Extension of bruker precursor information (2nd attempt)

pwiz/data/msdata/Serializer_MGF.cpp

@@ -96,7 +96,7 @@ void Serializer_MGF::Impl::write(ostream& os, const MSData& msd,
                 throw;
         }
 
-        Scan* scan = !s->scanList.empty() ? &s->scanList.scans[0] : 0;
+        const Scan& scan = !s->scanList.empty() ? s->scanList.scans[0] : Scan();
 
         if (s->cvParam(MS_ms_level).valueAs<int>() > 1 &&
             !s->precursors.empty() &&
@@ -105,19 +105,29 @@ void Serializer_MGF::Impl::write(ostream& os, const MSData& msd,
             os << "BEGIN IONS\n";
 
             const SelectedIon& si = s->precursors[0].selectedIons[0];
-            CVParam scanTimeParam = scan ? scan->cvParam(MS_scan_start_time) : CVParam();
+            CVParam scanTimeParam = scan.cvParam(MS_scan_start_time);
             CVParam chargeParam = si.cvParam(MS_charge_state);
 
             CVParam spectrumTitle = s->cvParam(MS_spectrum_title);
             if (!spectrumTitle.empty())
-                os << "TITLE=" << spectrumTitle.value << '\n';
+                os << "TITLE=" << spectrumTitle.value;
             else if (titleIsThermoDTA)
             {
-                string scan = id::value(s->id, "scan");
-                os << "TITLE=" << thermoBasename << '.' << scan << '.' << scan << '.' << chargeParam.value << '\n';
+                string scan_string = id::value(s->id, "scan");
+                os << "TITLE=" << thermoBasename << '.' << scan_string << '.' << scan_string << '.' << chargeParam.value;
             }
             else
-                os << "TITLE=" << s->id << '\n';
+                os << "TITLE=" << s->id;
+
+            CVParam collisionalCrossSectionalArea = scan.cvParam(MS_collisional_cross_sectional_area);
+            if (!collisionalCrossSectionalArea.empty())
+            {
+                os << ", " << "ccs=" << collisionalCrossSectionalArea.valueFixedNotation() << '\n';
+            }
+            else
+            {
+                os << '\n';
+            }
 
             if (!scanTimeParam.empty())
                 os << "RTINSECONDS=" << scanTimeParam.timeInSeconds() << '\n';
@@ -132,6 +142,11 @@ 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 << "ION_MOBILITY=" << si.cvParam(MS_selected_ion_m_z).valueFixedNotation() << " " << inverseReduceIonMobility.valueFixedNotation();
+            os << '\n';
+
             if (chargeParam.empty())
             {
                 vector<string> charges;

pwiz/data/msdata/Serializer_MGF_Test.cpp

@@ -122,6 +122,8 @@ void initializeTinyMGF(MSData& msd)
     s21.scanList.scans.push_back(Scan());
     Scan& s21scan = s21.scanList.scans.back();
     s21scan.set(MS_scan_start_time, 42.0, UO_second);
+    s21scan.set(MS_inverse_reduced_ion_mobility, 421.0, MS_volt_second_per_square_centimeter);
+    s21scan.set(MS_collisional_cross_sectional_area, 1.376, UO_square_angstrom);
 
     s21.setMZIntensityArrays(vector<double>(), vector<double>(), MS_number_of_detector_counts);
     BinaryData<double>& s21_mz = s21.getMZArray()->data;
@@ -154,7 +156,7 @@ void testWriteRead(const MSData& msd)
     DiffConfig diffConfig;
     diffConfig.ignoreIdentity = true;
     diffConfig.ignoreChromatograms = true;
-
+    
     Diff<MSData, DiffConfig> diff(msd, msd2, diffConfig);
     if (os_ && diff) *os_ << diff << endl; 
     unit_assert(!diff);
@@ -203,5 +205,4 @@ int main(int argc, char* argv[])
     }
 
