n Runs multiple search engines on any number of MGF peak lists using the SearchGUI.\n-\n-By default X! Tandem, OMSSA, MS-GF+, Myrimatch and Comet are run. Optionally, Amanda and Tide engines can also be run.\n+Default: X! Tandem, OMSSA and MS-GF+ are executed.\n+Optional: MyriMatch, MS-Amanda, Comet and Tide can be executed.\n \n </help>\n <expand macro="citations" />\n' |
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| diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_certificate_result2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peptide_shaker_certificate_result2.txt Tue Jun 16 23:43:39 2015 -0400 |
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| @@ -0,0 +1,67 @@ +Project Details1: PeptideShaker Version: 0.39.1 +2: Date: Thu Jun 04 20:07:16 CEST 2015 +3: Experiment: Galaxy_Experiment_2015060420071433441234 +4: Sample: Sample_2015060420071433441234 +5: Replicate Number: 1 +6: Identification Algorithms: OMSSA, X!Tandem, MS-GF+ and Comet +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: H2O, NH3 +5: Neutral Losses Sequence Dependence: Yes +6: Fragment Ion m/z Tolerance: 0.5 |
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| diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_hierarchical_result2.tabular --- a/test-data/peptide_shaker_hierarchical_result2.tabular Sun May 31 09:05:57 2015 -0400 +++ b/test-data/peptide_shaker_hierarchical_result2.tabular Tue Jun 16 23:43:39 2015 -0400 |
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| b'@@ -1,78 +1,79 @@\n-\tMain Accession\tDescription\tMW [kDa]\tCoverage [%]\tPossible Coverage [%]\tSpectrum Counting NSAF \tConfidently Localized Modification Sites\t# Confidently Localized Modification Sites\tAmbiguously Localized Modification Sites\t#Ambiguously Localized Modification Sites\tPI\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|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67\t\t69.88215372568374\t3757.96\t92.52\t0.014450915311500504\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\t39\t39\t100.0\t0\tDoubtful\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\tPI\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|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67\t\t69.88215372568374\t92.52\t37.58\t0.01785479771710408\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-1.1\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\tISITTYEEEIEDLHATAR\tLK; LK\tIN; IN\t\t\t\t2\t2\t100.0\t0\tDoubtful\n+1.1\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\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-1.1.1\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\tISITTYEEEIEDLHATAR\tNH2-ISITTYEEEIEDLHATAR-COOH\t\t\ttinyspectra.mgf\tCmpd 752, +MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167716836995\t0\t6.659655420038472\t0\t\t\t\t100.0\tDoubtful\n-1.1.2\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\tISITTYEEEIEDLHATAR\tNH2-ISITTYEEEIEDLHAT'..b'in\t\t-1.0\t590.64518\t3+\t3+\t1768.9107986836998\t0\t1.6433558579610066\t0\t\t\t\t100.0\tDoubtful\n+1.15.2\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\tKGDIIATVDEWGPVNR\tNH2-KGDIIATVDEWGPVNR-COOH\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 582, +MSn(590.6452), 63.2 min\t\t-1.0\t590.64518\t3+\t3+\t1768.9107986836998\t0\t1.6433558579610066\t0\t\t\t\t100.0\tDoubtful\n+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\t\t69.9696370486838\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 2.1\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-2.1.1\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\ttinyspectra.mgf\tCmpd 748, +MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.1444886837\t0\t6.210765906697086\t0\t\t\t\t100.0\tDoubtful\n-2.1.2\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\ttinyspectra.mgf\tCmpd 748, MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.1444886837\t0\t6.210765906697086\t0\t\t\t\t100.0\tDoubtful\n+2.1.1\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\tCmpd 748, MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.1444886837\t0\t6.210765906697086\t0\t\t\t\t100.0\tDoubtful\n+2.1.2\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\tCmpd 748, +MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.1444886837\t0\t6.210765906697086\t0\t\t\t\t100.0\tDoubtful\n' |
