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Extension of bruker precursor information #2780

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77056d6
Feature Reader Bruker with extended precursor info
xjasg Nov 6, 2023
4ebd57a
Test files changed, collisional Cross Sectional Area added
xjasg Nov 7, 2023
a2542c1
Test files changed
xjasg Nov 8, 2023
39f02e7
mzXML and MGF Reader/Writer externded
xjasg Nov 19, 2023
b8a18b6
Bugfix Typo
xjasg Nov 25, 2023
99dc650
reset
xjasg Nov 25, 2023
0e2b8f7
Testfiles with minor changes restored
xjasg Nov 25, 2023
46c5c1e
Restore
xjasg Nov 25, 2023
94f0673
Restore
xjasg Nov 25, 2023
0044ecd
Restore
xjasg Nov 25, 2023
92c0c3c
Restore
xjasg Nov 25, 2023
6595094
Restore
xjasg Nov 25, 2023
a124919
Restore
xjasg Nov 25, 2023
0ed625d
Restore
xjasg Nov 25, 2023
3fcf17c
restore
xjasg Nov 25, 2023
ed0c92f
restore
xjasg Nov 25, 2023
d09439c
restore
xjasg Nov 25, 2023
1a64df3
Restore
xjasg Nov 25, 2023
f6d2d53
Merge branch 'master' into feature/bruker_precursors
chambm Dec 5, 2023
9c3be9c
Implementation Waters analog channel reader (not tested yet)
Andre99999999 Aug 29, 2023
88a6f42
Cleanup after review
Andre99999999 Aug 30, 2023
00c941d
Cleanup tabs
Andre99999999 Aug 30, 2023
6188a47
remove spaces from channelname
Andre99999999 Aug 31, 2023
12f366f
Bugfix push changed files
Andre99999999 Sep 8, 2023
20ea13d
Tab vs. spaces
Andre99999999 Sep 8, 2023
9c09d4d
Analog channel name
Andre99999999 Sep 10, 2023
4e74556
Trim changed
Andre99999999 Sep 8, 2023
9f9d163
Cleanup / small Refactoring
xjasg Sep 10, 2023
6634123
Bugfix use separate field for channel index for analog channels
xjasg Sep 11, 2023
6ab86fb
Rework after review pwiz
xjasg Sep 18, 2023
80ee13e
Revert IO.cpp and ChromatogramList_Waters.hpp
xjasg Sep 21, 2023
c72729c
Tab vs. space
xjasg Sep 21, 2023
08b1943
Test Data
xjasg Sep 24, 2023
63df37b
New Test data + Bugfix idToIndexMap for analog channels not set before.
xjasg Sep 27, 2023
45d9b22
Temporary zip file removed
xjasg Sep 27, 2023
04d17d6
Change test, don't look for ms info in Spectren without this.
xjasg Sep 28, 2023
2d2e251
Performance measurement for the reading of analog channels
xjasg Sep 29, 2023
6d5a5da
Cleanup
xjasg Sep 30, 2023
d0b7f5a
Remove test data from wrong location
xjasg Oct 3, 2023
e6235bc
Checkin Test data - gitignore did not allow it before
xjasg Oct 3, 2023
26523e5
Bugfix use better way to check if there is at least 1 MS Spectrum wit…
xjasg Oct 4, 2023
ccb8d49
* fixed compile issues
chambm Oct 4, 2023
4e644cd
* fixed tribool logic
chambm Oct 5, 2023
8e6aac4
Rework Review
xjasg Mar 29, 2024
8f14c24
Bugfix
xjasg Mar 29, 2024
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1 change: 1 addition & 0 deletions libraries/boost_aux/libs/nowide/src/iostream.cpp
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Expand Up @@ -8,6 +8,7 @@
#define BOOST_NOWIDE_SOURCE
#include <boost/nowide/iostream.hpp>
#include <boost/nowide/convert.hpp>
#include <boost/locale/utf.hpp>
#include <stdio.h>
#include <vector>

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2 changes: 1 addition & 1 deletion pwiz/data/common/ParamTypes.hpp
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Expand Up @@ -139,7 +139,7 @@ struct PWIZ_API_DECL CVParam
return !operator==(that);
}

bool empty() const {return cvid==CVID_Unknown && value.empty() && units==CVID_Unknown;}
bool empty() const { return cvid == CVID_Unknown && value.empty() && units == CVID_Unknown; }
};