     TEST_EPILOG
-}
-
+}

pwiz/data/msdata/Serializer_mzXML.cpp

@@ -441,6 +441,7 @@ struct PrecursorInfo
     string collisionEnergy;
     string activation;
     double windowWideness;
+
 
     bool empty() const 
     {
@@ -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);

pwiz/data/msdata/SpectrumList_MGF.cpp

@@ -40,6 +40,9 @@ using namespace pwiz::util;
 
 namespace {
 
+const char* startTagCCSInTitle = "ccs=";
+const char* endTagsCCSInTitle[] = { " ", ",",";","\t" };
+
 class SpectrumList_MGFImpl : public SpectrumList_MGF
 {
     public:
@@ -218,10 +221,18 @@ class SpectrumList_MGFImpl : public SpectrumList_MGF
                                 // Some formats omit RTINSECONDS and store the retention time
                                 // in the title field instead.
                                 double scanTimeMin = getRetentionTimeFromTitle(value);
+
                                 if (scanTimeMin > 0)
                                     scan.set(MS_scan_start_time, scanTimeMin * 60, UO_second);
 
-                                spectrum.set(MS_spectrum_title, value);
+                                double ccs = getCCSFromTitle(value);
+
+                                if (ccs >= 0)
+                                {
+                                    scan.cvParams.push_back(CVParam(MS_collisional_cross_sectional_area, ccs, UO_square_angstrom));
+                                }
+
+                                spectrum.set(MS_spectrum_title, removeCCSFromTitle(value));
                             }
                             else if (name == "PEPMASS")
                             {
@@ -235,6 +246,13 @@ class SpectrumList_MGFImpl : public SpectrumList_MGF
                                 else
                                     selectedIon.set(MS_selected_ion_m_z, value, MS_m_z);
                             }
+                            else if (name == "ION_MOBILITY")
+                            {
+                                bal::trim(value);
+                                size_t delim = value.find_last_of(' ');
+
+                                scan.cvParams.push_back(CVParam(MS_inverse_reduced_ion_mobility, value.substr(delim + 1, value.size() - delim - 1), MS_volt_second_per_square_centimeter));
+                            }
                             else if (name == "CHARGE")
                             {
                                 bal::trim_if(value, bal::is_any_of(" \t\r"));
@@ -330,6 +348,62 @@ class SpectrumList_MGFImpl : public SpectrumList_MGF
         spectrum.set(MS_base_peak_intensity, basePeakIntensity);
     }
 
+    static size_t FindEndTag(const string& title, size_t start)
+    {
+        for (int i = 0; i < sizeof(endTagsCCSInTitle) / sizeof(endTagsCCSInTitle[0]); i++)
+        {
+            const size_t tmpEnd = title.find(endTagsCCSInTitle[i], start);
+            if (tmpEnd != string::npos)
+            {
+                return tmpEnd;
+            }
+        }
+
+        return title.length();
+    }
+
+    /**
+    * Parse the spectrum title to look for CCS.
+    */
+    static double getCCSFromTitle(const string& title)
+    {
+	    size_t start = title.find(startTagCCSInTitle, 0);
+
+        if (start == string::npos)
+            return -1; // not found
+
+        start += strlen(startTagCCSInTitle);
+
+        try
+        {
+            return boost::lexical_cast<double>(title.substr(start, FindEndTag(title, start + strlen(startTagCCSInTitle)) - start));
+        }
+        catch (...)
+        {
+            return -1;
+        }
+    }
+
+    /**
+     * Parse the spectrum title to look for CCS.
+    */
+    static string removeCCSFromTitle(const string& title)
+    {
+        size_t start = title.find(startTagCCSInTitle, 0);
+
+        if (start == string::npos)
+            return title; // not found
+
+        try
+        {
+            return title.substr(0, start - 2) + title.substr(FindEndTag(title, start));
+        }
+        catch (...)
+        {
+            return title;
+        }
+    }
+
     /**
      * Parse the spectrum title to look for retention times.  If there are
      * two times, return the center of the range.  Possible formats to look
@@ -346,7 +420,6 @@ class SpectrumList_MGFImpl : public SpectrumList_MGF
         double secondTime = 0;
         for(int format_idx = 0; format_idx < 2; format_idx++)
         {
-
             size_t position = 0;
             firstTime = getTime(title, startTags[format_idx], 
                                 endTags[format_idx], position);
@@ -376,7 +449,7 @@ class SpectrumList_MGFImpl : public SpectrumList_MGF
      * Update position to the end of the parsed double.
      */
     double getTime(const string& title, const char* startTag,
-                   const char* endTag, size_t position) const
+                   const char* endTag, size_t& position) const
     {
         size_t start = title.find(startTag, position);
         if( start == string::npos )
@@ -403,7 +476,6 @@ class SpectrumList_MGFImpl : public SpectrumList_MGF
         size_t lineCount = 0;
         bool inBeginIons = false;
         vector<SpectrumIdentity>::iterator curIdentityItr;
-        map<string, size_t>::iterator curIdToIndexItr;
 
