- added ignoreScheduledLimitsForChromatograms flag for telling pwiz t…

…o try to get SIM/SRM chromatograms from the entire time range instead of within the scheduled limits; works around a bug(?) with Sciex WIFF where it records the wrong scheduled limits but the data is actually there if you tell it to ignore the limits (reported by Phillip and Celeste)
ProteoWizard · May 15, 2023 · 64ac83d · 64ac83d
1 parent 45ae8f2
commit 64ac83d
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Showing 7 changed files with 30 additions and 22 deletions.
diff --git a/pwiz/data/msdata/Reader.cpp b/pwiz/data/msdata/Reader.cpp
@@ -52,6 +52,7 @@ Reader::Config::Config()
     , sortAndJitter(false)
     , globalChromatogramsAreMs1Only(false)
     , ddaProcessing(false)
+    , ignoreScheduledLimitsForChromatograms(false)
 {
 }
 
@@ -74,6 +75,7 @@ Reader::Config::Config(const Config& rhs)
     isolationMzAndMobilityFilter = rhs.isolationMzAndMobilityFilter;
     sortAndJitter = rhs.sortAndJitter;
     globalChromatogramsAreMs1Only = rhs.globalChromatogramsAreMs1Only;
+    ignoreScheduledLimitsForChromatograms = rhs.ignoreScheduledLimitsForChromatograms;
 }
 
 // default implementation; most Readers don't need to worry about multi-run input files

diff --git a/pwiz/data/msdata/Reader.hpp b/pwiz/data/msdata/Reader.hpp
@@ -96,6 +96,10 @@ class PWIZ_API_DECL Reader
         // to the same precursor from the same survey scan, and lockmass-correcting the precursor mass (if the lockmass refiner is active).
         bool ddaProcessing;
 
+        /// when true, scheduled SIM/SRM chromatograms will try to get an XIC covering the entire range instead of just the scheduled range
+        /// (useful if the instrument recorded extra data outside the scheduled limits, currently only applicable to Sciex WIFF)
+        bool ignoreScheduledLimitsForChromatograms;
+
         Config();
         Config(const Config& rhs);
     };

diff --git a/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp b/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp
@@ -251,7 +251,7 @@ PWIZ_API_DECL ChromatogramPtr ChromatogramList_ABI::chromatogram(size_t index, D
             result->setTimeIntensityArrays(std::vector<double>(), std::vector<double>(), UO_minute, MS_number_of_detector_counts);
 
             pwiz::util::BinaryData<double> times, intensities;
-            experiment->getSIC(ie.transition, times, intensities);
+            experiment->getSIC(ie.transition, times, intensities, config_.ignoreScheduledLimitsForChromatograms);
             result->defaultArrayLength = times.size();
 
             if (getBinaryData)
@@ -290,7 +290,7 @@ PWIZ_API_DECL ChromatogramPtr ChromatogramList_ABI::chromatogram(size_t index, D
             result->setTimeIntensityArrays(std::vector<double>(), std::vector<double>(), UO_minute, MS_number_of_detector_counts);
 
             pwiz::util::BinaryData<double> times, intensities;
-            experiment->getSIC(ie.transition, times, intensities);
+            experiment->getSIC(ie.transition, times, intensities, config_.ignoreScheduledLimitsForChromatograms);
             result->defaultArrayLength = times.size();
 
             if (getBinaryData)

diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp
@@ -130,9 +130,9 @@ struct ExperimentImpl : public Experiment
     virtual size_t getSRMSize() const;
     virtual void getSRM(size_t index, Target& target) const;
 
-    virtual double getSIC(size_t index, pwiz::util::BinaryData<double>& times, pwiz::util::BinaryData<double>& intensities) const;
+    virtual double getSIC(size_t index, pwiz::util::BinaryData<double>& times, pwiz::util::BinaryData<double>& intensities, bool ignoreScheduledLimits) const;
     virtual void getSIC(size_t index, pwiz::util::BinaryData<double>& times, pwiz::util::BinaryData<double>& intensities,
-                        double& basePeakX, double& basePeakY) const;
+                        double& basePeakX, double& basePeakY, bool ignoreScheduledLimits) const;
 
     virtual void getAcquisitionMassRange(double& startMz, double& stopMz) const;
     virtual ScanType getScanType() const;
@@ -609,7 +609,7 @@ void ExperimentImpl::getSRM(size_t index, Target& target) const
     CATCH_AND_FORWARD
 }
 
-double ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData<double>& times, pwiz::util::BinaryData<double>& intensities) const
+double ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData<double>& times, pwiz::util::BinaryData<double>& intensities, bool ignoreScheduledLimits) const
 {
     try
     {
@@ -620,7 +620,13 @@ double ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData<double>& time
         getSRM(index, target);
 