| b |
| diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_peptides_phoshorylation_result2.tabular --- a/test-data/peptide_shaker_peptides_phoshorylation_result2.tabular Sun May 31 09:05:57 2015 -0400 +++ b/test-data/peptide_shaker_peptides_phoshorylation_result2.tabular Tue Jun 16 23:43:39 2015 -0400 |
| b |
| b'@@ -1,17 +1,17 @@\n \tProtein(s)\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\tDecoy\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\tISITTYEEEIEDLHATAR\tNH2-ISITTYEEEIEDLHATAR-COOH\tLK; LK\tIN; IN\t\t\t\t\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-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\tMR; MR\tYQ; YQ\t\t\t\t\t\t\t\t2\t2\t100.0\t0\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\tNLLLDANKENGELK\tNH2-NLLLDANKENGELK-COOH\tAK; AK\tIS; IS\t\t\t\t\t\t\t\t4\t4\t100.0\t0\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\tSLQAENEQLR\tNH2-SLQAENEQLR-COOH\tVR; VR\tLK; LK\t\t\t\t\t\t\t\t2\t2\t100.0\t0\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\tINEDRIDELQDKVNK\tNH2-INEDRIDELQDKVNK-COOH\tAR; AR\tLI; LI\t\t\t\t\t\t\t\t2\t2\t100.0\t0\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\tMEIITITNQLQR\tNH2-MEIITITNQLQR-COOH\tMK; MK\tSN; SN\t\t\t\t\t\t\t\t2\t2\t100.0\t0\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\tLHVEMESMIEELQMLMDAK\tNH2-LHVEMESMIEELQMLMDAK-COOH\tNK; NK\tLS; LS\t\t\t\t\t\t\t\t3\t3\t100.0\t0\tDoubtful\n-8\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\tNH2-YESQLSQIR-COOH\tAR; AR\tQS; QS\t\t\t\t\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-9\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\tVGNLEEELEFLR\tNH2-VGNLEEELEFLR-COOH\tQK; QK\tSV; SV\t\t\t\t\t\t\t\t4\t4\t100.0\t0\tDoubtful\n-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; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10\tKGDIIATVDEWGPVNR\tNH2-KGDIIATVDEWGPVNR-COOH\tAK; AK; AK\tNS; NS; NS\t\t\t\t\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-11\tcds.comp41779_c0_seq'..b'1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10\tLISATSISPEHK\tNH2-LISATSISPEHK-COOH\tDR; DR; DR\tID; ID; ID\t\t\t\t\t\t\t\t4\t4\t100.0\t0\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\tISITTYEEEIEDLHATAR\tNH2-ISITTYEEEIEDLHATAR-COOH\tLK; LK\tIN; IN\t\t\t\t\t\t\t\t2\t2\t100.0\t0\tDoubtful\n+8\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\tVGNLEEELEFLR\tNH2-VGNLEEELEFLR-COOH\tQK; QK\tSV; SV\t\t\t\t\t\t\t\t4\t4\t100.0\t0\tDoubtful\n+9\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\tSK; SK; SK\tSK; SK; SK\t\t\t\t\t\t\t\t2\t2\t100.0\t0\tDoubtful\n+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\tSLQAENEQLR\tNH2-SLQAENEQLR-COOH\tVR; VR\tLK; LK\t\t\t\t\t\t\t\t2\t2\t100.0\t0\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\tLHVEMESMIEELQMLMDAK\tNH2-LHVEMESMIEELQMLMDAK-COOH\tNK; NK\tLS; LS\t\t\t\t\t\t\t\t4\t4\t100.0\t0\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\tKGDIIATVDEWGPVNR\tNH2-KGDIIATVDEWGPVNR-COOH\tAK; AK; AK\tNS; NS; NS\t\t\t\t\t\t\t\t2\t2\t100.0\t0\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\tEFDVEPLKEAYQAEIDEAK\tNH2-EFDVEPLKEAYQAEIDEAK-COOH\tRR; RR\tNL; NL\t\t\t\t\t\t\t\t2\t2\t100.0\t0\tDoubtful\n+14\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\tASLGMAAGVAGGIATK\tNH2-ASLGMAAGVAGGIATK-COOH\tGR; GR\tDM; DM\t\t\t\t\t\t\t\t2\t2\t100.0\t0\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\tYESQLSQIR\tNH2-YESQLSQIR-COOH\tAR; AR\tQS; QS\t\t\t\t\t\t\t\t2\t2\t100.0\t0\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\tMEIITITNQLQR\tNH2-MEIITITNQLQR-COOH\tMK; MK\tSN; SN\t\t\t\t\t\t\t\t2\t2\t100.0\t0\tDoubtful\n' |
| b |
| diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_peptides_result2.tabular --- a/test-data/peptide_shaker_peptides_result2.tabular Sun May 31 09:05:57 2015 -0400 +++ b/test-data/peptide_shaker_peptides_result2.tabular Tue Jun 16 23:43:39 2015 -0400 |
| b |
| b'@@ -1,17 +1,17 @@\n \tProtein(s)\tSequence\tModified Sequence\tAAs Before\tAAs After\tVariable Modifications\tFixed Modifications\tLocalization Confidence\t#Validated PSMs\t#PSMs\tConfidence\tDecoy\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\tISITTYEEEIEDLHATAR\tNH2-ISITTYEEEIEDLHATAR-COOH\tLK; LK\tIN; IN\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-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\tMR; MR\tYQ; YQ\t\t\t\t2\t2\t100.0\t0\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\tNLLLDANKENGELK\tNH2-NLLLDANKENGELK-COOH\tAK; AK\tIS; IS\t\t\t\t4\t4\t100.0\t0\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\tSLQAENEQLR\tNH2-SLQAENEQLR-COOH\tVR; VR\tLK; LK\t\t\t\t2\t2\t100.0\t0\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\tINEDRIDELQDKVNK\tNH2-INEDRIDELQDKVNK-COOH\tAR; AR\tLI; LI\t\t\t\t2\t2\t100.0\t0\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\tMEIITITNQLQR\tNH2-MEIITITNQLQR-COOH\tMK; MK\tSN; SN\t\t\t\t2\t2\t100.0\t0\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\tLHVEMESMIEELQMLMDAK\tNH2-LHVEMESMIEELQMLMDAK-COOH\tNK; NK\tLS; LS\t\t\t\t3\t3\t100.0\t0\tDoubtful\n-8\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\tNH2-YESQLSQIR-COOH\tAR; AR\tQS; QS\t\t\t\t2\t2\t100.0\t0\tDoubtful\n-9\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\tVGNLEEELEFLR\tNH2-VGNLEEELEFLR-COOH\tQK; QK\tSV; SV\t\t\t\t4\t4\t100.0\t0\tDoubtful\n-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; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10\tKGDIIATVDEWGPVNR\tNH2-KGDIIATVDEWGPVNR-COOH\tAK; AK; AK\tNS; NS; NS\t\t\t\t2\t2\t100.0\t0\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_se'..b'RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10\tLISATSISPEHK\tNH2-LISATSISPEHK-COOH\tDR; DR; DR\tID; ID; ID\t\t\t\t4\t4\t100.0\t0\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\tISITTYEEEIEDLHATAR\tNH2-ISITTYEEEIEDLHATAR-COOH\tLK; LK\tIN; IN\t\t\t\t2\t2\t100.0\t0\tDoubtful\n+8\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\tVGNLEEELEFLR\tNH2-VGNLEEELEFLR-COOH\tQK; QK\tSV; SV\t\t\t\t4\t4\t100.0\t0\tDoubtful\n+9\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\tSK; SK; SK\tSK; SK; SK\t\t\t\t2\t2\t100.0\t0\tDoubtful\n+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\tSLQAENEQLR\tNH2-SLQAENEQLR-COOH\tVR; VR\tLK; LK\t\t\t\t2\t2\t100.0\t0\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\tLHVEMESMIEELQMLMDAK\tNH2-LHVEMESMIEELQMLMDAK-COOH\tNK; NK\tLS; LS\t\t\t\t4\t4\t100.0\t0\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\tKGDIIATVDEWGPVNR\tNH2-KGDIIATVDEWGPVNR-COOH\tAK; AK; AK\tNS; NS; NS\t\t\t\t2\t2\t100.0\t0\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\tEFDVEPLKEAYQAEIDEAK\tNH2-EFDVEPLKEAYQAEIDEAK-COOH\tRR; RR\tNL; NL\t\t\t\t2\t2\t100.0\t0\tDoubtful\n+14\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\tASLGMAAGVAGGIATK\tNH2-ASLGMAAGVAGGIATK-COOH\tGR; GR\tDM; DM\t\t\t\t2\t2\t100.0\t0\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\tYESQLSQIR\tNH2-YESQLSQIR-COOH\tAR; AR\tQS; QS\t\t\t\t2\t2\t100.0\t0\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\tMEIITITNQLQR\tNH2-MEIITITNQLQR-COOH\tMK; MK\tSN; SN\t\t\t\t2\t2\t100.0\t0\tDoubtful\n' |
| b |
| diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_peptides_result3.tabular --- a/test-data/peptide_shaker_peptides_result3.tabular Sun May 31 09:05:57 2015 -0400 +++ b/test-data/peptide_shaker_peptides_result3.tabular Tue Jun 16 23:43:39 2015 -0400 |
| b |
| @@ -0,0 +1,17 @@ + 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 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_proteins_phoshorylation_result2.tabular --- a/test-data/peptide_shaker_proteins_phoshorylation_result2.tabular Sun May 31 09:05:57 2015 -0400 +++ b/test-data/peptide_shaker_proteins_phoshorylation_result2.tabular Tue Jun 16 23:43:39 2015 -0400 |
