| Previous changeset 1:86770eea5b09 (2017-03-04) Next changeset 3:abed51712ed0 (2017-04-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4ca7fcd1587c906db3314048a223d23b63b3f038 |
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modified:
datatypes_conf.xml nested_collection.py nested_collection.xml percolator.xml test-data/percolatorOut.xml test-data/target_ds2_withperco.mzid test-data/target_ds3_withperco.mzid |
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added:
percolator_converters.xml test-data/percolatorOut_alloptions.xml |
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removed:
msgf2pin.xml percolator_datatypes.py |
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| diff -r 86770eea5b09 -r 7a0951d0e13e datatypes_conf.xml --- a/datatypes_conf.xml Sat Mar 04 20:36:03 2017 -0500 +++ b/datatypes_conf.xml Fri Mar 10 03:20:52 2017 -0500 |
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| @@ -5,7 +5,7 @@ </datatype_files> <registration> <datatype extension="percin" type="galaxy.datatypes.data:Text" subclass="true" /> - <datatype extension="percout" type="galaxy.datatypes.percolator:PercolatorOutXml" /> + <datatype extension="percout" type="galaxy.datatypes.xml:GenericXml" subclass="true" /> <datatype extension="meta2pin" type="galaxy.datatypes.data:Text" subclass="true" /> </registration> </datatypes> |
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| diff -r 86770eea5b09 -r 7a0951d0e13e msgf2pin.xml --- a/msgf2pin.xml Sat Mar 04 20:36:03 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,116 +0,0 @@ -<tool id="msgfplus2pin" name="MS-GF+ output to Pin converter" version="3.0.1"> - <description>to create Percolator input files</description> - <requirements> - <requirement type="package" version="3.0">percolator</requirement> - </requirements> - <stdio> - <exit_code range="1:"/> - </stdio> - <command><![CDATA[ - mkdir target && mkdir decoy && - - #if $mzids.inputtype == "multi" - #for $key in $mzids.target.keys() - ln -s '$mzids.target[$key]' 'target/$key' && - echo 'target/$key' >> targetmeta && - #end for - #for $key in $mzids.decoy.keys() - ln -s '$mzids.decoy[$key]' 'decoy/$key' && - echo 'decoy/$key' >> decoymeta && - #end for - msgf2pin -o $pinout -e $enzyme - #if $matches - -m $matches - #end if - $aafreq $ptm $pngase $isotope targetmeta decoymeta - - #else - ln -s '$mzids.target' 'target/$target.display_name' && - ln -s '$mzids.decoy' 'decoy/$decoy.display_name' && - msgf2pin -o $pinout -e $enzyme - #if $matches - -m $matches - #end if - $aafreq $ptm $pngase $isotope - 'target/$mzids.target.display_name' 'decoy/$mzids.decoy.display_name' - #end if - ]]></command> - <inputs> - <conditional name="mzids"> - <param name="inputtype" type="select" display="radio"> - <option value="single">Single mzIdentML</option> - <option value="multi">Multiple mzIdentMLs</option> - </param> - <when value="single"> - <param name="target" type="data" format="mzid" label="Target MSGF+ results" /> - <param name="decoy" type="data" format="mzid" label="Decoy MSGF+ results" /> - </when> - <when value="multi"> - <param name="target" type="data_collection" collection_type="list" format="mzid" label="Target MSGF+ results" /> - <param name="decoy" type="data_collection" collection_type="list" format="mzid" label="Decoy MSGF+ results" /> - </when> - </conditional> - <param name="enzyme" type="select" label="Enzyme used"> - <option value="trypsin">trypsin</option> - <option value="no_enzyme">no enzyme</option> - <option value="elastase">elastase</option> - <option value="pepsin">pepsin</option> - <option value="proteinasek">proteinase K</option> - <option value="thermolysin">thermolysin</option> - <option value="chymotrypsin">chymotrypsin</option> - <option value="lys-n">lys-N</option> - <option value="lys-c">lys-C</option> - <option value="arg-c">arg-C</option> - <option value="asp-n">asp-N</option> - <option value="glu-c">glu-C</option> - </param> - <param name="matches" type="integer" optional="true" label="Max number of PSMs for a spectrum" /> - <param name="aafreq" type="boolean" label="Calculate amino acid frequency features" truevalue="-a" falsevalue="" /> - <param name="ptm" type="boolean" label="Calculate feature for number of PTMs" truevalue="-b" falsevalue="" /> - <param name="pngase" type="boolean" label="Calculate feature based on N-linked glycosylation resulting from PNGaseF" truevalue="-N" falsevalue="" /> - <param name="isotope" type="boolean" label="Calculate mass difference to closest isotope instead of avg. mass" truevalue="-M" falsevalue="" /> - </inputs> - <outputs> - <data format="percin" name="pinout"/> - </outputs> - <tests> - <test> - <param name="mzids|inputtype" value="single" /> - <param name="mzids|target" value="target.mzid" /> - <param name="mzids|decoy" value="decoy.mzid" /> - <param name="ptm" value="true"/> - <param name="matches" value="1"/> - <output name="pinout" value="percolatorInresult.txt" compare="sim_size" delta="20" /> - </test> - <test> - <param name="mzids|inputtype" value="multi" /> - <param