Merge branch '1.4.3' into zontal

# Conflicts:
#	RawFileParser.cs
#	Writer/MetadataWriter.cs
#	Writer/MzMlSpectrumWriter.cs

Author: zhaoheting-zontal

RawFileParser.cs

@@ -141,7 +141,6 @@ private static void ProcessFile(ParseInput parseInput)
                 if (rawFile.GetInstrumentCountOfType(Device.MS) != 0)
                 {
                     rawFile.SelectInstrument(Device.MS, 1);
-
                     rawFile.IncludeReferenceAndExceptionData = !parseInput.ExData;
 
                     // Get the first and last scan from the RAW file
@@ -154,7 +153,7 @@ private static void ProcessFile(ParseInput parseInput)
                         throw new RawFileParserException("Empty RAW file, no output will be produced");
                     }
                 }
-                
+
                 if (parseInput.MetadataFormat != MetadataFormat.NONE)
                 {
                     MetadataWriter metadataWriter = new MetadataWriter(parseInput);

Writer/MetadataWriter.cs

@@ -46,7 +46,7 @@ public MetadataWriter(ParseInput parseInput)
         /// </summary>
         public void WriteMetadata(IRawDataPlus rawFile, int firstScanNumber, int lastScanNumber)
         {
-            if (rawFile.SelectMsData())
+            if(rawFile.SelectMsData())
             {
                 for (var scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++)
                 {
@@ -112,8 +112,6 @@ public void WriteMetadata(IRawDataPlus rawFile, int firstScanNumber, int lastSca
                 }
             }
 
-            
-
             if (minCharge == 100000000000000)
             {
                 minCharge = 0;
@@ -177,6 +175,7 @@ private void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int last
                         rawFile.GetInstrumentData().HardwareVersion));
                 }
             }
+            
 
             // MS Data
             if (rawFile.SelectMsData())
@@ -216,7 +215,7 @@ private void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int last
                 metadata.addScanSetting(new CVTerm("MS:1000016", "MS", "scan start time",
                     startTime.ToString(CultureInfo.InvariantCulture)));
                 metadata.addScanSetting(new CVTerm("", "", "expected runtime",
-                    rawFile.RunHeader.ExpectedRuntime.ToString(CultureInfo.InvariantCulture)));            
+                    rawFile.RunHeader.ExpectedRuntime.ToString(CultureInfo.InvariantCulture)));
                 metadata.addScanSetting(new CVTerm("MS:1000011", "MS", "mass resolution",
                     rawFile.RunHeaderEx.MassResolution.ToString(CultureInfo.InvariantCulture)));
                 metadata.addScanSetting(new CVTerm("UO:0000002", "MS", "mass unit",
@@ -371,7 +370,7 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
                     output.Add("Firmware version=" + rawFile.GetInstrumentData().HardwareVersion);
                 }
             }
-
+            
             // MS Data
             if (rawFile.SelectMsData())
             {

Writer/MzMlSpectrumWriter.cs

@@ -68,6 +68,8 @@ public MzMlSpectrumWriter(ParseInput parseInput) : base(parseInput)
             _mzMlNamespace.Add(string.Empty, "http://psi.hupo.org/ms/mzml");
             _doIndexing = ParseInput.OutputFormat == OutputFormat.IndexMzML;
             _osOffset = Environment.NewLine == "\n" ? 0 : 1;
+            _precursorScanNumbers[""] = -1;
+            _precursorTree[-1] = new PrecursorInfo();
         }
 
         /// <inheritdoc />
@@ -1416,61 +1418,52 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
                     _precursorScanNumber = GetParentFromScanString(result.Groups[1].Value);
                 }
 
-                if (_precursorScanNumber > 0)
+                //finding precursor scan failed
+                if (_precursorScanNumber == -2)
                 {
+                    Log.Warn($"Cannot find precursor scan for scan# {scanNumber}");
+                    _precursorTree[-2] = new PrecursorInfo(0, msLevel, FindLastReaction(scanEvent, msLevel), new PrecursorType[0]);
+                }
 