| [ |
| @@ -1,3 +1,3 @@ - Main Accession Description Gene Name Chromosome MW [kDa] Coverage [%] Possible Coverage [%] Spectrum Counting NSAF Confident Phosphosites #Confident Phosphosites Ambiguous Phosphosites #Ambiguous Phosphosites PI Secondary Accessions Protein Group #Validated Peptides #Peptides #Unique #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 69.88215372568374 3757.96 92.52 0.014450915311500504 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 39 39 100.0 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 69.9696370486838 325.2 100.0 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 2 2 100.0 0 Doubtful + Main Accession Description Gene Name Chromosome MW [kDa] Possible Coverage [%] Coverage [%] Spectrum Counting NSAF Confident Phosphosites #Confident Phosphosites Ambiguous Phosphosites #Ambiguous Phosphosites PI Secondary Accessions Protein Group #Validated Peptides #Peptides #Unique #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 69.88215372568374 92.52 37.58 0.01785479771710408 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 40 40 100.0 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 69.9696370486838 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 2 2 100.0 0 Doubtful |
| b |
| diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_proteins_result2.tabular --- a/test-data/peptide_shaker_proteins_result2.tabular Sun May 31 09:05:57 2015 -0400 +++ b/test-data/peptide_shaker_proteins_result2.tabular Tue Jun 16 23:43:39 2015 -0400 |
| [ |
| @@ -1,3 +1,3 @@ - Main Accession Description Gene Name Chromosome MW [kDa] Coverage [%] Possible Coverage [%] Spectrum Counting NSAF Confidently Localized Modification Sites # Confidently Localized Modification Sites Ambiguously Localized Modification Sites #Ambiguously Localized Modification Sites PI Secondary Accessions Protein Group #Validated Peptides #Peptides #Unique #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 69.88215372568374 3757.96 92.52 0.014450915311500504 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 39 39 100.0 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 69.9696370486838 325.2 100.0 0.0032520325203252032 Related Proteins cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 1 1 1 2 2 100.0 0 Doubtful + Main Accession Description Gene Name Chromosome MW [kDa] Possible Coverage [%] Coverage [%] Spectrum Counting NSAF Confidently Localized Modification Sites # Confidently Localized Modification Sites Ambiguously Localized Modification Sites #Ambiguously Localized Modification Sites PI Secondary Accessions Protein Group #Validated Peptides #Peptides #Unique #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 69.88215372568374 92.52 37.58 0.01785479771710408 Related Proteins cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 15 15 15 40 40 100.0 0 Doubtful +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 69.9696370486838 100.0 3.25 0.0032520325203252032 Related Proteins cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 1 1 1 2 2 100.0 0 Doubtful |
| b |
| diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_psm_phoshorylation_result2.tabular --- a/test-data/peptide_shaker_psm_phoshorylation_result2.tabular Sun May 31 09:05:57 2015 -0400 +++ b/test-data/peptide_shaker_psm_phoshorylation_result2.tabular Tue Jun 16 23:43:39 2015 -0400 |
| [ |
| b'@@ -1,42 +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]\tDecoy\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\tISITTYEEEIEDLHATAR\t\t\ttinyspectra.mgf\tCmpd 752, +MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167716836995\t0\t6.659655420038472\t0\t\t\t\t\t\t\t\t100.0\tDoubtful\n-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\t\t\ttinyspectra.mgf\tCmpd 748, +MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.1444886837\t0\t6.210765906697086\t0\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\tNLLLDANKENGELK\t\t\ttinyspectra.mgf\tCmpd 204, +MSn(524.2825), 35.5 