From 6c8d555cabf6f29e5b5fe1e126aef296850de785 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Wed, 3 Oct 2018 22:17:11 +0200
Subject: [PATCH] grab specific informations from MS-GF+ mzidentML files
---
.../peptide_list_view/peptidetablemodel.cpp | 4 +-
src/input/identificationpwizreader.cpp | 61 +++++++++++++++++++
2 files changed, 63 insertions(+), 2 deletions(-)
diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp
index 6ca588d3b..efe5c63f6 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.cpp
+++ b/src/gui/peptide_list_view/peptidetablemodel.cpp
@@ -651,7 +651,7 @@ PeptideTableModel::getTitle(std::int8_t column)
return "MS-GF spectral E-value";
break;
case(std::int8_t)PeptideListColumn::msgfplus_isotope_error:
- return "MS-GF istotope error";
+ return "MS-GF isotope error";
break;
case(std::int8_t)PeptideListColumn::comet_xcorr:
@@ -788,7 +788,7 @@ PeptideTableModel::getDescription(std::int8_t column)
return "MS-GF spectral E-value";
break;
case(std::int8_t)PeptideListColumn::msgfplus_isotope_error:
- return "MS-GF istotope error";
+ return "MS-GF isotope error";
break;
case(std::int8_t)PeptideListColumn::comet_xcorr:
return "The Comet result 'XCorr'";
diff --git a/src/input/identificationpwizreader.cpp b/src/input/identificationpwizreader.cpp
index 0666dc909..f8ef38faa 100644
--- a/src/input/identificationpwizreader.cpp
+++ b/src/input/identificationpwizreader.cpp
@@ -200,6 +200,11 @@ IdentificationPwizReader::getIdentificationEngine(
{
identification_engine = IdentificationEngine::mascot;
}
+ else if(analysis_software_p.get()->softwareName.hasCVParam(
+ pwiz::cv::MS_MS_GF_))
+ {
+ identification_engine = IdentificationEngine::MSGFplus;
+ }
else
{
return IdentificationEngine::unknown;
@@ -521,6 +526,62 @@ IdentificationPwizReader::read(
}
+ //<cvParam cvRef="PSI-MS" accession="MS:1002049"
+ // name="MS-GF:RawScore" value="164"/>
+ QVariant MSGFplus_rawscore = getQVariantDoubleParam(
+ spid_item.get(), pwiz::cv::MS_MS_GF_RawScore);
+ if(!MSGFplus_rawscore.isNull())
+ {
+ p_peptide_evidence->setParam(
+ PeptideEvidenceParam::msgfplus_raw, MSGFplus_rawscore);
+ }
+ //<cvParam cvRef = "PSI-MS" accession = "MS:1002050" name
+ //="MS-GF:DeNovoScore" value = "170" />
+
+ QVariant MSGFplus_denovoscore = getQVariantDoubleParam(
+ spid_item.get(), pwiz::cv::MS_MS_GF_DeNovoScore);
+ if(!MSGFplus_denovoscore.isNull())
+ {
+ p_peptide_evidence->setParam(
+ PeptideEvidenceParam::msgfplus_denovo,
+ MSGFplus_denovoscore);
+ }
+
+ //<cvParam cvRef = "PSI-MS" accession = "MS:1002052" name
+ //="MS-GF:SpecEValue" value = "5.4876387E-19"/>
+
+ QVariant MSGFplus_specevalue = getQVariantDoubleParam(
+ spid_item.get(), pwiz::cv::MS_MS_GF_SpecEValue);
+ if(!MSGFplus_specevalue.isNull())
+ {
+ p_peptide_evidence->setParam(
+ PeptideEvidenceParam::msgfplus_SpecEValue,
+ MSGFplus_specevalue);
+ }
+ //<cvParam cvRef = "PSI-MS" accession = "MS:1002053" name =
+ //"MS-GF:EValue" value = "1.0822937E-11" />
+
+ QVariant MSGFplus_evalue = getQVariantDoubleParam(
+ spid_item.get(), pwiz::cv::MS_MS_GF_EValue);
+ if(!MSGFplus_evalue.isNull())
+ {
+ p_peptide_evidence->setParam(
+ PeptideEvidenceParam::msgfplus_EValue, MSGFplus_evalue);
+ p_peptide_evidence->setEvalue(MSGFplus_evalue.toDouble());
+ }
+
+ //<userParam name="IsotopeError" value="0"/>
+ QVariant isotope_error =
+ QVariant(QString::fromStdString(
+ spid_item.get()->userParam("IsotopeError").value)
+ .toInt());
+ if(!isotope_error.isNull())
+ {
+ p_peptide_evidence->setParam(
+ PeptideEvidenceParam::msgfplus_isotope_error,
+ isotope_error);
+ }
+
for(pwiz::identdata::PeptideEvidencePtr peptide_evidence_sp :
spid_item.get()->peptideEvidencePtr)
{
--
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