linker parameter added (CXL)

CrossLinker/nbproject/private/private.xml

@@ -38,6 +38,17 @@
             <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/PeakPairFinder.java</file>
             <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/PrecursorCrossPepFinder.java</file>
         </group>
-        <group name="DIA-Umpire_Release"/>
+        <group name="DIA-Umpire_Release">
+            <file>file:/C:/Users/Cct/Documents/GitHub/DIA-Umpire/CrossLinker/src/crosslinker/Linker.java</file>
+            <file>file:/C:/Users/Cct/Documents/GitHub/DIA-Umpire/CrossLinker/src/Exec/CrossLinkerDetection.java</file>
+            <file>file:/C:/Users/Cct/Documents/GitHub/DIA-Umpire/CrossLinker/src/crosslinker/FragmentPair.java</file>
+            <file>file:/C:/Users/Cct/Documents/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/PrecursorCrossPepFinder.java</file>
+            <file>file:/C:/Users/Cct/Documents/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/MS2PeakPairFinder.java</file>
+            <file>file:/C:/Users/Cct/Documents/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/PeakPairFinder.java</file>
+            <file>file:/C:/Users/Cct/Documents/GitHub/DIA-Umpire/CrossLinker/src/crosslinker/CrossLinkerHandler.java</file>
+            <file>file:/C:/Users/Cct/Documents/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/CrosslinkerPepFinder.java</file>
+            <file>file:/C:/Users/Cct/Documents/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/CXL_MALDI.java</file>
+            <file>file:/C:/Users/Cct/Documents/GitHub/DIA-Umpire/CrossLinker/src/crosslinker/CrossLinkerScanResult.java</file>
+        </group>
     </open-files>
 </project-private>

CrossLinker/src/CXL_PeakPairFinder/CXL_MALDI.java

@@ -12,6 +12,7 @@
 import MSUmpire.PeptidePeakClusterDetection.PDHandlerMS1;
 import MSUmpire.SpectrumParser.MALDIDataParser;
 import MSUmpire.Utility.ConsoleLogger;
+import crosslinker.Linker;
 import java.io.FileWriter;
 import java.io.IOException;;
 import java.util.ArrayList;
@@ -37,6 +38,7 @@ public static void main(String[] args) throws IOException, InterruptedException,
         int NoCPUs=10;
         InstrumentParameter parameter=null;
         LCMSPeakBase lCMSPeakBase = null;
+        Linker linker=new Linker();
         parameter = new InstrumentParameter(InstrumentParameter.InstrumentType.MALDI);
         MALDIDataParser parser = new MALDIDataParser(FilePath);
         parser.cycletime = 120f / 576f;
@@ -67,7 +69,7 @@ public static void main(String[] args) throws IOException, InterruptedException,
         //detection.DetectSingleMZTraces(scans);
         //lCMSPeakBase.ExportPeakCurveResult();
 
-        CrosslinkerPepFinder finder = new CrosslinkerPepFinder(lCMSPeakBase,0f);
+        CrosslinkerPepFinder finder = new CrosslinkerPepFinder(lCMSPeakBase,0f,linker);
         lCMSPeakBase.parameter.MS1PPM=200;
         lCMSPeakBase.parameter.RTtol=1f;
         finder.FindAllPairPeaks(NoCPUs);

CrossLinker/src/CXL_PeakPairFinder/CrosslinkerPepFinder.java

@@ -4,11 +4,11 @@
  */
 package CXL_PeakPairFinder;
 