min\t\t-1.0\t524.28252\t3+\t3+\t1569.8362346836998\t0\t-6.678342042310128\t0\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\tSLQAENEQLR\t\t\ttinyspectra.mgf\tCmpd 39, +MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942146837\t0\t2.0632379154490605\t0\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\tINEDRIDELQDKVNK\t\t\ttinyspectra.mgf\tCmpd 81, +MSn(610.3171), 27.0 min\t\t-1.0\t610.31708\t3+\t3+\t1827.9326546837003\t0\t-1.7717994436305495\t0\t\t\t\t\t\t\t\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\tMEIITITNQLQR\t\t\ttinyspectra.mgf\tCmpd 636, +MSn(730.3981), 66.9 min\t\t-1.0\t730.39814\t2+\t2+\t1458.7864506836997\t0\t-3.233580283650776\t0\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\tLHVEMESMIEELQMLMDAK\t\t\ttinyspectra.mgf\tCmpd 1198, +MSn(1139.0413), 115.6 min\t\t-1.0\t1139.04127\t2+\t2+\t2276.0560846836997\t0\t5.224764535153943\t0\t\t\t\t\t\t\t\t100.0\tDoubtful\n-8\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\ttinyspectra.mgf\tCmpd 67, +MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669286837\t0\t7.00561302556395\t0\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:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70'..b'0560846836997\t0\t5.228393373659577\t0\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\tLHVEMESMIEELQMLMDAK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 1198, +MSn(1139.0413), 115.6 min\t\t-1.0\t1139.04127\t2+\t2+\t2276.0560846836997\t0\t5.224764535153943\t0\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\tISITTYEEEIEDLHATAR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 752, +MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167716836995\t0\t6.659655420038472\t0\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, 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\tCmpd 75, +MSn(641.8547), 26.7 min\t\t-1.0\t641.85466\t2+\t2+\t1281.6928656837001\t0\t1.4811651380377848\t0\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\tSHVVGAGLGGGSMGSMNQSMSLHGGR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 220, +MSn(824.3852), 36.3 min\t\t-1.0\t824.38516\t3+\t3+\t2470.1263816837\t0\t2.9391347559636922\t0\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, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10\tKGDIIATVDEWGPVNR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 582, +MSn(590.6452), 63.2 min\t\t-1.0\t590.64518\t3+\t3+\t1768.9107986836998\t0\t1.6433558579610066\t0\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\tISTGYITENIGGFR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 588, +MSn(764.3961), 63.5 min\t\t-1.0\t764.39611\t2+\t2+\t1526.7728996836997\t0\t3.1184077735785474\t0\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\tEFDVEPLKEAYQAEIDEAK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 736, +MSn(742.0258), 75.1 min\t\t-1.0\t742.02585\t3+\t3+\t2223.0583016837\t0\t-1.1594749443833878\t0\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, 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\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 758, +MSn(847.7508), 76.8 min\t\t-1.0\t847.75082\t3+\t3+\t2540.2241966836996\t0\t2.5298047449054923\t0\t\t\t\t\t\t\t\t100.0\tDoubtful\n' |
| b |
| diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_psm_result1.tabular --- a/test-data/peptide_shaker_psm_result1.tabular Sun May 31 09:05:57 2015 -0400 +++ b/test-data/peptide_shaker_psm_result1.tabular Tue Jun 16 23:43:39 2015 -0400 |
| [ |