name="mzids|target"> - <collection type="list"> - <element name="target1" value="target.mzid" /> - <element name="target2" value="target.mzid" /> - </collection> - </param> - <param name="mzids|decoy"> - <collection type="list"> - <element name="decoy1" value="decoy.mzid" /> - <element name="decoy2" value="decoy.mzid" /> - </collection> - </param> - <param name="ptm" value="true"/> - <param name="matches" value="1"/> - <output name="pinout" value="percolatorInresult_multifractions.txt" compare="sim_size" delta="20" /> - </test> - </tests> - <help> -The percolator converter msgf2pin converts mzIdentML to input for percolator. -Target and decoy inputs are MzIdentML-files of MS-GF+ from -separate target and decoy searches. Internal MS-GF+ target/decoy -analysis should be turned off, and the addFeatures options turned on. -Multiple MzIdentML-files can be merged by passing lists of these. -For successful results, the different runs should be generated under -similar conditions. - </help> - <citations> - <citation type="doi">10.1021/pr400937n</citation> - </citations> -</tool> |
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| diff -r 86770eea5b09 -r 7a0951d0e13e nested_collection.py --- a/nested_collection.py Sat Mar 04 20:36:03 2017 -0500 +++ b/nested_collection.py Fri Mar 10 03:20:52 2017 -0500 |
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| @@ -44,7 +44,7 @@ for batchcount, (pool_id, batch) in enumerate(get_batches_of_galaxyfiles( args.realnames, args.batchsize, args.poolids)): for fncount, batchfile in enumerate([args.galaxyfiles[index] for index in batch]): - dsetname = '{}___batch{}_inputfn{}.mzid'.format(pool_id, batchcount, fncount) + dsetname = '{}_batch{}___inputfn{}.mzid'.format(pool_id, batchcount, fncount) print('producing', dsetname) os.symlink(batchfile, dsetname) |
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| diff -r 86770eea5b09 -r 7a0951d0e13e nested_collection.xml --- a/nested_collection.xml Sat Mar 04 20:36:03 2017 -0500 +++ b/nested_collection.xml Fri Mar 10 03:20:52 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="batched_set_list_creator" name="Create nested list" version="3.0.1"> +<tool id="batched_set_list_creator" name="Create nested list" version="3.1"> <description>based on filenames and batch sizes</description> <stdio> <exit_code range="1:" /> @@ -32,7 +32,7 @@ </inputs> <outputs> <collection name="batched_fractions" type="list:list" label="Pooled batched data"> - <discover_datasets pattern="[a-zA-z0-9_]*___(?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)\.mzid" ext="mzid" visible="true" /> + <discover_datasets pattern="(?P<identifier_0>\w+[^_][^_][^_])___(?P<identifier_1>[^_]+)\.mzid" ext="mzid" visible="true" /> </collection> </outputs> <tests> @@ -47,11 +47,11 @@ </collection> </param> <output_collection name="batched_fractions" type="list:list"> - <element name="batch0"> + <element name="pool0_batch0"> <element name="inputfn0" file="empty_file1.mzid"/> <element name="inputfn1" file="empty_file2.mzid"/> </element> - <element name="batch1"> + <element name="pool0_batch1"> <element name="inputfn0" file="empty_file3.mzid"/> <element name="inputfn1" file="empty_file4.mzid"/> </element> @@ -75,12 +75,12 @@ </collection> </param> <output_collection name="batched_fractions" type="list:list"> - <element name="batch0"> + <element name="set1_batch0"> <element name="inputfn0" file="empty_file1.mzid"/> <element name="inputfn1" file="empty_file2.mzid"/> <element name="inputfn2" file="empty_file3.mzid"/> </element> - <element name="batch1"> + <element name="set2_batch1"> <element name="inputfn0" file="empty_file4.mzid"/> <element name="inputfn1" file="empty_file5.mzid"/> <element name="inputfn2" file="empty_file6.mzid"/> @@ -106,18 +106,18 @@ </collection> </param> <output_collection name="batched_fractions" type="list:list"> - <element name="batch0"> + <element name="set1_batch0"> <element name="inputfn0" file="empty_file1.mzid"/> <element name="inputfn1" file="empty_file2.mzid"/> </element> - <element name="batch1"> + <element name="set1_batch1"> <element name="inputfn0" file="empty_file3.mzid"/> </element> - <element name="batch2"> + <element name="set2_batch2"> <element name="inputfn0" file="empty_file4.mzid"/> <element name="inputfn1" file="empty_file5.mzid"/> </element> - <element name="batch3"> + <element name="set2_batch3"> <element name="inputfn0" file="empty_file6.mzid"/> </element> </output_collection> |
