Changes for dealing with newer relatively complex Bruker DiaPASEF modes, e.g. "Diagonal" PASEF or "MiDia" PASEF…

pwiz/analysis/spectrum_processing/SpectrumList_IonMobility.cpp

@@ -48,6 +48,7 @@ SpectrumList_IonMobility::SpectrumList_IonMobility(const msdata::SpectrumListPtr
 {
     units_ = IonMobilityUnits::none;
     has_mzML_combined_ion_mobility_ = false;
+ //   isPassEntireDiaPasefFrame_ = false;
     if (dynamic_cast<detail::SpectrumList_Agilent*>(&*innermost()) != NULL)
     {
         equipment_ = IonMobilityEquipment::AgilentDrift;
@@ -66,6 +67,7 @@ SpectrumList_IonMobility::SpectrumList_IonMobility(const msdata::SpectrumListPtr
         {
             equipment_ = IonMobilityEquipment::BrukerTIMS;
             units_ = IonMobilityUnits::inverse_reduced_ion_mobility_Vsec_per_cm2;
+            //isPassEntireDiaPasefFrame_ = (dynamic_cast<detail::SpectrumList_Bruker*>(&*innermost()))->isPassEntireDiaPasefFrame();
         }
     }
     else if (dynamic_cast<detail::SpectrumList_Thermo*>(&*innermost()) != NULL)
@@ -110,19 +112,24 @@ SpectrumList_IonMobility::SpectrumList_IonMobility(const msdata::SpectrumListPtr
                     units_ = IonMobilityUnits::drift_time_msec;
                 for (const auto& binaryArray : spectrum->binaryDataArrayPtrs)
                 {
-                    CVID ionMobilityArrayType = binaryArray->cvParamChild(MS_ion_mobility_array).cvid;
-                    if (ionMobilityArrayType == CVID_Unknown)
+                    if (binaryArray->cvParamChild(MS_scanning_quadrupole_position_lower_bound_m_z_array).cvid != CVID_Unknown)
+                    {
+                        //isPassEntireDiaPasefFrame_ = true;
+                        continue;
+                    }
+                    CVID ionMobilityArrayType = binaryArray->cvParamChild(MS_ion_mobility_array).cvid;
+                    if (ionMobilityArrayType == CVID_Unknown)
                         continue;
 
-                    if (ionMobilityArrayType == MS_raw_ion_mobility_array || ionMobilityArrayType == MS_mean_ion_mobility_array)
-                    {
+                    if (ionMobilityArrayType == MS_raw_ion_mobility_array || ionMobilityArrayType == MS_mean_ion_mobility_array)
+                    {
                         has_mzML_combined_ion_mobility_ = true;
                         units_ = IonMobilityUnits::drift_time_msec;
                         probe = probeLimit; // No need to look further
                         break;
-                    }
-                    else if (ionMobilityArrayType == MS_raw_inverse_reduced_ion_mobility_array || ionMobilityArrayType == MS_mean_inverse_reduced_ion_mobility_array)
-                    {
+                    }
+                    else if (ionMobilityArrayType == MS_raw_inverse_reduced_ion_mobility_array || ionMobilityArrayType == MS_mean_inverse_reduced_ion_mobility_array)
+                    {
                         has_mzML_combined_ion_mobility_ = true;
                         units_ = IonMobilityUnits::inverse_reduced_ion_mobility_Vsec_per_cm2;
                         probe = probeLimit; // No need to look further
@@ -135,6 +142,11 @@ SpectrumList_IonMobility::SpectrumList_IonMobility(const msdata::SpectrumListPtr
                 spectrum = inner->spectrum(0, true);
                 for (const auto& binaryArray : spectrum->binaryDataArrayPtrs)
                 {
+                    if (binaryArray->cvParamChild(MS_scanning_quadrupole_position_lower_bound_m_z_array).cvid != CVID_Unknown)
+                    {
+                        //isPassEntireDiaPasefFrame_ = true;
+                        continue;
+                    }
                     CVID ionMobilityArrayType = binaryArray->cvParamChild(MS_ion_mobility_array).cvid;
                     if (ionMobilityArrayType == CVID_Unknown)
                         continue;
@@ -165,6 +177,11 @@ PWIZ_API_DECL SpectrumList_IonMobility::IonMobilityUnits SpectrumList_IonMobilit
     return units_;
 }
 
+//PWIZ_API_DECL bool SpectrumList_IonMobility::isPassEntireDiaPasefFrame() const
+//{
+ //   return isPassEntireDiaPasefFrame_;
+//}
+
 PWIZ_API_DECL bool SpectrumList_IonMobility::accept(const msdata::SpectrumListPtr& inner)
 {
     return true; // We'll wrap anything, but getIonMobilityUnits() may well return "none"

pwiz/analysis/spectrum_processing/SpectrumList_IonMobility.hpp

@@ -66,11 +66,15 @@ class PWIZ_API_DECL SpectrumList_IonMobility : public msdata::SpectrumListWrappe
     /// for Waters SONAR data, given a "drift" bin return the nominal m/z filter value of that bin.  If bin is outside the SONAR range, return value will be 0
     virtual double sonarBinToPrecursorMz(int bin) const;
 