| b'@@ -1,42 +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]\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\tISITTYEEEIEDLHATAR\t\t\ttinyspectra.mgf\tCmpd 752, +MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167716836995\t0\t6.659655420038472\t0\t\t\t\t100.0\tDoubtful\n-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\t\t\ttinyspectra.mgf\tCmpd 748, +MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.1444886837\t0\t6.210765906697086\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\tNLLLDANKENGELK\t\t\ttinyspectra.mgf\tCmpd 204, +MSn(524.2825), 35.5 min\t\t-1.0\t524.28252\t3+\t3+\t1569.8362346836998\t0\t-6.678342042310128\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\tSLQAENEQLR\t\t\ttinyspectra.mgf\tCmpd 39, +MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942146837\t0\t2.0632379154490605\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\tINEDRIDELQDKVNK\t\t\ttinyspectra.mgf\tCmpd 81, +MSn(610.3171), 27.0 min\t\t-1.0\t610.31708\t3+\t3+\t1827.9326546837003\t0\t-1.7717994436305495\t0\t\t\t\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\tMEIITITNQLQR\t\t\ttinyspectra.mgf\tCmpd 636, +MSn(730.3981), 66.9 min\t\t-1.0\t730.39814\t2+\t2+\t1458.7864506836997\t0\t-3.233580283650776\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\tLHVEMESMIEELQMLMDAK\t\t\ttinyspectra.mgf\tCmpd 1198, +MSn(1139.0413), 115.6 min\t\t-1.0\t1139.04127\t2+\t2+\t2276.0560846836997\t0\t5.224764535153943\t0\t\t\t\t100.0\tDoubtful\n-8\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\ttinyspectra.mgf\tCmpd 67, +MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669286837\t0\t7.00561302556395\t0\t\t\t\t100.0\tDoubtful\n-9\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\ttinyspectra.mgf\tCmpd'..b'15.6 min\t\t-1.0\t759.69661\t3+\t3+\t2276.0560846836997\t0\t5.228393373659577\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\tLHVEMESMIEELQMLMDAK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 1198, +MSn(1139.0413), 115.6 min\t\t-1.0\t1139.04127\t2+\t2+\t2276.0560846836997\t0\t5.224764535153943\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\tISITTYEEEIEDLHATAR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 752, +MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167716836995\t0\t6.659655420038472\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, 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\tCmpd 75, +MSn(641.8547), 26.7 min\t\t-1.0\t641.85466\t2+\t2+\t1281.6928656837001\t0\t1.4811651380377848\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\tSHVVGAGLGGGSMGSMNQSMSLHGGR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 220, +MSn(824.3852), 36.3 min\t\t-1.0\t824.38516\t3+\t3+\t2470.1263816837\t0\t2.9391347559636922\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, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10\tKGDIIATVDEWGPVNR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 582, +MSn(590.6452), 63.2 min\t\t-1.0\t590.64518\t3+\t3+\t1768.9107986836998\t0\t1.6433558579610066\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\tISTGYITENIGGFR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 588, +MSn(764.3961), 63.5 min\t\t-1.0\t764.39611\t2+\t2+\t1526.7728996836997\t0\t3.1184077735785474\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\tEFDVEPLKEAYQAEIDEAK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 736, +MSn(742.0258), 75.1 min\t\t-1.0\t742.02585\t3+\t3+\t2223.0583016837\t0\t-1.1594749443833878\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, 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\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 758, +MSn(847.7508), 76.8 min\t\t-1.0\t847.75082\t3+\t3+\t2540.2241966836996\t0\t2.5298047449054923\t0\t\t\t\t100.0\tDoubtful\n' |
| b |
| diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_psm_result2.tabular --- a/test-data/peptide_shaker_psm_result2.tabular Sun May 31 09:05:57 2015 -0400 +++ b/test-data/peptide_shaker_psm_result2.tabular Tue Jun 16 23:43:39 2015 -0400 |
| [ |