-                    try
+                try
+                {
+                    try //since there is no direct way to get the number of reactions available, it is necessary to try and fail
+                    {
+                        scanEvent.GetReaction(_precursorTree[_precursorScanNumber].ReactionCount);
+                    }
+                    catch (ArgumentOutOfRangeException ex)
                     {
-                        try //since there is no direct way to get the number of reactions available, it is necessary to try and fail
+                        Log.Debug($"Using Tribrid decision tree fix for scan# {scanNumber}");
+                        //Is it a decision tree scheduled scan on tribrid?
+                        if (msLevel == _precursorTree[_precursorScanNumber].MSLevel)
                         {
-                            scanEvent.GetReaction(_precursorTree[_precursorScanNumber].ReactionCount);
+                            _precursorScanNumber = GetParentFromScanString(result.Groups[1].Value);
                         }
-                        catch (ArgumentOutOfRangeException ex)
+                        else
                         {
-                            Log.Debug($"Using Tribrid decision tree fix for scan# {scanNumber}");
-                            //Is it a decision tree scheduled scan on tribrid?
-                            if (msLevel == _precursorTree[_precursorScanNumber].MSLevel)
-                            {
-                                _precursorScanNumber = GetParentFromScanString(result.Groups[1].Value);
-                            }
-                            else
-                            {
-                                throw new RawFileParserException(
-                                    $"Tribrid decision tree fix failed - cannot get reaction# {_precursorTree[_precursorScanNumber].ReactionCount} from {scanEvent.ToString()}",
-                                    ex);
-                            }
+                            throw new RawFileParserException(
+                                $"Tribrid decision tree fix failed - cannot get reaction# {_precursorTree[_precursorScanNumber].ReactionCount} from {scanEvent.ToString()}",
+                                ex);
                         }
-
-                        // Construct and set the precursor list element of the spectrum
-                        spectrum.precursorList =
-                            ConstructPrecursorList(_precursorScanNumber, scanEvent, charge, monoisotopicMz, isolationWidth,
-                                SPSMasses, out var reactionCount);
-
-                        //save precursor information for later reference
-                        _precursorTree[scanNumber] = new PrecursorInfo(_precursorScanNumber, msLevel, reactionCount, spectrum.precursorList.precursor);
                     }
-                    catch (Exception e)
-                    {
-                        var extra = (e.InnerException is null) ? "" : $"\n{e.InnerException.StackTrace}";
 
-                        Log.Warn($"Failed creating precursor list for scan# {scanNumber} - precursor information for this and dependent scans will be empty\nException details:{e.Message}\n{e.StackTrace}\n{extra}");
-                        ParseInput.NewWarn();
-
-                        _precursorTree[scanNumber] = new PrecursorInfo(_precursorScanNumber, 1, 0, new PrecursorType[0]);
-
-                    }
+                    // Construct and set the precursor list element of the spectrum
+                    spectrum.precursorList =
+                        ConstructPrecursorList(_precursorScanNumber, scanEvent, charge, monoisotopicMz, isolationWidth,
+                            SPSMasses, out var reactionCount);
 
+                    //save precursor information for later reference
+                    _precursorTree[scanNumber] = new PrecursorInfo(_precursorScanNumber, msLevel, reactionCount, spectrum.precursorList.precursor);
                 }
-                else
+                catch (Exception e)
                 {
-                    spectrum.precursorList = new PrecursorListType
-                    {
-                        count = "0",
-                        precursor = new PrecursorType[0]
-                    };
+                    var extra = (e.InnerException is null) ? "" : $"\n{e.InnerException.StackTrace}";
+
+                    Log.Warn($"Failed creating precursor list for scan# {scanNumber} - precursor information for this and dependent scans will be empty\nException details:{e.Message}\n{e.StackTrace}\n{extra}");
+                    ParseInput.NewWarn();
+
+                    _precursorTree[scanNumber] = new PrecursorInfo(_precursorScanNumber, 1, 0, new PrecursorType[0]);
 
-                    Log.Error($"Failed finding precursor for {scanNumber}");
-                    ParseInput.NewError();
                 }
             }
             else
@@ -1995,6 +1988,45 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
             return spectrum;
         }
 