-import MSUmpire.BaseDataStructure.InstrumentParameter;
 import MSUmpire.BaseDataStructure.XYData;
 import MSUmpire.LCMSPeakStructure.LCMSPeakBase;
 import MSUmpire.PeakDataStructure.PeakCluster;
 import MSUmpire.SpectralProcessingModule.ScanPeakGroup;
+import crosslinker.Linker;
 import java.util.ArrayList;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
@@ -27,9 +27,11 @@ public class CrosslinkerPepFinder {
     public ArrayList<PrecursorCrossPepFinder> IntactPepList;
     public ArrayList<MS2PeakPairFinder> IntactPepListMS2;
     public float medianIntensity=-1f;
-    public CrosslinkerPepFinder(LCMSPeakBase LCMSPeakBase,float medianIntensity) {
+    Linker linker;
+    public CrosslinkerPepFinder(LCMSPeakBase LCMSPeakBase,float medianIntensity, Linker linker) {
         this.LCMSPeakBase = LCMSPeakBase;
         this.medianIntensity=medianIntensity;
+        this.linker=linker;
     }
 
      public void FindPairPeakMS2(ArrayList<ScanPeakGroup> MS2PeakGroups, int NoCPUs) {
@@ -41,7 +43,7 @@ public void FindPairPeakMS2(ArrayList<ScanPeakGroup> MS2PeakGroups, int NoCPUs)
          IntactPepListMS2 = new ArrayList<>();
          //For each scan
          for (ScanPeakGroup scan : MS2PeakGroups) {
-             MS2PeakPairFinder finder = new MS2PeakPairFinder(scan, LCMSPeakBase.parameter);
+             MS2PeakPairFinder finder = new MS2PeakPairFinder(scan, LCMSPeakBase.parameter, linker);
              executorPool.execute(finder);
              //finder.run();
              IntactPepListMS2.add(finder);
@@ -71,7 +73,7 @@ public void FindAllPairPeaks(int NoCPUs) {
         for (int i = 0; i < LCMSPeakBase.PeakClusters.size(); i++) {
             PeakCluster peakCluster = LCMSPeakBase.PeakClusters.get(i);
             if (peakCluster.NeutralMass() >= mzRange.getX() && peakCluster.NeutralMass() <= mzRange.getY()) {
-                PeakPairFinder unit = new PeakPairFinder(peakCluster, LCMSPeakBase.GetPeakClusterMassSearchTree(), LCMSPeakBase.parameter);
+                PeakPairFinder unit = new PeakPairFinder(peakCluster, LCMSPeakBase.GetPeakClusterMassSearchTree(), LCMSPeakBase.parameter, linker);
                 templist.add(unit);
                 executorPool.execute(unit);
             }
@@ -102,7 +104,7 @@ public void FindAllPairPeaks(int NoCPUs) {
                         //For any two peak pairs, check if they co-elute together (RT diff < RTtol)
                         if (lowmass.lowMassPeak.NeutralMass()<=highmass.lowMassPeak.NeutralMass() 
                                 && Math.abs(lowmass.lowMassPeak.PeakHeightRT[0] - highmass.lowMassPeak.PeakHeightRT[0]) < LCMSPeakBase.parameter.RTtol) {
-                            PrecursorCrossPepFinder intactLinkedPep = new PrecursorCrossPepFinder(lowmass, highmass, LCMSPeakBase.GetPeakClusterMassSearchTree(), LCMSPeakBase.parameter);
+                            PrecursorCrossPepFinder intactLinkedPep = new PrecursorCrossPepFinder(lowmass, highmass, LCMSPeakBase.GetPeakClusterMassSearchTree(), LCMSPeakBase.parameter, linker);
                             IntactPepList.add(intactLinkedPep);
                             executorPool.execute(intactLinkedPep);
                         }

CrossLinker/src/CXL_PeakPairFinder/MS2PeakPairFinder.java

@@ -22,7 +22,7 @@
 import MSUmpire.BaseDataStructure.InstrumentParameter;
 import MSUmpire.SpectralProcessingModule.IsotopePeakGroup;
 import MSUmpire.SpectralProcessingModule.ScanPeakGroup;
-import crosslinker.DC4;
+import crosslinker.Linker;
 import java.util.ArrayList;
 import net.sf.javaml.core.kdtree.KDTree;
 import net.sf.javaml.core.kdtree.KeyDuplicateException;
@@ -37,6 +37,7 @@ public class MS2PeakPairFinder implements Runnable {
 
     public ScanPeakGroup ScanPeak;
     InstrumentParameter parameter;
+    Linker linker;
     private KDTree PeakClusterKDTree;
     public ArrayList<PairGroupMS2> PeakPairGroupList;
     public ArrayList<PeakPair> peakPairs = new ArrayList<>();
@@ -77,9 +78,10 @@ private IsotopePeakGroup FindTargetMWPeak(IsotopePeakGroup peakCluster, float ta
         return BestPeak;
     }
 