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| diff -r 86770eea5b09 -r 7a0951d0e13e percolator.xml --- a/percolator.xml Sat Mar 04 20:36:03 2017 -0500 +++ b/percolator.xml Fri Mar 10 03:20:52 2017 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="percolator" name="Percolator" version="3.0.1"> +<tool id="percolator" name="Percolator" version="3.1.0"> <description>accurate peptide identification</description> <requirements> - <requirement type="package" version="3.0">percolator</requirement> + <requirement type="package" version="3.1">percolator</requirement> </requirements> <stdio> <exit_code range="1:"/> @@ -13,6 +13,7 @@ #else -J '$percoout' #end if + $tdmethod #if $cpos -p $cpos #end if @@ -37,18 +38,22 @@ $quickval $unitnorm $override $onlypsms </command> <inputs> - <param name="output_type" label="What filetype to output" type="select" display="radio"> - <option value="xml" selected="true">percolator XML (for further processing)</option> - <option value="tsv">Tab-separated</option> + <param name="output_type" label="What to output" type="select" display="radio"> + <option value="xml" selected="true">Percolator output (XML)</option> + <option value="tsv">Computed features of input (Tab separated)</option> </param> <param name="input" type="data" format="percin" label="Percolator input data" /> + <param name="tdmethod" type="select" label="Target decoy method"> + <option value="-y" selected="true">Mix-max</option> + <option value="-Y">Target-decoy competition (also good when unequal amounts of target/decoy PSMs)</option> + </param> <param name="cpos" label="Penalty for mistakes on positive examples" type="float" optional="true" /> <param name="cneg" label="Penalty for mistakes on negative examples" type="float" optional="true" /> <param name="trainfdr" label="FDR threshold to define positive examples" type="float" optional="true" help="Set by cross validation if 0."/> <param name="testfdr" label="FDR threshold for evaluating best cross validation result" type="float" optional="true" /> <param name="maxiter" label="Maximal number of iterations" type="integer" optional="true" /> <param name="quickval" label="Quicker execution by reduced internal cross-validation" type="boolean" truevalue="-x" falsevalue=""/> - <param name="default_direction" label="Most informative feature given as feature number" type="integer" optional="true" /> + <param name="default_direction" label="Most informative feature given as feature name." help="Can be negated to indicate lower value=better, e.g -featureName" type="text" optional="true" /> <param name="unitnorm" type="boolean" label="Unit normalization instead of standard deviation" truevalue="-u" falsevalue=""/> <param name="override" label="Override error check?" help="and no fallback on default score vector in case of suspect score vector" type="boolean" truevalue="-O" falsevalue=""/> <param name="seed" label="Seed of random number generator" type="integer" optional="true" /> @@ -70,8 +75,25 @@ </test> <test> <param name="input" value="percolatorTab" /> + <param name="output_type" value="xml" /> + <param name="tdmethod" value="-Y" /> + <param name="cpos" value="0.00001" /> + <param name="cneg" value="0.00001" /> + <param name="trainfdr" value="0.1" /> + <param name="testfdr" value="0.1" /> + <param name="maxiter" value="5" /> + <param name="quickval" value="-x" /> + <param name="default_direction" value="RawScore" /> + <param name="unitnorm" value="-u" /> + <param name="override" value="-O" /> + <param name="seed" value="2" /> + <param name="onlypsms" value="-U" /> + <output name="percoout" value="percolatorOut_alloptions.xml" lines_diff="2" /> + </test> + <test> + <param name="input" value="percolatorTab" /> <param name="output_type" value="tsv" /> - <output name="percoout" value="percolatorOut.txt" /> + <output name="percoout" value="percolatorOut.txt" lines_diff="1" /> </test> </tests> <help>The first step in analyzing an mass spectrometry assay is to match the harvested spectra against a target database using database search engines such as Sequest and Mascot, a process that renders list of peptide-spectrum matches. However, it is not trivial to assess the accuracy of these identifications. |
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| diff -r 86770eea5b09 -r 7a0951d0e13e percolator_converters.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/percolator_converters.xml Fri Mar 10 03:20:52 2017 -0500 |
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| @@ -0,0 +1,121 @@ +<tool id="percolator_input_converters" name="Search engine output to Pin converter" version="3.1"> + <description>to create Percolator input files</description> + <requirements> + <requirement type="package" version="3.1">percolator</requirement> + </requirements> + <stdio> + <exit_code range="1:"/> + </stdio> + <command><![CDATA[ + mkdir target && mkdir decoy && + + #if $mzids.inputtype == "multi" + #for $key in $mzids.target.keys() + ln -s '$mzids.target[$key]' 'target/$key' && + echo 'target/$key' >> targetmeta && + #end for + #for $key in $mzids.decoy.keys() + ln -s '$mzids.decoy[$key]' 'decoy/$key' && + echo 'decoy/$key' >> decoymeta && + #end for + $searchengine -o $pinout -e $enzyme + #if $matches + -m $matches + #end if + $aafreq $ptm $pngase $isotope targetmeta decoymeta + + #else + ln -s '$mzids.target' 'target/$target.display_name' && + ln -s '$mzids.decoy' 'decoy/$decoy.display_name' && + $searchengine -o $pinout -e $enzyme + #if $matches + -m $matches + #end if + $aafreq $ptm $pngase $isotope + 'target/$mzids.target.display_name' 'decoy/$mzids.decoy.display_name' + #end if + ]]></command> + <inputs> + <param name="searchengine" type="select" label="Search engine used"> + <option value="msgf2pin">MSGF+ (mzIdentML)</option> + <option value="tandem2pin">X!Tandem (tandem)</option> + <option value="sqt2pin">Crux (SQT output)</option> + </param> + <conditional name="mzids"> + <param name="inputtype" type="select" display="radio"> + <option value="single">Single mzIdentML</option> + <option value="multi">Multiple mzIdentMLs</option> + </param> + <when value="single"> + <param name="target" type="data" format="mzid" label="Target MSGF+ results" /> + <param name="decoy" type="data" format="mzid" label="Decoy MSGF+ results" /> + </when> + <when value="multi"> + <param name="target" type="data_collection" collection_type="list" format="mzid" label="Target MSGF+ results" /> + <param name="decoy" type="data_collection" collection_type="list" format="mzid" label="Decoy MSGF+ results" /> + </when> + </conditional> + <param name="enzyme" type="select" label="Enzyme used"> + <option value="trypsin">trypsin</option> + <option value="no_enzyme">no enzyme</option> + <option value="elastase">elastase</option> + <option value="pepsin">pepsin</option> + <option value="proteinasek">proteinase K</option> + <option value="thermolysin">thermolysin</option> + <option value="chymotrypsin">chymotrypsin</option> + <option value="lys-n">lys-N</option> + <option value="lys-c">lys-C</option> + <option value="arg-c">arg-C</option> + <option value="asp-n">asp-N</option> + <option value="glu-c">glu-C</option> + </param> + <param name="matches" type="integer" optional="true" label="Max number of PSMs for a spectrum" /> + <param name="aafreq" type="boolean" label="Calculate amino acid frequency features" truevalue="-a" falsevalue="" /> + <param name="ptm" type="boolean" label="Calculate feature for number of PTMs" truevalue="-b" falsevalue="" /> + <param name="pngase" type="boolean" label="Calculate feature based on N-linked glycosylation resulting from PNGaseF" truevalue="-N" falsevalue="" /> + <param name="isotope" type="boolean" label="Calculate mass difference to closest isotope instead of avg. mass" truevalue="-M" falsevalue="" /> + </inputs> + <outputs> + <data format="percin" name="pinout"/> + </outputs> + <tests> + <test> + <param name="mzids|inputtype" value="single" /> + <param name="mzids|target" value="target.mzid" /> + <param name="mzids|decoy" value="decoy.mzid" /> + <param name="ptm" value="true"/> + <param name="matches" value="1"/> + <output name="pinout" value="percolatorInresult.txt" compare="sim_size" delta="20" /> + </test> + <test> + <param name="mzids|inputtype" value="multi" /> + <param name="mzids|target"> + <collection type="list"> + <element name="target1" value="target.mzid" /> + <element name="target2" value="target.mzid" /> + </collection> + </param> + <param name="mzids|decoy"> + <collection type="list"> + <element name="decoy1" value="decoy.mzid" /> + <element name="decoy2" value="decoy.mzid" /> + </collection> + </param> + <param name="ptm" value="true"/> + <param name="matches" value="1"/> + <output name="pinout" value="percolatorInresult_multifractions.txt" compare="sim_size" delta="20" /> + </test> + </tests> + <help> +The percolator converter msgf2pin converts mzIdentML to input for percolator. +Target and decoy inputs are MzIdentML-files of MS-GF+ from +separate target and decoy searches. Internal MS-GF+ target/decoy +analysis should be turned off, and the addFeatures options turned on. +Multiple MzIdentML-files can be merged by passing lists of these. +For successful results, the different runs should be generated under +similar conditions. + </help> + <citations> + <citation type="doi">10.1021/pr400937n</citation> + </citations> +</tool> |
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| diff -r 86770eea5b09 -r 7a0951d0e13e percolator_datatypes.py --- a/percolator_datatypes.py Sat Mar 04 20:36:03 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,7 +0,0 @@ -from galaxy.datatypes.proteomics import ProteomicsXml - - -class PercolatorOutXml(ProteomicsXml): - """Percolator output data in XML format""" - file_ext = 'percout' - blurb = 'percolator out XML' |
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| diff -r 86770eea5b09 -r 7a0951d0e13e test-data/percolatorOut.xml --- a/test-data/percolatorOut.xml Sat Mar 04 20:36:03 2017 -0500 +++ b/test-data/percolatorOut.xml Fri Mar 10 03:20:52 2017 -0500 |