+        private int FindLastReaction(IScanEvent scanEvent, int msLevel)
+        {
+            int lastReactionIndex = msLevel - 2;
+
+            //iteratively trying find the last available index for reaction
+            while(true)
+            {
+                try
+                {
+                    scanEvent.GetReaction(lastReactionIndex + 1);
+                }
+                catch (ArgumentOutOfRangeException)
+                {
+                    //stop trying
+                    break;
+                }
+
+                lastReactionIndex++;
+            }
+
+            //supplemental activation flag is on -> one of the levels (not necissirily the last one) used supplemental activation
+            //check last two activations
+            if (scanEvent.SupplementalActivation == TriState.On) 
+            {
+                var lastActivation = scanEvent.GetReaction(lastReactionIndex).ActivationType;
+                var beforeLastActivation = scanEvent.GetReaction(lastReactionIndex - 1).ActivationType;
+
+                if ((beforeLastActivation == ActivationType.ElectronTransferDissociation || beforeLastActivation == ActivationType.ElectronCaptureDissociation) &&
+                    (lastActivation == ActivationType.CollisionInducedDissociation || lastActivation == ActivationType.HigherEnergyCollisionalDissociation))
+                    return lastReactionIndex - 1; //ETD or ECD followed by HCD or CID -> supplemental activation in the last level (move the last reaction one step back)
+                else
+                    return lastReactionIndex;
+            }
+            else //just use the last one
+            {
+                return lastReactionIndex;
+            }
+        }
+
         private SpectrumType ConstructPDASpectrum(int scanNumber, int instrumentNumber)
         {
             // Get each scan from the RAW file
@@ -2257,19 +2289,24 @@ private PrecursorListType ConstructPrecursorList(int precursorScanNumber, IScanE
             // Get precursors from earlier levels
             var prevPrecursors = _precursorTree[precursorScanNumber];
 
-            var spectrumRef = "";
+            string spectrumRef = null;
             int msLevel = (int)scanEvent.MSOrder;
             IReaction reaction = null;
             var precursorMz = 0.0;
             reactionCount = prevPrecursors.ReactionCount;
 
-            spectrumRef = ConstructSpectrumTitle((int)Device.MS, 1, precursorScanNumber);
             reaction = scanEvent.GetReaction(reactionCount);
 
-            precursorMz = reaction.PrecursorMass;
-
             //if isolation width was not found in the trailer, try to get one from the reaction
             if (isolationWidth == null) isolationWidth = reaction.IsolationWidth;
+            if (isolationWidth < 0) isolationWidth = null;
+
+            precursorMz = reaction.PrecursorMass;
+
+            if (precursorScanNumber > 0)
+            {
+                spectrumRef = ConstructSpectrumTitle((int)Device.MS, 1, precursorScanNumber);
+            }
 
             var precursor = new PrecursorType
             {
@@ -2307,7 +2344,7 @@ private PrecursorListType ConstructPrecursorList(int precursorScanNumber, IScanE
                 });
             }
 
-            if (selectedIonMz > ZeroDelta)
+            if (selectedIonMz > ZeroDelta && precursorScanNumber > 0)
             {
                 var selectedIonIntensity = CalculatePrecursorPeakIntensity(_rawFile, precursorScanNumber, reaction.PrecursorMass, isolationWidth,
                     ParseInput.NoPeakPicking.Contains(msLevel - 1));
@@ -2488,6 +2525,51 @@ private PrecursorListType ConstructPrecursorList(int precursorScanNumber, IScanE
                     spectrumRef = spectrumRef
                 };
 