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1 change: 1 addition & 0 deletions pwiz/data/identdata/ExtendedReadTest.cpp
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Expand Up @@ -24,6 +24,7 @@
#include "DefaultReaderList.hpp"
#include "IO.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include "pwiz/utility/misc/unit.hpp"

using namespace pwiz::identdata;

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10 changes: 10 additions & 0 deletions pwiz/data/msdata/Serializer_MGF.cpp
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Expand Up @@ -132,6 +132,16 @@ void Serializer_MGF::Impl::write(ostream& os, const MSData& msd,
os << " " << intensityParam.valueFixedNotation();
os << '\n';

CVParam inverseReduceIonMobility = scan->cvParam(MS_inverse_reduced_ion_mobility);
if (!inverseReduceIonMobility.empty())
os << "INVREION=" << inverseReduceIonMobility.valueFixedNotation();
os << '\n';

CVParam collisionalCrossSectionalArea = scan->cvParam(MS_collisional_cross_sectional_area);
if (!collisionalCrossSectionalArea.empty())
os << "COLLCROSSSA=" << collisionalCrossSectionalArea.valueFixedNotation();
os << '\n';

if (chargeParam.empty())
{
vector<string> charges;
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4 changes: 2 additions & 2 deletions pwiz/data/msdata/Serializer_mzXML.cpp
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Expand Up @@ -441,6 +441,7 @@ struct PrecursorInfo
string collisionEnergy;
string activation;
double windowWideness;


bool empty() const
{
Expand Down Expand Up @@ -514,7 +515,6 @@ vector<PrecursorInfo> getPrecursorInfo(const Spectrum& spectrum,
return result;
}


void write_precursors(XMLWriter& xmlWriter, const vector<PrecursorInfo>& precursorInfo)
{
xmlWriter.pushStyle(XMLWriter::StyleFlag_InlineInner);
Expand All @@ -535,7 +535,7 @@ void write_precursors(XMLWriter& xmlWriter, const vector<PrecursorInfo>& precurs
attributes.add("activationMethod", it->activation);
if (it->windowWideness != 0)
attributes.add("windowWideness", it->windowWideness);