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| b'@@ -4,34 +4,46 @@\n xmlns:p="http://per-colator.com/percolator_out/15" \n xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" \n xsi:schemaLocation="http://per-colator.com/percolator_out/15 https://github.com/percolator/percolator/raw/pout-1-5/src/xml/percolator_out.xsd" \n-p:majorVersion="3" p:minorVersion="00" p:percolator_version="Percolator version 3.00">\n+p:majorVersion="3" p:minorVersion="01" p:percolator_version="Percolator version 3.01">\n \n <process_info>\n- <command_line>percolator -j testpin -X percolator30Out.xml --decoy-xml-output</command_line>\n+ <command_line>percolator -X percotest -j percolatorTab --decoy-xml-output</command_line>\n <other_command_line></other_command_line>\n- <pi_0_psms>1</pi_0_psms>\n- <pi_0_peptides>1</pi_0_peptides>\n- <psms_qlevel>60</psms_qlevel>\n- <peptides_qlevel>60</peptides_qlevel>\n+ <pi_0_psms>0.790264</pi_0_psms>\n+ <pi_0_peptides>0.805704</pi_0_peptides>\n+ <psms_qlevel>0</psms_qlevel>\n+ <peptides_qlevel>0</peptides_qlevel>\n </process_info>\n \n <psms>\n- <psm p:psm_id="dataset_2_SII_259_1_9758_3_1" p:decoy="false">\n- <svm_score>2.813409</svm_score>\n- <q_value>0.000000e+00</q_value>\n- <pep>1.126167e-05</pep>\n- <exp_mass>1020.5000</exp_mass>\n- <calc_mass>1020.180</calc_mass>\n- <peptide_seq n="K" c="V" seq="[UNIMOD:737]TDEFQLHTNVNDGTEFGGSIYQK[UNIMOD:737]"/>\n- <protein_id>ENSP00000378484.3</protein_id>\n- <protein_id>ENSP00000265333.3</protein_id>\n- <protein_id>ENSP00000378487.2</protein_id>\n- <p_value>6.357e-04</p_value>\n+ <psm p:psm_id="dataset_2_SII_438_1_9937_2_1" p:decoy="false">\n+ <svm_score>0.000000</svm_score>\n+ <q_value>2.195178e-02</q_value>\n+ <pep>6.523451e-02</pep>\n+ <exp_mass>1111.0600</exp_mass>\n+ <calc_mass>1111.070</calc_mass>\n+ <peptide_seq n="K" c="A" seq="[UNIMOD:737]YQLQSQENFEAFMK[UNIMOD:737]"/>\n+ <protein_id>ENSP00000295834.3</protein_id>\n+ <protein_id>ENSP00000377351.3</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_3_SII_386_1_9885_4_1" p:decoy="false">\n+ <svm_score>0.000</svm_score>\n+ <q_value>2.195e-02</q_value>\n+ <pep>6.523e-02</pep>\n+ <exp_mass>573.8040</exp_mass>\n+ <calc_mass>573.810</calc_mass>\n+ <peptide_seq n="K" c="G" seq="[UNIMOD:737]TYFPHFDLSHGSAQVK[UNIMOD:737]"/>\n+ <protein_id>ENSP00000322421.5</protein_id>\n+ <protein_id>ENSP00000380899.1</protein_id>\n+ <protein_id>ENSP00000251595.6</protein_id>\n+ <protein_id>ENSP00000380908.1</protein_id>\n+ <p_value>0.000e+00</p_value>\n </psm>\n <psm p:psm_id="dataset_3_SII_343_1_9842_3_1" p:decoy="false">\n- <svm_score>2.556</svm_score>\n- <q_value>0.000e+00</q_value>\n- <pep>3.128e-05</pep>\n+ <svm_score>0.000</svm_score>\n+ <q_value>2.195e-02</q_value>\n+ <pep>6.523e-02</pep>\n <exp_mass>804.7940</exp_mass>\n <calc_mass>804.802</calc_mass>\n <peptide_seq n="R" c="A" seq="[UNIMOD:737]VAPEEHPVLLTEAPLNPK[UNIMOD:737]"/>\n@@ -50,140 +62,35 @@\n <protein_id>ENSP00000460660.1</protein_id>\n <protein_id>ENSP00000466346.1</protein_id>\n <protein_id>ENSP00000477968.1</protein_id>\n- <p_value>6.357e-04</p_value>\n- </psm>\n- <psm p:psm_id="dataset_3_SII_386_1_9885_4_1" p:decoy="false">\n- <svm_score>2.202</svm_score>\n- <q_value>0.000e+00</q_value>\n- <pep>1.274e-04</pep>\n- <exp_mass>573.8040</exp_mass>\n- <calc_mass>573.810</calc_mass>\n- <peptide_seq n="K" c="G" seq="[UNIMOD:737]TYFPHFDLSHGSAQVK[UNIMOD:737]"/>\n- <protein_id>ENSP00000322421.5</protein_id>\n- <protein_id>ENSP00000380899.1</protein_id>\n- <protein_id>ENSP00000251595.6</protein_id>\n- <protein_id>ENSP00000380908.1</protein_id>\n- <p_value>6.357e-04</p_value>\n- </psm>\n- <psm p:psm_id="dataset_3_SII_176_1_9675_2_1" p:decoy="false">\n- <svm_score>1.673</svm_score>\n- <q_value>0.000e+00</q_value>\n- <pep>1.038e-03</pe'..b'_ENSP00000344055.4</protein_id>\n- <p_value>9.970e-01</p_value>\n- <psm_ids>\n- <psm_id>dataset_88023_SII_10106_1_10106_6_1</psm_id>\n- </psm_ids>\n- </peptide>\n- <peptide p:peptide_id="[UNIMOD:737]M[UNIMOD:35]TM[UNIMOD:35]RGGPC[UNIMOD:4]HK[UNIMOD:737]RPTK[UNIMOD:737]AK[UNIMOD:737]EK[UNIMOD:737]RNK[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]RK[UNIMOD:737]EILR" p:decoy="true">\n- <svm_score>-2.304</svm_score>\n- <q_value>1.000e+00</q_value>\n- <pep>1.000e+00</pep>\n- <exp_mass>1003.3000</exp_mass>\n- <calc_mass>1003.300</calc_mass>\n- <protein_id>decoy_ENSP00000428940.1</protein_id>\n- <protein_id>decoy_ENSP00000427937.1</protein_id>\n- <protein_id>decoy_ENSP00000276659.5</protein_id>\n- <protein_id>decoy_ENSP00000428614.1</protein_id>\n- <p_value>9.978e-01</p_value>\n- <psm_ids>\n- <psm_id>dataset_88023_SII_10224_1_10224_6_1</psm_id>\n- </psm_ids>\n- </peptide>\n- <peptide p:peptide_id="[UNIMOD:737]QREK[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]ELERWLEEK[UNIMOD:737]K[UNIMOD:737]LEELK[UNIMOD:737]LK[UNIMOD:737]K[UNIMOD:737]ELAK[UNIMOD:737]" p:decoy="true">\n- <svm_score>-2.508</svm_score>\n- <q_value>1.000e+00</q_value>\n- <pep>1.000e+00</pep>\n- <exp_mass>979.6190</exp_mass>\n- <calc_mass>979.460</calc_mass>\n- <protein_id>decoy_ENSP00000261461.2</protein_id>\n- <protein_id>decoy_ENSP00000442866.1</protein_id>\n- <p_value>9.985e-01</p_value>\n- <psm_ids>\n- <psm_id>dataset_88023_SII_10081_1_10081_6_1</psm_id>\n- </psm_ids>\n- </peptide>\n- <peptide p:peptide_id="[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]RK[UNIMOD:737]HK[UNIMOD:737]K[UNIMOD:737]EK[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]DK[UNIMOD:737]" p:decoy="true">\n- <svm_score>-2.583</svm_score>\n- <q_value>1.000e+00</q_value>\n- <pep>1.000e+00</pep>\n- <exp_mass>846.0940</exp_mass>\n- <calc_mass>846.257</calc_mass>\n- <protein_id>decoy_ENSP00000272139.4</protein_id>\n- <p_value>9.993e-01</p_value>\n- <psm_ids>\n- <psm_id>dataset_88023_SII_10136_1_10136_6_1</psm_id>\n- </psm_ids>\n- </peptide>\n- <peptide