| b'@@ -1,42 +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]\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\tISITTYEEEIEDLHATAR\t\t\ttinyspectra.mgf\tCmpd 752, +MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167716836995\t0\t6.659655420038472\t0\t\t\t\t100.0\tDoubtful\n-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\t\t\ttinyspectra.mgf\tCmpd 748, +MSn(789.0604), 76.1 min\t\t-1.0\t789.06034\t3+\t3+\t2364.1444886837\t0\t6.210765906697086\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\tNLLLDANKENGELK\t\t\ttinyspectra.mgf\tCmpd 204, +MSn(524.2825), 35.5 min\t\t-1.0\t524.28252\t3+\t3+\t1569.8362346836998\t0\t-6.678342042310128\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\tSLQAENEQLR\t\t\ttinyspectra.mgf\tCmpd 39, +MSn(594.3056), 25.0 min\t\t-1.0\t594.30561\t2+\t2+\t1186.5942146837\t0\t2.0632379154490605\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\tINEDRIDELQDKVNK\t\t\ttinyspectra.mgf\tCmpd 81, +MSn(610.3171), 27.0 min\t\t-1.0\t610.31708\t3+\t3+\t1827.9326546837003\t0\t-1.7717994436305495\t0\t\t\t\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\tMEIITITNQLQR\t\t\ttinyspectra.mgf\tCmpd 636, +MSn(730.3981), 66.9 min\t\t-1.0\t730.39814\t2+\t2+\t1458.7864506836997\t0\t-3.233580283650776\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\tLHVEMESMIEELQMLMDAK\t\t\ttinyspectra.mgf\tCmpd 1198, +MSn(1139.0413), 115.6 min\t\t-1.0\t1139.04127\t2+\t2+\t2276.0560846836997\t0\t5.224764535153943\t0\t\t\t\t100.0\tDoubtful\n-8\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\ttinyspectra.mgf\tCmpd 67, +MSn(562.2947), 26.3 min\t\t-1.0\t562.29468\t2+\t2+\t1122.5669286837\t0\t7.00561302556395\t0\t\t\t\t100.0\tDoubtful\n-9\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\ttinyspectra.mgf\tCmpd'..b'15.6 min\t\t-1.0\t759.69661\t3+\t3+\t2276.0560846836997\t0\t5.228393373659577\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\tLHVEMESMIEELQMLMDAK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 1198, +MSn(1139.0413), 115.6 min\t\t-1.0\t1139.04127\t2+\t2+\t2276.0560846836997\t0\t5.224764535153943\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\tISITTYEEEIEDLHATAR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 752, +MSn(697.6842), 76.3 min\t\t-1.0\t697.68418\t3+\t3+\t2090.0167716836995\t0\t6.659655420038472\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, 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\tCmpd 75, +MSn(641.8547), 26.7 min\t\t-1.0\t641.85466\t2+\t2+\t1281.6928656837001\t0\t1.4811651380377848\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\tSHVVGAGLGGGSMGSMNQSMSLHGGR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 220, +MSn(824.3852), 36.3 min\t\t-1.0\t824.38516\t3+\t3+\t2470.1263816837\t0\t2.9391347559636922\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, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10\tKGDIIATVDEWGPVNR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 582, +MSn(590.6452), 63.2 min\t\t-1.0\t590.64518\t3+\t3+\t1768.9107986836998\t0\t1.6433558579610066\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\tISTGYITENIGGFR\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 588, +MSn(764.3961), 63.5 min\t\t-1.0\t764.39611\t2+\t2+\t1526.7728996836997\t0\t3.1184077735785474\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\tEFDVEPLKEAYQAEIDEAK\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 736, +MSn(742.0258), 75.1 min\t\t-1.0\t742.02585\t3+\t3+\t2223.0583016837\t0\t-1.1594749443833878\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, 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\t\t\tsearchgui_tinyspectra1.mgf\tCmpd 758, +MSn(847.7508), 76.8 min\t\t-1.0\t847.75082\t3+\t3+\t2540.2241966836996\t0\t2.5298047449054923\t0\t\t\t\t100.0\tDoubtful\n' |
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| @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="searchgui" version="1.27"> - <repository changeset_revision="6ad0463c0e64" name="package_searchgui_1_27" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="searchgui" version="1.28"> + <repository changeset_revision="0d8bbd52ae42" name="package_searchgui_1_28" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="peptide_shaker" version="0.38"> - <repository changeset_revision="958037b48c33" name="package_peptideshaker_0_38" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="peptide_shaker" version="0.40"> + <repository changeset_revision="9a4d33da1cce" name="package_peptideshaker_0_40" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |