Centroid/Profile in PROXI

Centroid/Profile detection in PROXI when profile spectrum requested

Author: caetera

Query/ProxiSpectrumReader.cs

@@ -72,8 +72,6 @@ public List<ProxiSpectrum> Retrieve()
                         // Get the scan event for this scan number
                         var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
 
-                        var isCentroid = true;
-
                         IReaction reaction = null;
                         if (scanEvent.MSOrder != MSOrderType.Ms)
                         {
@@ -161,7 +159,7 @@ public List<ProxiSpectrum> Retrieve()
                         proxiSpectrum.AddAttribute(accession: "MS:10000512", name: "filter string",
                             value: scanEvent.ToString());
 
-                        if (!queryParameters.noPeakPicking)
+                        if (!queryParameters.noPeakPicking) //centroiding requested
                         {
                             proxiSpectrum.AddAttribute(accession: "MS:1000525", name: "spectrum representation",
                                 value: "centroid spectrum", valueAccession: "MS:1000127");
@@ -175,9 +173,8 @@ public List<ProxiSpectrum> Retrieve()
                                     proxiSpectrum.AddIntensities(scan.CentroidScan.Intensities);
                                 }
                             }
-                            else // otherwise take the profile data
+                            else // otherwise take the low res segmented data
                             {
-                                // Get the segmented (low res and profile) scan data
                                 // if the spectrum is profile perform centroiding
                                 var segmentedScan = scanEvent.ScanData == ScanDataType.Profile
                                     ? Scan.ToCentroid(scan).SegmentedScan
@@ -187,11 +184,21 @@ public List<ProxiSpectrum> Retrieve()
                                 proxiSpectrum.AddIntensities(segmentedScan.Intensities);
                             }
                         }
-                        else // use the profile data as is
+                        else // use the segmented data as is
                         {
-                            proxiSpectrum.AddAttribute(accession: "MS:1000525", name: "spectrum representation",
-                                value: "profile spectrum", valueAccession: "MS:1000128");
-
+                            switch (scanEvent.ScanData) //check if the data is centroided already
+                            {
+                                case ScanDataType.Centroid:
+                                    proxiSpectrum.AddAttribute(accession: "MS:1000525", name: "spectrum representation",
+                                        value: "centroid spectrum", valueAccession: "MS:1000127");
+                                    break;
+
+                                case ScanDataType.Profile:
+                                    proxiSpectrum.AddAttribute(accession: "MS:1000525", name: "spectrum representation",
+                                        value: "profile spectrum", valueAccession: "MS:1000128");
+                                    break;
+                            }
+                            
                             // Get the segmented (low res and profile) scan data
                             proxiSpectrum.AddMz(scan.SegmentedScan.Positions);
                             proxiSpectrum.AddIntensities(scan.SegmentedScan.Intensities);

Writer/MgfSpectrumWriter.cs

@@ -141,9 +141,8 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
                                     }
                                 }
                             }
-                            else // otherwise take the profile data
+                            else // otherwise take segmented (low res) scan data
                             {
-                                // Get the segmented (low res and profile) scan data
                                 // if the spectrum is profile perform centroiding
                                 var segmentedScan = scanEvent.ScanData == ScanDataType.Profile
                                     ? Scan.ToCentroid(scan).SegmentedScan
@@ -160,7 +159,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
                                 }
                             }
                         }
-                        else // use the profile data as is
+                        else // use the segmented data as is
                         {
                             // Get the segmented (low res and profile) scan data
                             for (var i = 0; i < scan.SegmentedScan.Positions.Length; i++)

Writer/MzMlSpectrumWriter.cs

@@ -993,12 +993,11 @@ private SpectrumType ConstructSpectrum(int scanNumber)
                         intensities = scan.CentroidScan.Intensities;
                     }
                 }
-                else // otherwise take the profile data
+                else // otherwise take the segmented (low res) scan
                 {
                     basePeakMass = scan.ScanStatistics.BasePeakMass;
                     basePeakIntensity = scan.ScanStatistics.BasePeakIntensity;
 
-                    // Get the segmented (low res and profile) scan data
                     // if the spectrum is profile perform centroiding
                     var segmentedScan = scanEvent.ScanData == ScanDataType.Profile
                         ? Scan.ToCentroid(scan).SegmentedScan
@@ -1013,15 +1012,15 @@ private SpectrumType ConstructSpectrum(int scanNumber)
                     }
                 }
             }
-            else // use the profile data as is
+            else // use the segmented data as is
             {
                 basePeakMass = scan.ScanStatistics.BasePeakMass;
                 basePeakIntensity = scan.ScanStatistics.BasePeakIntensity;
 
-                // Get the segmented (low res and profile) scan data
+                // Get the segmented scan data
                 if (scan.SegmentedScan.Positions.Length > 0)
                 {
-                    switch (scanEvent.ScanData)
+                    switch (scanEvent.ScanData) //check if the data centroided already
                     {
                         case ScanDataType.Centroid:
                             spectrumCvParams.Add(new CVParamType