p:peptide_id="[UNIMOD:737]TK[UNIMOD:737]K[UNIMOD:737]ERK[UNIMOD:737]EEM[UNIMOD:35]TSEK[UNIMOD:737]K[UNIMOD:737]EVTLEK[UNIMOD:737]K[UNIMOD:737]RPTREEM[UNIMOD:35]RK[UNIMOD:737]EVILEK[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]RK[UNIMOD:737]ETSEK[UNIMOD:737]TK[UNIMOD:737]" p:decoy="true">\n- <svm_score>-2.593</svm_score>\n- <q_value>1.000e+00</q_value>\n- <pep>1.000e+00</pep>\n- <exp_mass>1548.7900</exp_mass>\n- <calc_mass>1548.780</calc_mass>\n- <protein_id>decoy_ENSP00000362455.3</protein_id>\n- <p_value>1.000e+00</p_value>\n- <psm_ids>\n- <psm_id>dataset_88023_SII_2545_1_2545_6_1</psm_id>\n+ <peptide p:peptide_id="[UNIMOD:737]LHEC[UNIMOD:4]EPSC[UNIMOD:4]VSWESWVEWSGDVPC[UNIMOD:4]LSTC[UNIMOD:4]TIR" p:decoy="true">\n+ <svm_score>-1.388</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>780.3480</exp_mass>\n+ <calc_mass>779.953</calc_mass>\n+ <protein_id>decoy_ENSP00000385143.2</protein_id>\n+ <protein_id>decoy_ENSP00000412652.1</protein_id>\n+ <protein_id>decoy_ENSP00000394303.2</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ <psm_ids>\n+ <psm_id>dataset_88023_SII_9728_1_9728_5_1</psm_id>\n+ </psm_ids>\n+ </peptide>\n+ <peptide p:peptide_id="[UNIMOD:737]MC[UNIMOD:4]DQC[UNIMOD:4]C[UNIMOD:4]VC[UNIMOD:4]QDLVDR" p:decoy="false">\n+ <svm_score>-1.404</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>1045.4500</exp_mass>\n+ <calc_mass>1044.440</calc_mass>\n+ <protein_id>ENSP00000423323.1</protein_id>\n+ <protein_id>ENSP00000426402.1</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ <psm_ids>\n+ <psm_id>dataset_2_SII_240_1_9739_2_1</psm_id>\n </psm_ids>\n </peptide>\n </peptides>\n' |
| b |
| diff -r 86770eea5b09 -r 7a0951d0e13e test-data/percolatorOut_alloptions.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/percolatorOut_alloptions.xml Fri Mar 10 03:20:52 2017 -0500 |
| [ |
| b'@@ -0,0 +1,21498 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+<percolator_output \n+xmlns="http://per-colator.com/percolator_out/15" \n+xmlns:p="http://per-colator.com/percolator_out/15" \n+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" \n+xsi:schemaLocation="http://per-colator.com/percolator_out/15 https://github.com/percolator/percolator/raw/pout-1-5/src/xml/percolator_out.xsd" \n+p:majorVersion="3" p:minorVersion="01" p:percolator_version="Percolator version 3.01">\n+\n+ <process_info>\n+ <command_line>percolator -X percotest -j percolatorTab -Y -p 0.00001 -n 0.00001 -t 0.1 -F 0.1 -i 5 -S 2 -V RawScore -x -u -O -U --decoy-xml-output</command_line>\n+ <other_command_line></other_command_line>\n+ <pi_0_psms>1</pi_0_psms>\n+ <psms_qlevel>0</psms_qlevel>\n+ </process_info>\n+\n+ <psms>\n+ <psm p:psm_id="dataset_3_SII_77_1_9576_2_1" p:decoy="false">\n+ <svm_score>0.000000</svm_score>\n+ <q_value>1.000000e+00</q_value>\n+ <pep>1.000000e+00</pep>\n+ <exp_mass>419.7500</exp_mass>\n+ <calc_mass>420.250</calc_mass>\n+ <peptide_seq n="R" c="P" seq="[UNIMOD:737]PPPGSR"/>\n+ <protein_id>ENSP00000361434.5</protein_id>\n+ <protein_id>ENSP00000436727.1</protein_id>\n+ <protein_id>ENSP00000361429.3</protein_id>\n+ <protein_id>ENSP00000391998.3</protein_id>\n+ <protein_id>ENSP00000387435.3</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_9148_1_9148_2_1" p:decoy="true">\n+ <svm_score>0.000</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>401.7190</exp_mass>\n+ <calc_mass>402.223</calc_mass>\n+ <peptide_seq n="K" c="P" seq="[UNIMOD:737]PGMGGR"/>\n+ <protein_id>decoy_ENSP00000412580.2</protein_id>\n+ <protein_id>decoy_ENSP00000347042.5</protein_id>\n+ <protein_id>decoy_ENSP00000346437.3</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_6492_1_6492_2_1" p:decoy="true">\n+ <svm_score>0.000</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>474.7240</exp_mass>\n+ <calc_mass>475.225</calc_mass>\n+ <peptide_seq n="R" c="-" seq="[UNIMOD:737]PVC[UNIMOD:4]C[UNIMOD:4]QG"/>\n+ <protein_id>decoy_ENSP00000357675.1</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_2_SII_492_1_9991_5_1" p:decoy="false">\n+ <svm_score>-0.017</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>900.4430</exp_mass>\n+ <calc_mass>900.646</calc_mass>\n+ <peptide_seq n="R" c="S" seq="[UNIMOD:737]PRLK[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]K[UNIMOD:737]RK[UNIMOD:737]K[UNIMOD:737]R"/>\n+ <protein_id>ENSP00000485049.1</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_9938_1_9938_3_1" p:decoy="true">\n+ <svm_score>-0.056</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>342.8710</exp_mass>\n+ <calc_mass>343.206</calc_mass>\n+ <peptide_seq n="R" c="P" seq="[UNIMOD:737]LRC[UNIMOD:4]PPR"/>\n+ <protein_id>decoy_ENSP00000263408.4</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_9732_1_9732_3_1" p:decoy="true">\n+ <svm_score>-0.073</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>304.8620</exp_mass>\n+ <calc_mass>305.194</calc_mass>\n+ <peptide_seq n="R" c="P" seq="[UNIMOD:737]DALPLR"/>\n+ <protein_id>decoy_ENSP00000400713.2</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_9301_1_9301_2_1" p:decoy="true">\n+ <svm_score>-0.113</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>401.7200</exp_mass>\n+ <calc_mass>402.223</calc_mass>\n+ <peptide_seq n="K" c="P" s'..b'+ <protein_id>decoy_ENSP00000487145.1</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_10309_1_10309_2_1" p:decoy="true">\n+ <svm_score>-1.604</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>961.0350</exp_mass>\n+ <calc_mass>960.541</calc_mass>\n+ <peptide_seq n="R" c="Q" seq="[UNIMOD:737]ERQRLVEM[UNIMOD:35]QEK[UNIMOD:737]"/>\n+ <protein_id>decoy_ENSP00000369627.1</protein_id>\n+ <protein_id>decoy_ENSP00000369625.3</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_10289_1_10289_2_1" p:decoy="true">\n+ <svm_score>-1.605</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>1008.0300</exp_mass>\n+ <calc_mass>1007.530</calc_mass>\n+ <peptide_seq n="R" c="S" seq="[UNIMOD:737]LNM[UNIMOD:35]YSEIEDALNK[UNIMOD:737]"/>\n+ <protein_id>decoy_ENSP00000473469.1</protein_id>\n+ <protein_id>decoy_ENSP00000473565.1</protein_id>\n+ <protein_id>decoy_ENSP00000369792.2</protein_id>\n+ <protein_id>decoy_ENSP00000354301.3</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_10381_1_10381_2_1" p:decoy="true">\n+ <svm_score>-1.612</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>1114.6200</exp_mass>\n+ <calc_mass>1114.110</calc_mass>\n+ <peptide_seq n="R" c="-" seq="[UNIMOD:737]AAEVLEVTC[UNIMOD:4]GELIIVGVPE"/>\n+ <protein_id>decoy_ENSP00000447539.1</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_10339_1_10339_2_1" p:decoy="true">\n+ <svm_score>-1.613</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>1292.6700</exp_mass>\n+ <calc_mass>1291.660</calc_mass>\n+ <peptide_seq n="K" c="C" seq="[UNIMOD:737]VTWDMC[UNIMOD:4]YLEK[UNIMOD:737]QM[UNIMOD:35]M[UNIMOD:35]K[UNIMOD:737]"/>\n+ <protein_id>decoy_ENSP00000367319.2</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_10223_1_10223_2_1" p:decoy="true">\n+ <svm_score>-1.624</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>1298.7000</exp_mass>\n+ <calc_mass>1297.690</calc_mass>\n+ <peptide_seq n="R" c="S" seq="[UNIMOD:737]NQDEINPESC[UNIMOD:4]RK[UNIMOD:737]LYTLR"/>\n+ <protein_id>decoy_ENSP00000260283.4</protein_id>\n+ <protein_id>decoy_ENSP00000437905.1</protein_id>\n+ <protein_id>decoy_ENSP00000432076.1</protein_id>\n+ <protein_id>decoy_ENSP00000436319.1</protein_id>\n+ <protein_id>decoy_ENSP00000436522.1</protein_id>\n+ <protein_id>decoy_ENSP00000431399.1</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_10036_1_10036_2_1" p:decoy="true">\n+ <svm_score>-1.634</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>998.5300</exp_mass>\n+ <calc_mass>997.517</calc_mass>\n+ <peptide_seq n="K" c="A" seq="[UNIMOD:737]DLDSQM[UNIMOD:35]QQQALDK[UNIMOD:737]"/>\n+ <protein_id>decoy_ENSP00000364691.4</protein_id>\n+ <protein_id>decoy_ENSP00000402626.2</protein_id>\n+ <protein_id>decoy_ENSP00000480016.1</protein_id>\n+ <protein_id>decoy_ENSP00000478281.1</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ <psm p:psm_id="dataset_88023_SII_10444_1_10444_2_1" p:decoy="true">\n+ <svm_score>-1.740</svm_score>\n+ <q_value>1.000e+00</q_value>\n+ <pep>1.000e+00</pep>\n+ <exp_mass>1068.5600</exp_mass>\n+ <calc_mass>1068.550</calc_mass>\n+ <peptide_seq n="R" c="L" seq="[UNIMOD:737]ESLELIDM[UNIMOD:35]C[UNIMOD:4]RQLDLR"/>\n+ <protein_id>decoy_ENSP00000347667.3</protein_id>\n+ <protein_id>decoy_ENSP00000352608.2</protein_id>\n+ <p_value>0.000e+00</p_value>\n+ </psm>\n+ </psms>\n+\n+</percolator_output>\n' |
| b |
| diff -r 86770eea5b09 -r 7a0951d0e13e test-data/target_ds2_withperco.mzid --- a/test-data/target_ds2_withperco.mzid Sat Mar 04 20:36:03 2017 -0500 +++ b/test-data/target_ds2_withperco.mzid Fri Mar 10 03:20:52 2017 -0500 |
| b |
| @@ -151,6 +151,12 @@ <userParam value="4.3375416" name="StdevRelErrorAll"/> <userParam value="-5.0645747" name="MeanRelErrorTop7"/> <userParam value="4.3375416" name="StdevRelErrorTop7"/> + <userParam name="percolator:score" value="-1.404"/> + <userParam name="percolator:psm_p_value" value="0.000e+00"/> + <userParam name="percolator:psm_q_value" value="1.000e+00"/> + <userParam name="percolator:psm_pep" value="1.000e+00"/> + <userParam name="percolator:peptide_q_value" value="1.000e+00"/> + <userParam name="percolator:peptide_pep" value="1.000e+00"/> </SpectrumIdentificationItem> <cvParam accession="MS:1001115" cvRef="PSI-MS" value="9739" name="scan number(s)"/> </SpectrumIdentificationResult> @@ -291,8 +297,8 @@ <userParam value="6.192429" name="StdevRelErrorAll"/> <userParam value="-4.629228" name="MeanRelErrorTop7"/> <userParam value="6.192429" name="StdevRelErrorTop7"/> - <userParam name="percolator:score" value="-1.105"/> - <userParam name="percolator:psm_p_value" value="6.287e-01"/> + <userParam name="percolator:score" value="-1.147"/> + <userParam name="percolator:psm_p_value" value="0.000e+00"/> <userParam name="percolator:psm_q_value" value="1.000e+00"/> <userParam name="percolator:psm_pep" value="1.000e+00"/> <userParam name="percolator:peptide_q_value" value="1.000e+00"/> |