         ExtractedIonChromatogramSettings^ option = gcnew ExtractedIonChromatogramSettings(index);
-        if (target.startTime != target.endTime)
+        if (ignoreScheduledLimits)
+        {
+            option->StartCycle = 0;
+            option->EndCycle = convertRetentionTimeToCycle(cycleTimes().back());
+            option->UseStartEndCycle = true;
+        }
+        else if (target.startTime != target.endTime)
         {
             option->StartCycle = convertRetentionTimeToCycle(target.startTime);
             option->EndCycle = convertRetentionTimeToCycle(target.endTime);
@@ -636,9 +642,9 @@ double ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData<double>& time
 }
 
 void ExperimentImpl::getSIC(size_t index, pwiz::util::BinaryData<double>& times, pwiz::util::BinaryData<double>& intensities,
-                            double& basePeakX, double& basePeakY) const
+                            double& basePeakX, double& basePeakY, bool ignoreScheduledLimits) const
 {
-    basePeakY = getSIC(index, times, intensities);
+    basePeakY = getSIC(index, times, intensities, ignoreScheduledLimits);
 
     try
     {

diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp
@@ -190,9 +190,9 @@ struct PWIZ_API_DECL Experiment
 
     virtual size_t getSRMSize() const = 0;
     virtual void getSRM(size_t index, Target& target) const = 0;
-    virtual double getSIC(size_t index, pwiz::util::BinaryData<double>& times, pwiz::util::BinaryData<double>& intensities) const = 0;
+    virtual double getSIC(size_t index, pwiz::util::BinaryData<double>& times, pwiz::util::BinaryData<double>& intensities, bool ignoreScheduledLimits) const = 0;
     virtual void getSIC(size_t index, pwiz::util::BinaryData<double>& times, pwiz::util::BinaryData<double>& intensities,
-                        double& basePeakX, double& basePeakY) const = 0;
+                        double& basePeakX, double& basePeakY, bool ignoreScheduledLimits) const = 0;
 
     virtual void getAcquisitionMassRange(double& startMz, double& stopMz) const = 0;
     virtual ScanType getScanType() const = 0;

diff --git a/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp b/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile2.ipp
@@ -130,9 +130,9 @@ struct Experiment2Impl : public Experiment
     virtual size_t getSRMSize() const;
     virtual void getSRM(size_t index, Target& target) const;
 
-    virtual double getSIC(size_t index, pwiz::util::BinaryData<double>& times, pwiz::util::BinaryData<double>& intensities) const;
+    virtual double getSIC(size_t index, pwiz::util::BinaryData<double>& times, pwiz::util::BinaryData<double>& intensities, bool ignoreScheduledLimits) const;
     virtual void getSIC(size_t index, pwiz::util::BinaryData<double>& times, pwiz::util::BinaryData<double>& intensities,
-                        double& basePeakX, double& basePeakY) const;
+                        double& basePeakX, double& basePeakY, bool ignoreScheduledLimits) const;
 
     virtual void getAcquisitionMassRange(double& startMz, double& stopMz) const;
     virtual ScanType getScanType() const;
@@ -568,15 +568,15 @@ void Experiment2Impl::getSRM(size_t index, Target& target) const
     CATCH_AND_FORWARD
 }
 
-double Experiment2Impl::getSIC(size_t index, pwiz::util::BinaryData<double>& times, pwiz::util::BinaryData<double>& intensities) const
+double Experiment2Impl::getSIC(size_t index, pwiz::util::BinaryData<double>& times, pwiz::util::BinaryData<double>& intensities, bool ignoreScheduledLimits) const
 {
     double x, y;
-    getSIC(index, times, intensities, x, y);
+    getSIC(index, times, intensities, x, y, ignoreScheduledLimits);
     return y;
 }
 
 void Experiment2Impl::getSIC(size_t index, pwiz::util::BinaryData<double>& times, pwiz::util::BinaryData<double>& intensities,
-                            double& basePeakX, double& basePeakY) const
+                            double& basePeakX, double& basePeakY, bool ignoreScheduledLimits) const
 {
     try
     {

diff --git a/pwiz_tools/commandline/msconvert.cpp b/pwiz_tools/commandline/msconvert.cpp
@@ -70,15 +70,8 @@ struct Config : public Reader::Config
     Config()
         : outputPath("."), verbose(false), merge(false)
     {
-        simAsSpectra = false;
-        srmAsSpectra = false;
-        combineIonMobilitySpectra = false;
-        ignoreCalibrationScans = false;
-        reportSonarBins = false;
-        unknownInstrumentIsError = true;
         stripLocationFromSourceFiles = false;
         stripVersionFromSoftware = false;
-        ddaProcessing = false;
     }
 
     string outputFilename(const string& inputFilename, const MSData& inputMSData) const;
@@ -344,6 +337,9 @@ Config parseCommandLine(int argc, char** argv)
         ("ignoreCalibrationScans",
             po::value<bool>(&config.ignoreCalibrationScans)->zero_tokens(),
             ": do not process calibration scans (currently only applies to Waters lockmass function)")
+        ("ignoreScheduledLimitsForChromatograms",
+            po::value<bool>(&config.ignoreScheduledLimitsForChromatograms)->zero_tokens(),
+            ": scheduled SIM/SRM chromatograms will try to get an XIC covering the entire run time instead of just the scheduled limits")
         ("acceptZeroLengthSpectra",
             po::value<bool>(&config.acceptZeroLengthSpectra)->zero_tokens(),
             ": some vendor readers have an efficient way of filtering out empty spectra, but it takes more time to open the file")