xmlWriter.startElement("precursorMz", attributes);
xmlWriter.characters(it->mz, false);
xmlWriter.endElement();
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10 changes: 10 additions & 0 deletions pwiz/data/msdata/SpectrumList_MGF.cpp
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Expand Up @@ -235,6 +235,16 @@ class SpectrumList_MGFImpl : public SpectrumList_MGF
else
selectedIon.set(MS_selected_ion_m_z, value, MS_m_z);
}
else if (name == "INVREION")
{
bal::trim(value);
scan.cvParams.push_back(CVParam(MS_inverse_reduced_ion_mobility, value, MS_volt_second_per_square_centimeter));
}
else if (name == "COLLCROSSSA")
{
bal::trim(value);
scan.cvParams.push_back(CVParam(MS_collisional_cross_sectional_area, value, UO_square_angstrom));
}
else if (name == "CHARGE")
{
bal::trim_if(value, bal::is_any_of(" \t\r"));
Expand Down
1 change: 0 additions & 1 deletion pwiz/data/msdata/SpectrumList_mzXML.cpp
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Expand Up @@ -566,7 +566,6 @@ class HandlerScan : public SAXParser::Handler
bool getBinaryData_;
string scanNumber_;
string collisionEnergy_;
string activationMethod_;
HandlerPeaks handlerPeaks_;
HandlerPrecursor handlerPrecursor_;
CVID nativeIdFormat_;
Expand Down
14 changes: 7 additions & 7 deletions pwiz/data/vendor_readers/Bruker/Reader_Bruker_Test.data/100 fmol BSA.mzML
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@@ -1,7 +1,7 @@
<?xml version="1.0" encoding="utf-8"?>
<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="100 fmol BSA" version="1.1.0">
<cvList count="2">
<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
<cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>
</cvList>
<fileDescription>
Expand All @@ -10,27 +10,27 @@
<cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
</fileContent>
<sourceFileList count="5">
<sourceFile id="_x0031_00_x0020_fmol_x0020_BSA_x002f_0_B1_x002f_1_x002f_1SRef_x002f_fid" name="fid" location="file://C:\pwiz.git\pwiz\pwiz\data\vendor_readers\Bruker\Reader_Bruker_Test.data\100 fmol BSA\0_B1\1\1SRef">
<sourceFile id="_x0031_00_x0020_fmol_x0020_BSA_x002f_0_B1_x002f_1_x002f_1SRef_x002f_fid" name="fid" location="file://C:\github\pwiz\pwiz\data\vendor_readers\Bruker\Reader_Bruker_Test.data\100 fmol BSA\0_B1\1\1SRef">
<cvParam cvRef="MS" accession="MS:1000773" name="Bruker FID nativeID format" value=""/>
<cvParam cvRef="MS" accession="MS:1000825" name="Bruker FID format" value=""/>
<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="79443fd17d6e57a688190c83abeb6ec3a4949f04"/>
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<sourceFile id="_x0031_00_x0020_fmol_x0020_BSA_x002f_0_B2_x002f_1_x002f_1249.4898.LIFT_x002f_1SRef_x002f_fid" name="fid" location="file://C:\github\pwiz\pwiz\data\vendor_readers\Bruker\Reader_Bruker_Test.data\100 fmol BSA\0_B2\1\1249.4898.LIFT\1SRef">
<cvParam cvRef="MS" accession="MS:1000773" name="Bruker FID nativeID format" value=""/>
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<sourceFile id="_x0031_00_x0020_fmol_x0020_BSA_x002f_0_B2_x002f_1_x002f_1287.4500.LIFT_x002f_1SRef_x002f_fid" name="fid" location="file://C:\github\pwiz\pwiz\data\vendor_readers\Bruker\Reader_Bruker_Test.data\100 fmol BSA\0_B2\1\1287.4500.LIFT\1SRef">
<cvParam cvRef="MS" accession="MS:1000773" name="Bruker FID nativeID format" value=""/>
<cvParam cvRef="MS" accession="MS:1000825" name="Bruker FID format" value=""/>
<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="33cb1333474c96a4914441b2c11c518af11473bf"/>
</sourceFile>
<sourceFile id="_x0031_00_x0020_fmol_x0020_BSA_x002f_0_B2_x002f_1_x002f_1SRef_x002f_fid" name="fid" location="file://C:\pwiz.git\pwiz\pwiz\data\vendor_readers\Bruker\Reader_Bruker_Test.data\100 fmol BSA\0_B2\1\1SRef">
<sourceFile id="_x0031_00_x0020_fmol_x0020_BSA_x002f_0_B2_x002f_1_x002f_1SRef_x002f_fid" name="fid" location="file://C:\github\pwiz\pwiz\data\vendor_readers\Bruker\Reader_Bruker_Test.data\100 fmol BSA\0_B2\1\1SRef">
<cvParam cvRef="MS" accession="MS:1000773" name="Bruker FID nativeID format" value=""/>
<cvParam cvRef="MS" accession="MS:1000825" name="Bruker FID format" value=""/>
<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="9527cfe861f2411a5e5fca8254ce73e670fce29d"/>
</sourceFile>
<sourceFile id="_x0031_00_x0020_fmol_x0020_BSA_x002f_0_B3_x002f_1_x002f_1SRef_x002f_fid" name="fid" location="file://C:\pwiz.git\pwiz\pwiz\data\vendor_readers\Bruker\Reader_Bruker_Test.data\100 fmol BSA\0_B3\1\1SRef">
<sourceFile id="_x0031_00_x0020_fmol_x0020_BSA_x002f_0_B3_x002f_1_x002f_1SRef_x002f_fid" name="fid" location="file://C:\github\pwiz\pwiz\data\vendor_readers\Bruker\Reader_Bruker_Test.data\100 fmol BSA\0_B3\1\1SRef">
<cvParam cvRef="MS" accession="MS:1000773" name="Bruker FID nativeID format" value=""/>
<cvParam cvRef="MS" accession="MS:1000825" name="Bruker FID format" value=""/>
<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="e1cc8d437a8fc4ee30839c8fd5dbe34047a7ee44"/>
Expand All @@ -50,7 +50,7 @@
<software id="FlexControl" version="unknown">
<cvParam cvRef="MS" accession="MS:1000540" name="FlexControl" value=""/>
</software>
<software id="pwiz_Reader_Bruker" version="3.0.19105">
