Updated msconvert and Skyline to handle Agilent neutral loss/gain scan data

pwiz/data/vendor_readers/Agilent/Reader_Agilent.cpp

@@ -117,6 +117,8 @@ void fillInMetadata(const string& rawpath, MassHunterDataPtr rawfile, MSData& ms
     if (scanTypes & MSScanType_Scan)         msd.fileDescription.fileContent.set(MS_MS1_spectrum);
     if (scanTypes & MSScanType_ProductIon)   msd.fileDescription.fileContent.set(MS_MSn_spectrum);
     if (scanTypes & MSScanType_PrecursorIon) msd.fileDescription.fileContent.set(MS_precursor_ion_spectrum);
+    if (scanTypes & MSScanType_NeutralLoss)  msd.fileDescription.fileContent.set(MS_constant_neutral_loss_spectrum);
+    if (scanTypes & MSScanType_NeutralGain)  msd.fileDescription.fileContent.set(MS_constant_neutral_gain_spectrum);
     // other scan types are not enumerated
 
     if (!msd.fileDescription.fileContent.empty())

pwiz/data/vendor_readers/Agilent/Reader_Agilent_Detail.cpp

@@ -130,8 +130,8 @@ PWIZ_API_DECL CVID translateAsSpectrumType(MSScanType scanType)
     if (scanType == MSScanType_SelectedIon)         return MS_SIM_spectrum;
     if (scanType == MSScanType_TotalIon)            return MS_SIM_spectrum;
     if (scanType == MSScanType_MultipleReaction)    return MS_SRM_spectrum;
-    if (scanType == MSScanType_NeutralLoss)         return MS_constant_neutral_loss_scan_OBSOLETE;
-    if (scanType == MSScanType_NeutralGain)         return MS_constant_neutral_gain_scan_OBSOLETE;
+    if (scanType == MSScanType_NeutralLoss)         return MS_constant_neutral_loss_spectrum;
+    if (scanType == MSScanType_NeutralGain)         return MS_constant_neutral_gain_spectrum;
     throw runtime_error("[translateAsSpectrumType] Error parsing spectrum type.");
 }
 

pwiz/data/vendor_readers/Agilent/SpectrumList_Agilent.cpp

@@ -218,6 +218,7 @@ PWIZ_API_DECL SpectrumPtr SpectrumList_Agilent::spectrum(size_t index, DetailLev
     }
 
     double mzOfInterest = scanRecordPtr->getMZOfInterest();
+    bool isNeutralLossOrGainScan = scanType == MSScanType_NeutralLoss || scanType == MSScanType_NeutralGain;
     if (msLevel > 1 && mzOfInterest > 0)
     {
         Precursor precursor;
@@ -232,6 +233,10 @@ PWIZ_API_DECL SpectrumPtr SpectrumList_Agilent::spectrum(size_t index, DetailLev
             //product.isolationWindow.set(MS_isolation_window_lower_offset, isolationWidth/2, MS_m_z);
             //product.isolationWindow.set(MS_isolation_window_upper_offset, isolationWidth/2, MS_m_z);
         }
+        else if (isNeutralLossOrGainScan)
+        {
+            scan.set(MS_analyzer_scan_offset, mzOfInterest, MS_m_z); // Always positive, look at scan type to determine whether it's loss or gain
+        }
         else
         {
             precursor.isolationWindow.set(MS_isolation_window_target_m_z, mzOfInterest, MS_m_z);
@@ -367,7 +372,7 @@ PWIZ_API_DECL SpectrumPtr SpectrumList_Agilent::spectrum(size_t index, DetailLev
     }
 
 
-    if (reportMS2ForAllIonsScan)
+    if (reportMS2ForAllIonsScan || isNeutralLossOrGainScan)
     {
         // claim a target window that encompasses all ions
         Precursor& precursor = result->precursors.back();
@@ -733,6 +738,8 @@ PWIZ_API_DECL void SpectrumList_Agilent::createIndex() const
 			scanTypes & MSScanType_ProductIon ||
 			scanTypes & MSScanType_PrecursorIon ||
             scanTypes & MSScanType_SelectedIon ||
+            scanTypes & MSScanType_NeutralLoss ||
+            scanTypes & MSScanType_NeutralGain ||
             scanTypes & MSScanType_MultipleReaction)
 		{
 

pwiz_tools/Shared/CommonUtil/Spectra/SpectrumMetadata.cs

@@ -32,6 +32,7 @@ private enum Flags
             HasScanWindow = 2,
             HasTotalIonCurrent = 4,
             HasInjectionTime = 8,
+            HasConstantNeutralLoss = 16,
         }
         private ImmutableList<ImmutableList<SpectrumPrecursor>> _precursorsByMsLevel =
             ImmutableList<ImmutableList<SpectrumPrecursor>>.EMPTY;
@@ -161,6 +162,27 @@ private set
             }
         }
 