| b |
| diff -r 86770eea5b09 -r 7a0951d0e13e test-data/target_ds3_withperco.mzid --- a/test-data/target_ds3_withperco.mzid Sat Mar 04 20:36:03 2017 -0500 +++ b/test-data/target_ds3_withperco.mzid Fri Mar 10 03:20:52 2017 -0500 |
| b |
| @@ -125,6 +125,12 @@ <userParam value="9.273238" name="StdevRelErrorAll"/> <userParam value="0.79569435" name="MeanRelErrorTop7"/> <userParam value="9.273238" name="StdevRelErrorTop7"/> + <userParam name="percolator:score" value="-0.996"/> + <userParam name="percolator:psm_p_value" value="0.000e+00"/> + <userParam name="percolator:psm_q_value" value="1.000e+00"/> + <userParam name="percolator:psm_pep" value="1.000e+00"/> + <userParam name="percolator:peptide_q_value" value="1.000e+00"/> + <userParam name="percolator:peptide_pep" value="1.000e+00"/> </SpectrumIdentificationItem> <cvParam accession="MS:1001115" cvRef="PSI-MS" value="9576" name="scan number(s)"/> </SpectrumIdentificationResult> @@ -186,6 +192,12 @@ <userParam value="2.0159998" name="StdevRelErrorAll"/> <userParam value="-12.467069" name="MeanRelErrorTop7"/> <userParam value="2.0159998" name="StdevRelErrorTop7"/> + <userParam name="percolator:score" value="-1.105"/> + <userParam name="percolator:psm_p_value" value="0.000e+00"/> + <userParam name="percolator:psm_q_value" value="1.000e+00"/> + <userParam name="percolator:psm_pep" value="1.000e+00"/> + <userParam name="percolator:peptide_q_value" value="1.000e+00"/> + <userParam name="percolator:peptide_pep" value="1.000e+00"/> </SpectrumIdentificationItem> <cvParam accession="MS:1001115" cvRef="PSI-MS" value="9624" name="scan number(s)"/> </SpectrumIdentificationResult> @@ -217,6 +229,12 @@ <userParam value="6.908051" name="StdevRelErrorAll"/> <userParam value="-10.314375" name="MeanRelErrorTop7"/> <userParam value="6.908051" name="StdevRelErrorTop7"/> + <userParam name="percolator:score" value="-1.122"/> + <userParam name="percolator:psm_p_value" value="0.000e+00"/> + <userParam name="percolator:psm_q_value" value="1.000e+00"/> + <userParam name="percolator:psm_pep" value="1.000e+00"/> + <userParam name="percolator:peptide_q_value" value="1.000e+00"/> + <userParam name="percolator:peptide_pep" value="1.000e+00"/> </SpectrumIdentificationItem> <cvParam accession="MS:1001115" cvRef="PSI-MS" value="9597" name="scan number(s)"/> </SpectrumIdentificationResult> @@ -266,8 +284,8 @@ <userParam value="0.0" name="StdevRelErrorAll"/> <userParam value="7.1771297" name="MeanRelErrorTop7"/> <userParam value="0.0" name="StdevRelErrorTop7"/> - <userParam name="percolator:score" value="-1.307"/> - <userParam name="percolator:psm_p_value" value="8.449e-01"/> + <userParam name="percolator:score" value="-1.13"/> + <userParam name="percolator:psm_p_value" value="0.000e+00"/> <userParam name="percolator:psm_q_value" value="1.000e+00"/> <userParam name="percolator:psm_pep" value="1.000e+00"/> <userParam name="percolator:peptide_q_value" value="1.000e+00"/> @@ -322,8 +340,8 @@ <userParam value="6.8804927" name="StdevRelErrorAll"/> <userParam value="-3.5387955" name="MeanRelErrorTop7"/> <userParam value="6.8804927" name="StdevRelErrorTop7"/> - <userParam name="percolator:score" value="-1.42"/> - <userParam name="percolator:psm_p_value" value="9.186e-01"/> + <userParam name="percolator:score" value="-1.144"/> + <userParam name="percolator:psm_p_value" value="0.000e+00"/> <userParam name="percolator:psm_q_value" value="1.000e+00"/> <userParam name="percolator:psm_pep" value="1.000e+00"/> <userParam name="percolator:peptide_q_value" value="1.000e+00"/> @@ -356,6 +374,12 @@ <userParam value="7.9635553" name="StdevRelErrorAll"/> <userParam value="-2.0970254" name="MeanRelErrorTop7"/> <userParam value="7.9635553" name="StdevRelErrorTop7"/> + <userParam name="percolator:score" value="-1.153"/> + <userParam name="percolator:psm_p_value" value="0.000e+00"/> + <userParam name="percolator:psm_q_value" value="1.000e+00"/> + <userParam name="percolator:psm_pep" value="1.000e+00"/> + <userParam name="percolator:peptide_q_value" value="1.000e+00"/> + <userParam name="percolator:peptide_pep" value="1.000e+00"/> </SpectrumIdentificationItem> <cvParam accession="MS:1001115" cvRef="PSI-MS" value="9594" name="scan number(s)"/> </SpectrumIdentificationResult> @@ -384,6 +408,12 @@ <userParam value="1.2990792" name="StdevRelErrorAll"/> <userParam value="-9.696182" name="MeanRelErrorTop7"/> <userParam value="1.2990792" name="StdevRelErrorTop7"/> + <userParam name="percolator:score" value="-1.202"/> + <userParam name="percolator:psm_p_value" value="0.000e+00"/> + <userParam name="percolator:psm_q_value" value="1.000e+00"/> + <userParam name="percolator:psm_pep" value="1.000e+00"/> + <userParam name="percolator:peptide_q_value" value="1.000e+00"/> + <userParam name="percolator:peptide_pep" value="1.000e+00"/> </SpectrumIdentificationItem> <cvParam accession="MS:1001115" cvRef="PSI-MS" value="9681" name="scan number(s)"/> </SpectrumIdentificationResult> |