         while (std::getline(*is_, lineStr)) // need accurate line length, so do not use pwiz::util convenience wrapper
         {
@@ -421,7 +493,7 @@ class SpectrumList_MGFImpl : public SpectrumList_MGF
                 curIdentityItr->index = index_.size()-1;
                 curIdentityItr->id = "index=" + lexical_cast<string>(index_.size()-1);
                 curIdentityItr->sourceFilePosition = size_t(is_->tellg())-lineStr.length()-1;
-                curIdToIndexItr = idToIndex_.insert(pair<string, size_t>(curIdentityItr->id, index_.size()-1)).first;
+                idToIndex_.insert(pair<string, size_t>(curIdentityItr->id, index_.size() - 1)).first;
                 inBeginIons = true;
             }
             else if (lineStr.find("TITLE=") == 0)

pwiz/data/msdata/SpectrumList_mzXML.cpp

@@ -567,7 +567,6 @@ class HandlerScan : public SAXParser::Handler
     bool getBinaryData_;
     string scanNumber_;
     string collisionEnergy_;
-    string activationMethod_;
     HandlerPeaks handlerPeaks_;
     HandlerPrecursor handlerPrecursor_;
     CVID nativeIdFormat_;

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

@@ -158,6 +158,7 @@
               <selectedIon>
                 <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1221.992746500243" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                 <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="1"/>
+                <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="38916.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
               </selectedIon>
             </selectedIonList>
             <activation>
@@ -268,6 +269,7 @@
               <selectedIon>
                 <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1135.076451371559" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                 <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
+                <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="3367.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
               </selectedIon>
             </selectedIonList>
             <activation>
@@ -377,6 +379,7 @@
             <selectedIonList count="1">
               <selectedIon>
                 <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1426.71440688228" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+                <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="272.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
               </selectedIon>
             </selectedIonList>
             <activation>
@@ -487,6 +490,7 @@
               <selectedIon>
                 <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1318.158480438941" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                 <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
+                <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="693.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
               </selectedIon>
             </selectedIonList>
             <activation>
@@ -597,6 +601,7 @@
               <selectedIon>
                 <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1135.076451371559" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                 <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
+                <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="3367.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
               </selectedIon>
             </selectedIonList>
             <activation>
@@ -706,6 +711,7 @@
             <selectedIonList count="1">
               <selectedIon>
                 <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1426.71440688228" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+                <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="272.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
               </selectedIon>
             </selectedIonList>
             <activation>
@@ -816,6 +822,7 @@
               <selectedIon>
                 <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1318.158480438941" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                 <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
+                <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="693.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
               </selectedIon>
             </selectedIonList>
             <activation>
@@ -926,6 +933,7 @@
               <selectedIon>
                 <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1135.076451371559" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                 <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
+                <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="3367.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
               </selectedIon>
             </selectedIonList>
             <activation>
@@ -1035,6 +1043,7 @@
             <selectedIonList count="1">
               <selectedIon>
                 <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1426.71440688228" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+                <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="272.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
               </selectedIon>
             </selectedIonList>
             <activation>
@@ -1145,6 +1154,7 @@
               <selectedIon>
                 <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1318.158480438941" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                 <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
+                <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="693.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
               </selectedIon>
             </selectedIonList>
             <activation>
@@ -1255,6 +1265,7 @@
               <selectedIon>
                 <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1135.076451371559" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                 <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
+                <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="3367.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
               </selectedIon>
             </selectedIonList>
             <activation>
@@ -1364,6 +1375,7 @@
             <selectedIonList count="1">
               <selectedIon>
                 <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1426.71440688228" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+                <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="272.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
               </selectedIon>
             </selectedIonList>
             <activation>
@@ -1474,6 +1486,7 @@
               <selectedIon>
                 <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1318.158480438941" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                 <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
+                <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="693.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
               </selectedIon>
             </selectedIonList>
             <activation>
@@ -1584,6 +1597,7 @@
               <selectedIon>
                 <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1135.076451371559" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                 <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
+                <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="3367.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
               </selectedIon>
             </selectedIonList>
             <activation>