+    /// for Bruker TIMS data, returns true if the data represents an entire diaPASEF frame with isolation range arrays, as in diagonal PASEF mode
+  //  virtual bool isPassEntireDiaPasefFrame() const;
+
 private:
     enum class IonMobilityEquipment { None, AgilentDrift, WatersDrift, WatersSonar, BrukerTIMS, ThermoFAIMS, UIMFDrift, MobilIonDrift };
     IonMobilityEquipment equipment_;
     IonMobilityUnits units_;
     bool has_mzML_combined_ion_mobility_;
+    //bool isPassEntireDiaPasefFrame_;
     msdata::SpectrumListIonMobilityBase* sl_;
 };
 

pwiz/data/msdata/Reader.cpp

@@ -52,6 +52,8 @@ Reader::Config::Config()
     , sortAndJitter(false)
     , globalChromatogramsAreMs1Only(false)
     , ddaProcessing(false)
+    , passEntireDiaPasefFrame(false)
+    , includeIsolationArrays(true)
 {
 }
 
@@ -74,6 +76,8 @@ Reader::Config::Config(const Config& rhs)
     isolationMzAndMobilityFilter = rhs.isolationMzAndMobilityFilter;
     sortAndJitter = rhs.sortAndJitter;
     globalChromatogramsAreMs1Only = rhs.globalChromatogramsAreMs1Only;
+    passEntireDiaPasefFrame = rhs.passEntireDiaPasefFrame;
+    includeIsolationArrays = rhs.includeIsolationArrays;
 }
 
 void Reader::Config::instrumentMetadataError(const std::string& msg) const

pwiz/data/msdata/Reader.hpp

@@ -59,6 +59,12 @@ class PWIZ_API_DECL Reader
         /// when true, all drift bins/scans in a frame/block are written in combined form instead of as individual spectra
         bool combineIonMobilitySpectra;
 
+        /// when true, diaPASEF data is combined frame-by-frame instead of grouped by isolation window
+        bool passEntireDiaPasefFrame;
+
+        /// when true, include precursor isolation range arrays in Bruker DiaPASEF in passEntireDiaPasefFrame mode
+        bool includeIsolationArrays;
+
         /// when true, scans with only calibration data will be ignored (currently Waters lockmass only)
         bool ignoreCalibrationScans;
 

pwiz/data/vendor_readers/Bruker/Reader_Bruker.cpp

@@ -200,6 +200,19 @@ void fillInMetadata(const bfs::path& rootpath, MSData& msd, Reader_Bruker_Format
         auto serialNumber = compassDataPtr->getInstrumentSerialNumber();
         if (!serialNumber.empty())
             msd.run.defaultInstrumentConfigurationPtr->set(MS_instrument_serial_number, serialNumber);
+
+        // Write DIA-PASEF window group information if available
+        auto diaFrameMsMsWindowsTable = compassDataPtr->getDiaFrameMsMsWindowsTable();
+        if (!diaFrameMsMsWindowsTable.empty())
+        {
+            std::vector<std::string> lines;
+            boost::split(lines, diaFrameMsMsWindowsTable, boost::is_any_of(";"));
+            msd.run.defaultInstrumentConfigurationPtr->userParams.push_back(UserParam("DiaFrameMsMsWindowsTable", lines[0]));
+            for (size_t i = 1; i < lines.size(); ++i)
+            {
+                msd.run.defaultInstrumentConfigurationPtr->userParams.push_back(UserParam("WindowGroup", lines[i]));
+            }
+        }
     }
 
     msd.run.id = msd.id;
@@ -233,7 +246,7 @@ void Reader_Bruker::read(const string& filename,
         rootpath = rootpath.parent_path();
 
     CompassDataPtr compassDataPtr(CompassData::create(rootpath.string(), config.combineIonMobilitySpectra, format, 
-        config.preferOnlyMsLevel, config.allowMsMsWithoutPrecursor, config.isolationMzAndMobilityFilter));
+        config.preferOnlyMsLevel, config.allowMsMsWithoutPrecursor, config.passEntireDiaPasefFrame, config.includeIsolationArrays, config.isolationMzAndMobilityFilter));
 
     SpectrumList_Bruker* sl = new SpectrumList_Bruker(result, rootpath.string(), format, compassDataPtr, config);
     ChromatogramList_Bruker* cl = new ChromatogramList_Bruker(result, rootpath.string(), format, compassDataPtr, config);

pwiz/data/vendor_readers/Bruker/Reader_Bruker_Test.data/Hela_QC_PASEF_Slot1-first-6-frames-combineIMS-centroid.mzML

@@ -90,7 +90,6 @@
           <cvParam cvRef="MS" accession="MS:1000571" name="sum of spectra" value=""/>
           <scan spectrumRef="frame=1 scan=229">
             <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="3600.104777103251" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
-            <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.383376377915" unitCvRef="MS" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
             <scanWindowList count="1">
               <scanWindow>
                 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="100.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
@@ -202,7 +201,6 @@
           <cvParam cvRef="MS" accession="MS:1000571" name="sum of spectra" value=""/>
           <scan spectrumRef="frame=1 scan=297">
             <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="3600.104777103251" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
-            <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.311488568245" unitCvRef="MS" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
             <scanWindowList count="1">
               <scanWindow>
                 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="100.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
@@ -314,7 +312,6 @@
           <cvParam cvRef="MS" accession="MS:1000571" name="sum of spectra" value=""/>
           <scan spectrumRef="frame=2 scan=210">
             <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="3600.219602772449" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
-            <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.402904707999" unitCvRef="MS" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
             <scanWindowList count="1">
               <scanWindow>
                 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="100.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
@@ -424,7 +421,6 @@
           <cvParam cvRef="MS" accession="MS:1000571" name="sum of spectra" value=""/>
           <scan spectrumRef="frame=2 scan=251">
             <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="3600.219602772449" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
-            <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.360215217559" unitCvRef="MS" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
             <scanWindowList count="1">
               <scanWindow>
                 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="100.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
@@ -536,7 +532,6 @@
           <cvParam cvRef="MS" accession="MS:1000571" name="sum of spectra" value=""/>
           <scan spectrumRef="frame=2 scan=297">
             <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="3600.219602772449" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
-            <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.311488568245" unitCvRef="MS" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
             <scanWindowList count="1">
               <scanWindow>
                 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="100.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
@@ -648,7 +643,6 @@
           <cvParam cvRef="MS" accession="MS:1000571" name="sum of spectra" value=""/>
           <scan spectrumRef="frame=3 scan=210">
             <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="3600.332630267621" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
-            <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.402904707999" unitCvRef="MS" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
             <scanWindowList count="1">
               <scanWindow>
                 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="100.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
@@ -758,7 +752,6 @@
           <cvParam cvRef="MS" accession="MS:1000571" name="sum of spectra" value=""/>
           <scan spectrumRef="frame=3 scan=251">
             <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="3600.332630267621" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
-            <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.360215217559" unitCvRef="MS" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
             <scanWindowList count="1">
               <scanWindow>
                 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="100.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
@@ -870,7 +863,6 @@
           <cvParam cvRef="MS" accession="MS:1000571" name="sum of spectra" value=""/>
           <scan spectrumRef="frame=3 scan=297">
             <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="3600.332630267621" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
-            <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.311488568245" unitCvRef="MS" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
             <scanWindowList count="1">
               <scanWindow>
                 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="100.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
@@ -982,7 +974,6 @@
           <cvParam cvRef="MS" accession="MS:1000571" name="sum of spectra" value=""/>
           <scan spectrumRef="frame=4 scan=210">
             <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="3600.446653913667" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
-            <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.402904707999" unitCvRef="MS" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
             <scanWindowList count="1">
               <scanWindow>
                 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="100.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
@@ -1092,7 +1083,6 @@
           <cvParam cvRef="MS" accession="MS:1000571" name="sum of spectra" value=""/>
           <scan spectrumRef="frame=4 scan=251">
             <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="3600.446653913667" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
-            <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.360215217559" unitCvRef="MS" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
             <scanWindowList count="1">
               <scanWindow>
                 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="100.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
@@ -1204,7 +1194,6 @@
           <cvParam cvRef="MS" accession="MS:1000571" name="sum of spectra" value=""/>
           <scan spectrumRef="frame=4 scan=297">
             <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="3600.446653913667" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
-            <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.311488568245" unitCvRef="MS" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
             <scanWindowList count="1">
               <scanWindow>
                 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="100.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
@@ -1316,7 +1305,6 @@
           <cvParam cvRef="MS" accession="MS:1000571" name="sum of spectra" value=""/>
           <scan spectrumRef="frame=5 scan=210">
             <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="3600.560795150677" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
-            <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.402904707999" unitCvRef="MS" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
             <scanWindowList count="1">
               <scanWindow>
                 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="100.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
@@ -1426,7 +1414,6 @@
           <cvParam cvRef="MS" accession="MS:1000571" name="sum of spectra" value=""/>
           <scan spectrumRef="frame=5 scan=251">
             <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="3600.560795150677" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
-            <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.360215217559" unitCvRef="MS" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
             <scanWindowList count="1">
               <scanWindow>
                 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="100.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
@@ -1538,7 +1525,6 @@
           <cvParam cvRef="MS" accession="MS:1000571" name="sum of spectra" value=""/>
           <scan spectrumRef="frame=5 scan=297">
             <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="3600.560795150677" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
-            <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.311488568245" unitCvRef="MS" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
             <scanWindowList count="1">
               <scanWindow>
                 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="100.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
@@ -1650,7 +1636,6 @@
           <cvParam cvRef="MS" accession="MS:1000571" name="sum of spectra" value=""/>
           <scan>
             <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="3600.674356643713" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
-            <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.58380207594" unitCvRef="MS" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
             <scanWindowList count="1">
               <scanWindow>
                 <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="100.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>