Use CVTerm "Orbitrap" for FTMS scans in Orbitrap-based instruments

Author: caetera

Writer/MzMlSpectrumWriter.cs

@@ -279,6 +279,9 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
                     instrumentModel = OntologyMapping.GetInstrumentModel(instrumentData.Model);
                     SerializeCvParam(instrumentModel);
 
+                    //Update the definition of FTMS
+                    OntologyMapping.UpdateFTMSDefinition(instrumentData.Model);
+
                     SerializeCvParam(new CVParamType
                     {
                         cvRef = "MS",

Writer/OntologyMapping.cs

@@ -718,6 +718,38 @@ public static CVParamType GetInstrumentModel(string instrumentName)
             return instrumentModel;
         }
 
+        /// <summary>
+        /// Changes the mapping of `MassAnalyserFTMS` for Orbitrap-based instruments
+        /// updates OntologyMapping dictionarty in place
+        /// </summary>
+        /// <param name="instrumentName">the instrument name</param>
+        /// <returns>Void</returns>
+        public static void UpdateFTMSDefinition(string instrumentName)
+        {
+            instrumentName = instrumentName.ToUpper();
+
+            if (instrumentName.Contains("ORBITRAP") || instrumentName.Contains("EXACTIVE"))
+            {
+                MassAnalyzerTypes[MassAnalyzerType.MassAnalyzerFTMS] = new CVParamType
+                {
+                    accession = "MS:1000484",
+                    name = "orbitrap",
+                    cvRef = "MS",
+                    value = ""
+                };
+            }
+            else
+            {
+                MassAnalyzerTypes[MassAnalyzerType.MassAnalyzerFTMS] = new CVParamType
+                {
+                    accession = "MS:1000079",
+                    name = "fourier transform ion cyclotron resonance mass spectrometer",
+                    cvRef = "MS",
+                    value = ""
+                };
+            }
+        }
+
         /// <summary>
         /// Get a list of detectors for the given instrument
         /// </summary>