+                //Isolation window for SPS masses is the same as for the first precursor
+                SPSPrecursor.isolationWindow =
+                new ParamGroupType
+                {
+                    cvParam = new CVParamType[3]
+                };
+
+                SPSPrecursor.isolationWindow.cvParam[0] =
+                    new CVParamType
+                    {
+                        accession = "MS:1000827",
+                        name = "isolation window target m/z",
+                        value = SPSMasses[n].ToString(CultureInfo.InvariantCulture),
+                        cvRef = "MS",
+                        unitCvRef = "MS",
+                        unitAccession = "MS:1000040",
+                        unitName = "m/z"
+                    };
+                if (isolationWidth != null)
+                {
+                    var offset = isolationWidth.Value / 2 + reaction.IsolationWidthOffset;
+                    SPSPrecursor.isolationWindow.cvParam[1] =
+                        new CVParamType
+                        {
+                            accession = "MS:1000828",
+                            name = "isolation window lower offset",
+                            value = (isolationWidth.Value - offset).ToString(CultureInfo.InvariantCulture),
+                            cvRef = "MS",
+                            unitCvRef = "MS",
+                            unitAccession = "MS:1000040",
+                            unitName = "m/z"
+                        };
+                    SPSPrecursor.isolationWindow.cvParam[2] =
+                        new CVParamType
+                        {
+                            accession = "MS:1000829",
+                            name = "isolation window upper offset",
+                            value = offset.ToString(CultureInfo.InvariantCulture),
+                            cvRef = "MS",
+                            unitCvRef = "MS",
+                            unitAccession = "MS:1000040",
+                            unitName = "m/z"
+                        };
+                }
+
                 // Selected ion MZ only
                 SPSPrecursor.selectedIonList.selectedIon[0] =
                     new ParamGroupType
@@ -2530,8 +2612,7 @@ private PrecursorListType ConstructPrecursorList(int precursorScanNumber, IScanE
 
         private int GetParentFromScanString(string scanString)
         {
-            var result = _filterStringIsolationMzPattern.Match(scanString);
-            var parts = Regex.Split(result.Groups[1].Value, " ");
+            var parts = Regex.Split(scanString, " ");
 
             //find the position of the first (from the end) precursor with a different mass 
             //to account for possible supplementary activations written in the filter
@@ -2549,7 +2630,7 @@ private int GetParentFromScanString(string scanString)
                 return _precursorScanNumbers[parentFilter];
             }
 
-            return -1; //unsuccessful parsing
+            return -2; //unsuccessful parsing
         }
 
         /// <summary>

Writer/OntologyMapping.cs

@@ -68,6 +68,15 @@ public static class OntologyMapping
                         value = ""
                     }
                 },
+                {
+                    MassAnalyzerType.MassAnalyzerMRTOF, new CVParamType
+                    {
+                        accession = "MS:1003379",
+                        name = "asymmetric track lossless time-of-flight analyzer",
+                        cvRef = "MS",
+                        value = ""
+                    }
+                },
                 {
                     MassAnalyzerType.Any, new CVParamType
                     {
@@ -543,6 +552,15 @@ public static class OntologyMapping
                         value = ""
                     }
                 },
+                {
+                    "ORBITRAP ASCEND", new CVParamType
+                    {
+                        accession = "MS:1003356",
+                        name = "Orbitrap Ascend",
+                        cvRef = "MS",
+                        value = ""
+                    }
+                },
                 {
                     "ORBITRAP EXPLORIS 120", new CVParamType
                     {
@@ -570,6 +588,15 @@ public static class OntologyMapping
                         value = ""
                     }
                 },
+                {
+                    "ORBITRAP ASTRAL", new CVParamType
+                    {
+                        accession = "MS:1003378",
+                        name = "Orbitrap Astral",
+                        cvRef = "MS",
+                        value = ""
+                    }
+                },
                 {
                     "EXACTIVE", new CVParamType
                     {
@@ -730,6 +757,8 @@ public static List<CVParamType> GetDetectors(string instrumentAccession)
                 case "MS:1002732":
                 // ORBITRAP ECLIPSE    
                 case "MS:1003029":
+                // ORBITRAP ASCEND    
+                case "MS:1003356":
                 // ORBITRAP ID-X
                 case "MS:1003112":
                     detectors = new List<CVParamType>
@@ -768,6 +797,8 @@ public static List<CVParamType> GetDetectors(string instrumentAccession)
                 case "MS:1003094":
                 // ORBITRAP EXPLORIS 480
                 case "MS:1003028":
+                // ORBITRAP ASTRAL
+                case "MS:1003378":
                     detectors = new List<CVParamType>
                     {
                         new CVParamType

Writer/PrecursorInfo.cs

@@ -5,7 +5,7 @@
     /// </summary>
     public class PrecursorInfo
     {
-        //for future use
+        //Current MSLevel
         public int MSLevel { get; }
 
         //precursor scan number, 0 - means not a precursor