-    public MS2PeakPairFinder(ScanPeakGroup ScanPeak, InstrumentParameter parameter) {
+    public MS2PeakPairFinder(ScanPeakGroup ScanPeak, InstrumentParameter parameter, Linker linker) {
         this.ScanPeak = ScanPeak;
         this.parameter = parameter;
+        this.linker=linker;
     }
 
 
@@ -106,9 +108,9 @@ public void run() {
             IsotopePeakGroup PeakCluster = ScanPeak.peakGroupList.get(i);
             PairGroupMS2 Pairgroup = new PairGroupMS2(PeakCluster);
             //Calculate MW of peak pair
-            float pairmw = PeakCluster.NeutralMass() + DC4.DABCO;
+            float pairmw = PeakCluster.NeutralMass() + linker.Core;
             Pairgroup.HighMassPeak = FindTargetMWPeak(PeakCluster,pairmw);
-            float DeadEndpairMW = PeakCluster.NeutralMass() + DC4.DABCO + DC4.H2O + DC4.Arm;
+            float DeadEndpairMW = PeakCluster.NeutralMass() + linker.Core + linker.H2O + linker.Arm;
             Pairgroup.DeadEndpairs = FindTargetMWPeak(PeakCluster,DeadEndpairMW);
             PeakPairGroupList.add(Pairgroup);
         }
@@ -121,7 +123,7 @@ public void run() {
                         PairGroupMS2 highmass = PeakPairGroupList.get(j);
                         if (lowmass.LowMassPeak.NeutralMass() <= highmass.LowMassPeak.NeutralMass()) {
 
-                            float IntactMW = lowmass.LowMassPeak.NeutralMass() + highmass.LowMassPeak.NeutralMass() + DC4.DABCO;
+                            float IntactMW = lowmass.LowMassPeak.NeutralMass() + highmass.LowMassPeak.NeutralMass() + linker.Core;
 
                             //Check if the precursor mass value of the MS2 spectrum is the summation of MW values of low and high peak pairs
                             //If yes, then the two peak pairs are potentially crosslinking peptides

CrossLinker/src/CXL_PeakPairFinder/PeakPairFinder.java

@@ -22,7 +22,7 @@
 import MSUmpire.BaseDataStructure.InstrumentParameter;
 import MSUmpire.PeakDataStructure.PeakCluster;
 import MSUmpire.PeptidePeakClusterDetection.PeakCurveCorrCalc;
-import crosslinker.DC4;
+import crosslinker.Linker;
 import java.io.IOException;
 import java.util.HashMap;
 import net.sf.javaml.core.kdtree.KDTree;
@@ -37,15 +37,17 @@ public class PeakPairFinder implements Runnable {
 
     private PeakCluster TargetPeak;
     InstrumentParameter parameter;
+    Linker linker;
     private final KDTree PeakClusterKDTree;
     float lowrt = 0f;
     float highrt = 0f;
     public PairGroup pairgroup;
 
-    public PeakPairFinder(PeakCluster peakClusterA, KDTree PeakClusterKDTree, InstrumentParameter parameter) {
+    public PeakPairFinder(PeakCluster peakClusterA, KDTree PeakClusterKDTree, InstrumentParameter parameter, Linker linker) {
         this.TargetPeak = peakClusterA;
         this.PeakClusterKDTree = PeakClusterKDTree;
         this.parameter = parameter;
+        this.linker=linker;
         lowrt = peakClusterA.PeakHeightRT[0] - parameter.RTtol;
         if (lowrt < 0) {
             lowrt = 0f;
@@ -55,13 +57,13 @@ public PeakPairFinder(PeakCluster peakClusterA, KDTree PeakClusterKDTree, Instru
 