+        private double _constantNeutralLoss;
+
+        public double? ConstantNeutralLoss // As found in Constant Neutral Loss scans, where Q1 peaks are only reported if there's a Q3 peak with this mz offset. Positive value implies loss, negative value implies gain
+        {
+            get
+            {
+                return GetFlag(Flags.HasConstantNeutralLoss) ? _constantNeutralLoss : (double?)null;
+            }
+            private set
+            {
+                _constantNeutralLoss = value.GetValueOrDefault();
+                SetFlag(Flags.HasConstantNeutralLoss, _constantNeutralLoss != 0);
+            }
+        }
+
+        public SpectrumMetadata ChangeConstantNeutralLoss(double? value)
+        {
+            return ChangeProp(ImClone(this), im => im.ConstantNeutralLoss = value);
+        }
+
+
         public SpectrumMetadata ChangeTotalIonCurrent(double? value)
         {
             return ChangeProp(ImClone(this), im => im.TotalIonCurrent = value);

pwiz_tools/Shared/ProteowizardWrapper/MsDataFileImpl.cs

@@ -1397,6 +1397,7 @@ private SpectrumMetadata GetSpectrumMetadata(Spectrum spectrum)
 
             metadata = metadata.ChangeTotalIonCurrent(GetTotalIonCurrent(spectrum));
             metadata = metadata.ChangeInjectionTime(GetInjectionTime(spectrum));
+            metadata = metadata.ChangeConstantNeutralLoss(GetConstantNeutralLoss(spectrum));
             return metadata;
         }
 
@@ -1656,6 +1657,35 @@ private static string GetScanDescription(Spectrum spectrum)
             return count == 0 ? (double?) null : total;
         }
 
+        private double? GetConstantNeutralLoss(Spectrum spectrum) // If return value < 0, it's actually a neutral gain
+        {
+            try
+            {
+                if (spectrum.scanList.empty())
+                {
+                    return null;
+                }
+
+                CVParam paramOffset = spectrum.scanList.scans[0].cvParam(CVID.MS_analyzer_scan_offset);
+                if (paramOffset.empty())
+                {
+                    return null;
+                }
+
+                CVParam paramScanType = spectrum.scanList.scans[0].cvParam(CVID.MS_constant_neutral_gain_spectrum);
+                if (paramScanType.empty())
+                {
+                    return (double)paramOffset.value; // ConstantNeutralLoss is positive for loss, negative for gain;
+                }
+
+                return  -1.0 * (double)paramOffset.value; // ConstantNeutralLoss is positive for loss, negative for gain
+            }
+            catch (InvalidCastException)
+            {
+                return null;
+            }
+        }
+
         private static int GetPresetScanConfiguration(Spectrum spectrum)
         {
             try

pwiz_tools/Skyline/Model/Databinding/Entities/ColumnCaptions.resx

@@ -321,6 +321,9 @@
   <data name="ConfidenceLevel">
     <value>Confidence Level</value>
   </data>
+  <data name="ConstantNeutralLoss">
+    <value>Constant Neutral Loss</value>
+  </data>
   <data name="CountTruncated">
     <value>Count Truncated</value>
   </data>

pwiz_tools/Skyline/Model/Databinding/Entities/ColumnToolTips.resx

@@ -316,6 +316,9 @@ specific default collision energy equation within Skyline</value>
   <data name="ConfidenceLevel">
     <value>Confidence level which was used to determine the confidence interval around the fold change.</value>
   </data>
+  <data name="ConstantNeutralLoss">
+    <value>Analyzer offset value for constant neutral loss scan - use a negative value for neutral gain.</value>
+  </data>
   <data name="CountTruncated">
     <value>The number of transitions for a precursor that integrate a peak with a
 boundary at either end of the acquisition time range, where intensity at the end is

pwiz_tools/Skyline/Model/FullScanProperties.cs

@@ -119,6 +119,11 @@ public static FullScanProperties CreateProperties(MsDataSpectrum spectrum)
 
             res.IsCentroided = spectrum.Centroided.ToString(CultureInfo.CurrentCulture);
 
+            if (spectrum.Metadata.ConstantNeutralLoss.HasValue)
+            {
+                res.ConstantNeutralLoss = spectrum.Metadata.ConstantNeutralLoss.Value.ToString(Formats.Mz);
+            }
+
             if (spectrum.WindowGroup > 0)
             {
                 res.WindowGroup = spectrum.WindowGroup.ToString(CultureInfo.CurrentCulture); // For Bruker PASEF MS2
@@ -143,6 +148,7 @@ public static FullScanProperties CreateProperties(MsDataSpectrum spectrum)
         [Category("AcquisitionInfo")] public string ScanId { get; set; }
         [Category("AcquisitionInfo")] public string CE { get; set; }
         [Category("AcquisitionInfo")] public string MSLevel { get; set; }
+        [Category("AcquisitionInfo")] public string ConstantNeutralLoss { get; set; }
         [Category("AcquisitionInfo")] public InstrumentInfo Instrument { get; set; }
         [Category("AcquisitionInfo")] public string DataPoints { get; set; }
         [Category("AcquisitionInfo")] public string MzCount { get; set; }

