From 7f7e2e717042942a7195cd415032987c4f191139 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 22 Mar 2018 13:55:22 +0100
Subject: [PATCH] new column added to display experimental precursor m/z
---
src/grouping/ptm/ptmsamplescan.h | 8 ++++++
.../peptide_list_view/peptidetablemodel.cpp | 11 +++++++-
src/gui/peptide_list_view/peptidetablemodel.h | 25 ++++++++++---------
src/output/ods/ptm/ptmspectrasheet.cpp | 5 ++--
src/output/ods/spectrasheet.cpp | 12 ++++-----
5 files changed, 39 insertions(+), 22 deletions(-)
diff --git a/src/grouping/ptm/ptmsamplescan.h b/src/grouping/ptm/ptmsamplescan.h
index e06758f4..50427558 100644
--- a/src/grouping/ptm/ptmsamplescan.h
+++ b/src/grouping/ptm/ptmsamplescan.h
@@ -48,9 +48,17 @@ public:
PtmSampleScan(const PtmSampleScan& other);
~PtmSampleScan();
+ /** @brief get the best peptide Match (Evalue)
+ * peptide match are sorted in this sample/scan by Evalue
+ * The representative peptide match is the first in the sorted array
+ */
const PeptideMatch & getRepresentativePeptideMatch() const;
bool add(const PeptideMatch & peptide_match);
std::vector<unsigned int> getBestPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
+
+ /** @brief get all observed PTM positions for this sample/scan
+ * positions are intended in a peptide (not protein), from 0 (first amino acid) to size-1 (last amino acid)
+ */
std::vector<unsigned int> getObservedPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
const QString getHtmlSequence(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
std::vector<PeptideMatch> & getPeptideMatchList();
diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp
index 31fc935c..86689402 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.cpp
+++ b/src/gui/peptide_list_view/peptidetablemodel.cpp
@@ -68,7 +68,7 @@ int PeptideTableModel::rowCount(const QModelIndex &parent ) const {
return 0;
}
int PeptideTableModel::columnCount(const QModelIndex &parent ) const {
- return 19;
+ return 20;
}
QVariant PeptideTableModel::headerData(int section, Qt::Orientation orientation, int role) const
{
@@ -148,6 +148,9 @@ QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
case (std::int8_t)PeptideListColumn::charge:
return QVariant ((quint32) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getCharge());
break;
+ case (std::int8_t)PeptideListColumn::experimental_mz:
+ return QVariant ((qreal) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getExperimentalMz());
+ break;
case (std::int8_t)PeptideListColumn::sequence:
return _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getPeptideXtpSp().get()->getSequence();
break;
@@ -251,6 +254,9 @@ const QString PeptideTableModel::getTitle(std::int8_t column) {
case (std::int8_t) PeptideListColumn::charge:
return "charge";
break;
+ case (std::int8_t) PeptideListColumn::experimental_mz:
+ return "observed m/z";
+ break;
case (std::int8_t) PeptideListColumn::sequence:
return "sequence";
break;
@@ -317,6 +323,9 @@ const QString PeptideTableModel::getDescription(std::int8_t column) {
case (std::int8_t) PeptideListColumn::charge:
return "peptide charge";
break;
+ case (std::int8_t) PeptideListColumn::experimental_mz:
+ return "observed m/z (experimental m/z of precursor)";
+ break;
case (std::int8_t) PeptideListColumn::sequence:
return "peptide sequence";
break;
diff --git a/src/gui/peptide_list_view/peptidetablemodel.h b/src/gui/peptide_list_view/peptidetablemodel.h
index c79bd1b0..2281ede6 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.h
+++ b/src/gui/peptide_list_view/peptidetablemodel.h
@@ -39,18 +39,19 @@ enum class PeptideListColumn: std::int8_t {
rtmin=4,
rt=5,
charge=6,
- sequence=7,
- modifs=8,
- label=9,
- start=10,
- length=11,
- used=12,
- subgroups=13,
- Evalue=14,
- theoretical_mhplus=15,
- delta_mhplus=16,
- hyperscore=17,
- mascot_score=18
+ experimental_mz=7,
+ sequence=8,
+ modifs=9,
+ label=10,
+ start=11,
+ length=12,
+ used=13,
+ subgroups=14,
+ Evalue=15,
+ theoretical_mhplus=16,
+ delta_mhplus=17,
+ hyperscore=18,
+ mascot_score=19
};
class PeptideListWindow;
diff --git a/src/output/ods/ptm/ptmspectrasheet.cpp b/src/output/ods/ptm/ptmspectrasheet.cpp
index e337a379..49bc3ff8 100644
--- a/src/output/ods/ptm/ptmspectrasheet.cpp
+++ b/src/output/ods/ptm/ptmspectrasheet.cpp
@@ -56,7 +56,8 @@ void PtmSpectraSheet::writeCellHeader(PeptideListColumn column) {
void PtmSpectraSheet::writeHeaders(IdentificationGroup * p_ident) {
- // Group ID Peptide ID Sample Scan Rt (minutes) Sequence (top) Modifs (top) Number of subgroups Sub-groups Ids Best E-value Best hyperscore m/z Obs Charge MH+ Obs MH+ theo DeltaMH+ Delta-ppm
+ // Group ID Sub-group ID Phosphopeptide ID Sample Scan Rt Sequence (top) Modifs (top) Best position in peptide All observed positions in phosphopeptide Number of phosphoislands Phosphoislands Ids Best e-value Charge MH+ Obs MH+ theo DeltaMH+ Delta-ppm
+
//MS Sample : 20120906_balliau_extract_1_A01_urnb-1
const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
@@ -73,7 +74,7 @@ void PtmSpectraSheet::writeHeaders(IdentificationGroup * p_ident) {
_p_writer->writeCell("Peptide ID");
_p_writer->setCellAnnotation("MS sample name (MS run)");
_p_writer->writeCell("Sample");
- _p_writer->writeCell("Scan");
+ writeCellHeader(PeptideListColumn::scan);
_p_writer->setCellAnnotation("retention time in seconds");
_p_writer->writeCell("Rt (seconds)");
_p_writer->setCellAnnotation("experimental precursor m/z");
diff --git a/src/output/ods/spectrasheet.cpp b/src/output/ods/spectrasheet.cpp
index c10af12f..ffbd9aee 100644
--- a/src/output/ods/spectrasheet.cpp
+++ b/src/output/ods/spectrasheet.cpp
@@ -71,13 +71,11 @@ void SpectraSheet::writeHeaders(IdentificationGroup * p_ident) {
_p_writer->writeLine();
_p_writer->writeCell("Group ID");
_p_writer->writeCell("Peptide ID");
- _p_writer->setCellAnnotation("MS sample name (MS run)");
- _p_writer->writeCell("Sample");
- _p_writer->writeCell("Scan");
- _p_writer->setCellAnnotation("retention time in seconds");
- _p_writer->writeCell("Rt (seconds)");
- _p_writer->setCellAnnotation("experimental precursor m/z");
- _p_writer->writeCell("Precursor m/z");
+
+ writeCellHeader(PeptideListColumn::sample);
+ writeCellHeader(PeptideListColumn::scan);
+ writeCellHeader(PeptideListColumn::rt);
+ writeCellHeader(PeptideListColumn::experimental_mz);
_p_writer->setCellAnnotation("peptide sequence (best match)");
_p_writer->writeCell("Sequence (top)");
_p_writer->setCellAnnotation("peptide charge (best match)");
--
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