<software id="pwiz_Reader_Bruker" version="3.0.24089">
<cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
</software>
</softwareList>
Expand Down
8 changes: 4 additions & 4 deletions ...or_readers/Bruker/Reader_Bruker_Test.data/20percLaser_100fold_1_0_H6_MS-ms1-centroid.mzML
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@@ -1,20 +1,20 @@
<?xml version="1.0" encoding="utf-8"?>
<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="20percLaser_100fold_1_0_H6_MS" version="1.1.0">
<cvList count="2">
<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.99" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
<cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>
</cvList>
<fileDescription>
<fileContent>
<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
</fileContent>
<sourceFileList count="2">
<sourceFile id="_x0032_0percLaser_100fold_1_0_H6_MS.d_x005c_Analysis.tsf" name="Analysis.tsf" location="file://C:\dev\pwiz\pwiz\data\vendor_readers\Bruker\Reader_Bruker_Test.data\20percLaser_100fold_1_0_H6_MS.d">
<sourceFile id="_x0032_0percLaser_100fold_1_0_H6_MS.d_x005c_Analysis.tsf" name="Analysis.tsf" location="file://C:\github\pwiz\pwiz\data\vendor_readers\Bruker\Reader_Bruker_Test.data\20percLaser_100fold_1_0_H6_MS.d">
<cvParam cvRef="MS" accession="MS:1003283" name="Bruker TSF nativeID format" value=""/>
<cvParam cvRef="MS" accession="MS:1003282" name="Bruker TSF format" value=""/>
<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="f2ef8f5dd73702385dec525d9af542f01f4dfc41"/>
</sourceFile>
<sourceFile id="_x0032_0percLaser_100fold_1_0_H6_MS.d_x005c_Analysis.tsf_bin" name="Analysis.tsf_bin" location="file://C:\dev\pwiz\pwiz\data\vendor_readers\Bruker\Reader_Bruker_Test.data\20percLaser_100fold_1_0_H6_MS.d">
<sourceFile id="_x0032_0percLaser_100fold_1_0_H6_MS.d_x005c_Analysis.tsf_bin" name="Analysis.tsf_bin" location="file://C:\github\pwiz\pwiz\data\vendor_readers\Bruker\Reader_Bruker_Test.data\20percLaser_100fold_1_0_H6_MS.d">
<cvParam cvRef="MS" accession="MS:1003283" name="Bruker TSF nativeID format" value=""/>
<cvParam cvRef="MS" accession="MS:1003282" name="Bruker TSF format" value=""/>
<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="523917fb1b858272b4b98807f0f68eeacfe9e37d"/>
Expand All @@ -34,7 +34,7 @@
<software id="Compass" version="3.0.22">
<cvParam cvRef="MS" accession="MS:1000712" name="Compass" value=""/>
</software>
<software id="pwiz_Reader_Bruker" version="3.0.22236">
<software id="pwiz_Reader_Bruker" version="3.0.24089">
<cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
</software>
</softwareList>
Expand Down
8 changes: 4 additions & 4 deletions ...or_readers/Bruker/Reader_Bruker_Test.data/20percLaser_100fold_1_0_H6_MS-ms2-centroid.mzML
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@@ -1,19 +1,19 @@
<?xml version="1.0" encoding="utf-8"?>
<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="20percLaser_100fold_1_0_H6_MS" version="1.1.0">
<cvList count="2">
<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.99" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
<cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>
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<sourceFile id="_x0032_0percLaser_100fold_1_0_H6_MS.d_x005c_Analysis.tsf" name="Analysis.tsf" location="file://C:\github\pwiz\pwiz\data\vendor_readers\Bruker\Reader_Bruker_Test.data\20percLaser_100fold_1_0_H6_MS.d">
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<sourceFile id="_x0032_0percLaser_100fold_1_0_H6_MS.d_x005c_Analysis.tsf_bin" name="Analysis.tsf_bin" location="file://C:\github\pwiz\pwiz\data\vendor_readers\Bruker\Reader_Bruker_Test.data\20percLaser_100fold_1_0_H6_MS.d">
<cvParam cvRef="MS" accession="MS:1003283" name="Bruker TSF nativeID format" value=""/>
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Expand All @@ -33,7 +33,7 @@
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<cvParam cvRef="MS" accession="MS:1000712" name="Compass" value=""/>
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<software id="pwiz_Reader_Bruker" version="3.0.22236">
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<cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
</software>
</softwareList>
Expand Down
8 changes: 4 additions & 4 deletions pwiz/data/vendor_readers/Bruker/Reader_Bruker_Test.data/20percLaser_100fold_1_0_H6_MS.mzML
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@@ -1,20 +1,20 @@
<?xml version="1.0" encoding="utf-8"?>
<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="20percLaser_100fold_1_0_H6_MS" version="1.1.0">
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<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.117" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
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Expand All @@ -34,7 +34,7 @@
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6 changes: 3 additions & 3 deletions pwiz/data/vendor_readers/Bruker/Reader_Bruker_Test.data/CsI_Pos_0_G1_000003.mzML
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Expand All @@ -29,7 +29,7 @@
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