pwiz_tools/Skyline/Model/FullScanPropertiesRes.resx

@@ -319,4 +319,10 @@
   <data name="DissociationMethod" xml:space="preserve">
     <value>Dissociation Method</value>
   </data>
+  <data name="ConstantNeutralLoss" xml:space="preserve">
+    <value>Constant Neutral Loss</value>
+  </data>
+  <data name="Description_ConstantNeutralLoss" xml:space="preserve">
+    <value>Analyzer offset for Constant Neutral Loss spectrum (negative value for constant neutral gain)</value>
+  </data>
 </root>

pwiz_tools/Skyline/Model/Results/Spectra/SpectrumClass.cs

@@ -79,5 +79,9 @@ public double? CompensationVoltage
         public double? IsolationWindowWidth { get; private set; }
 
         public string DissociationMethod { get; private set; }
+
+        [Format(Formats.Mz)]
+        public double? ConstantNeutralLoss { get; private set; } // Negative value means neutral gain
+
     }
 }

pwiz_tools/Skyline/Model/Results/Spectra/SpectrumClassColumn.cs

@@ -77,10 +77,13 @@ public abstract class SpectrumClassColumn
         public static readonly SpectrumClassColumn DissociationMethod = MakeColumn(
             nameof(SpectrumClass.DissociationMethod), GetDissociationMethod);
 
+        public static readonly SpectrumClassColumn ConstantNeutralLoss = MakeColumn(
+            nameof(SpectrumClass.ConstantNeutralLoss), spectrum => spectrum.ConstantNeutralLoss);
+
         public static readonly ImmutableList<SpectrumClassColumn> ALL = ImmutableList.ValueOf(new[]
         {
             Ms1Precursors, Ms2Precursors, ScanDescription, CollisionEnergy, ScanWindowWidth, CompensationVoltage,
-            PresetScanConfiguration, MsLevel, Analyzer, IsolationWindowWidth, DissociationMethod
+            PresetScanConfiguration, MsLevel, Analyzer, IsolationWindowWidth, DissociationMethod, ConstantNeutralLoss
         });
 
         public static readonly ImmutableList<SpectrumClassColumn> MS1 = ImmutableList.ValueOf(new[]

pwiz_tools/Skyline/Model/Results/Spectra/SpectrumMetadatas.cs

@@ -47,6 +47,7 @@ public class SpectrumMetadatas : AbstractReadOnlyList<SpectrumMetadata>
         private readonly ImmutableList<double?> _compensationVoltages;
         private readonly ImmutableList<bool> _negativeCharges;
         private readonly ImmutableList<int> _msLevels;
+        private readonly ImmutableList<double?> _constantNeutralLosses;
 
         public SpectrumMetadatas(IEnumerable<SpectrumMetadata> enumerable)
         {
@@ -65,6 +66,7 @@ public SpectrumMetadatas(IEnumerable<SpectrumMetadata> enumerable)
             _compensationVoltages = collection.Select(m => m.CompensationVoltage).ToFactor().MaybeConstant();
             _negativeCharges = collection.Select(m => m.NegativeCharge).ToFactor().MaybeConstant();
             _msLevels = collection.Select(m => m.MsLevel).ToFactor().MaybeConstant();
+            _constantNeutralLosses = collection.Select(m => m.ConstantNeutralLoss).Nullables().MaybeConstant();
         }
 
         public SpectrumMetadatas(ResultFileMetaDataProto proto)
@@ -118,6 +120,7 @@ public SpectrumMetadatas(ResultFileMetaDataProto proto)
             }
             _spectrumPrecursors = spectrumPrecursorsList.ToFactor().MaybeConstant();
             _msLevels = IntegerList.FromIntegers(msLevels);
+            _constantNeutralLosses = proto.Spectra.Select(s => s.ConstantNeutralLoss).Nullables().MaybeConstant();
         }
 
         public override SpectrumMetadata this[int index]
@@ -132,6 +135,7 @@ public override SpectrumMetadata this[int index]
                     .ChangePresetScanConfiguration(_presetScanConfigurations[index])
                     .ChangeScanDescription(_scanDescriptions[index])
                     .ChangeTotalIonCurrent(_totalIonCurrents[index])
+                    .ChangeConstantNeutralLoss(_constantNeutralLosses[index])
                     .ChangeNegativeCharge(_negativeCharges[index]);
                 var precursorsByLevelLookup = _spectrumPrecursors[index].ToLookup(t=>t.MsLevel, t=>t.Precursor);
                 var precursors = Enumerable.Range(1, _msLevels[index] - 1)

pwiz_tools/Skyline/ProtocolBuffers/ChromatogramGroupData.proto

@@ -47,6 +47,7 @@ message ResultFileMetaDataProto {
 		google.protobuf.DoubleValue compensationVoltage = 11;
 		bool negativeCharge = 12;
 		int32 msLevel = 13;
+		google.protobuf.DoubleValue constantNeutralLoss = 14;
 	}
 
 	message Precursor {