# HG changeset patch # User galaxyp # Date 1626333061 0 # Node ID db6faafbf75b65142bf5fe98834ce3625ebef5c5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4" diff -r 000000000000 -r db6faafbf75b proteomiqon_peptidespectrummatching.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteomiqon_peptidespectrummatching.xml Thu Jul 15 07:11:01 2021 +0000 @@ -0,0 +1,195 @@ + + + iterates across all MS/MS scans in an MS run, determines precursor charge states and possible peptide spectrum matches. + + + 0.0.7 + + + proteomiqon-peptidespectrummatching + + > '$out_paramfile' && + #end if + ln -s '$instrumentOutput' '${basename}.mzlite' && + ln -s '$out_psm' '${basename}.psm' && + proteomiqon-peptidespectrummatching -i './${basename}.mzlite' -d '$peptideDB' -p '$paramfile' -o ./ + ]]> + + + + + + + + + +
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+ + `_ tool. + +Given raw a MS run in the mzite format, this tool iterates accross all recorded MS/MS scans and determines the charge state of precursor ions which were selected for fragmentation. +With this it is possible to query the peptide data base for every precursor ion mass +/- a tolerance (which defines the so called 'search space') and retrieve peptides that are +theoretical candidates for a match. For each of the peptide candidates we create an theoretical spectrum in silico and compare it to the measured MS/MS scan. + +.. image:: PSM.png + :width: 768pt + :height: 563pt + +To measure similarity we use our own implementations of three established search enginge scores: SEQUEST, Andromeda and XTandem. +The search space is extended by so called decoys. Decoys are reversed counterparts of peptides within the search space and allow +us to assign a false discovery rate to each scored peptide using the `PSMStatistics `_ tool. + +Further Reading +--------------- +Additional information about the tool can be found in the `documentation `_. + ]]> + +
\ No newline at end of file diff -r 000000000000 -r db6faafbf75b static/images/PSM.png Binary file static/images/PSM.png has changed diff -r 000000000000 -r db6faafbf75b test-data/result_1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_1.json Thu Jul 15 07:11:01 2021 +0000 @@ -0,0 +1,24 @@ + + + { + "ChargeStateDeterminationParams": { + "ExpectedMinimalCharge": 2, + "ExpectedMaximumCharge": 5, + "Width": 1.1, + "MinIntensity": 0.15, + "DeltaMinIntensity": 0.3, + "NrOfRndSpectra": 10000 + }, + "LookUpPPM": 30.0, + "nTerminalSeries": { "Case": "B" }, + "cTerminalSeries": { "Case": "Y" }, + "Andromeda": { + "PMinPMax": { + "Item1": 4, + "Item2": 10 + }, + "MatchingIonTolerancePPM": 100.0 + } + } + + \ No newline at end of file diff -r 000000000000 -r db6faafbf75b test-data/result_2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_2.json Thu Jul 15 07:11:01 2021 +0000 @@ -0,0 +1,24 @@ + + + { + "ChargeStateDeterminationParams": { + "ExpectedMinimalCharge": 2, + "ExpectedMaximumCharge": 5, + "Width": 1.1, + "MinIntensity": 0.15, + "DeltaMinIntensity": 0.3, + "NrOfRndSpectra": 10000 + }, + "LookUpPPM": 30.0, + "nTerminalSeries": { "Case": "A" }, + "cTerminalSeries": { "Case": "Z" }, + "Andromeda": { + "PMinPMax": { + "Item1": 4, + "Item2": 10 + }, + "MatchingIonTolerancePPM": 100.0 + } + } + + \ No newline at end of file diff -r 000000000000 -r db6faafbf75b test-data/result_3.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_3.json Thu Jul 15 07:11:01 2021 +0000 @@ -0,0 +1,24 @@ + + + { + "ChargeStateDeterminationParams": { + "ExpectedMinimalCharge": 2, + "ExpectedMaximumCharge": 5, + "Width": 1.1, + "MinIntensity": 0.15, + "DeltaMinIntensity": 0.3, + "NrOfRndSpectra": 10000 + }, + "LookUpPPM": 30.0, + "nTerminalSeries": { "Case": "C" }, + "cTerminalSeries": { "Case": "X" }, + "Andromeda": { + "PMinPMax": { + "Item1": 4, + "Item2": 10 + }, + "MatchingIonTolerancePPM": 100.0 + } + } + + \ No newline at end of file diff -r 000000000000 -r db6faafbf75b test-data/sample.db Binary file test-data/sample.db has changed diff -r 000000000000 -r db6faafbf75b test-data/sample.mzlite Binary file test-data/sample.mzlite has changed