     @Override
     public void run() {
-        //linked pair : x + DC4.DABCO
+        //linked pair : x + Linker.Core
         pairgroup=new PairGroup(TargetPeak);
 
         //calculate MW of peak pair
-        float pairmw= TargetPeak.NeutralMass()+DC4.DABCO;
+        float pairmw= TargetPeak.NeutralMass()+linker.Core;
         pairgroup.highMassPeak=FindTargetMWPeak(pairmw);        
-        float DeadEndpairMW = TargetPeak.NeutralMass()+ DC4.DABCO + DC4.H2O + DC4.Arm;
+        float DeadEndpairMW = TargetPeak.NeutralMass()+ linker.Core + linker.H2O + linker.Arm;
         pairgroup.DeadEndpairs=FindTargetMWPeak(DeadEndpairMW);
     }
 

CrossLinker/src/CXL_PeakPairFinder/PrecursorCrossPepFinder.java

@@ -9,7 +9,7 @@
 import MSUmpire.BaseDataStructure.InstrumentParameter;
 import MSUmpire.PeakDataStructure.PeakCluster;
 import MSUmpire.PeptidePeakClusterDetection.PeakCurveCorrCalc;
-import crosslinker.DC4;
+import crosslinker.Linker;
 import java.io.IOException;
 import java.util.HashMap;
 import net.sf.javaml.core.kdtree.KDTree;
@@ -29,17 +29,19 @@ public class PrecursorCrossPepFinder implements Runnable{
     public float MaxHighMassPeakCorr=0f;
     public float LowHighPeakCorr=0f;
     private float PrecCorssPeakPPM=1000f;
+    Linker linker;
     private InstrumentParameter parameter;
     float lowrt = 0f;
     float highrt = 0f;
     private final KDTree PeakClusterSearchTree;
     private CoElutePeak BestPrecursorPeak=null;
 
-    public PrecursorCrossPepFinder(PairGroup LowMassPeak, PairGroup HighMassPeak, KDTree PeakClusterSearchTree, InstrumentParameter parameter){
+    public PrecursorCrossPepFinder(PairGroup LowMassPeak, PairGroup HighMassPeak, KDTree PeakClusterSearchTree, InstrumentParameter parameter, Linker linker){
         this.LowMassPeakGroup=LowMassPeak;
         this.HighMassPeakGroup=HighMassPeak;
         this.PeakClusterSearchTree=PeakClusterSearchTree;
         this.parameter=parameter;
+        this.linker=linker;
         try {
             LowHighPeakCorr = PeakCurveCorrCalc.CalPeakCorr(LowMassPeak.lowMassPeak.MonoIsotopePeak, HighMassPeak.lowMassPeak.MonoIsotopePeak, parameter.NoPeakPerMin);
             if (Float.isNaN(LowHighPeakCorr)) {
@@ -53,7 +55,7 @@ public PrecursorCrossPepFinder(PairGroup LowMassPeak, PairGroup HighMassPeak, KD
         highrt = Math.min(LowMassPeak.lowMassPeak.PeakHeightRT[0],HighMassPeak.lowMassPeak.PeakHeightRT[0]) + parameter.RTtol;
     }
     public void FindPrecursorCrossPeak(){
-        float IntactMW = LowMassPeakGroup.lowMassPeak.NeutralMass()+HighMassPeakGroup.lowMassPeak.NeutralMass()+DC4.DABCO;
+        float IntactMW = LowMassPeakGroup.lowMassPeak.NeutralMass()+HighMassPeakGroup.lowMassPeak.NeutralMass()+linker.Core;
 
         float lowMW = InstrumentParameter.GetMzByPPM(IntactMW, 1, parameter.MS1PPM);
         float highMW = InstrumentParameter.GetMzByPPM(IntactMW, 1, -parameter.MS1PPM);

CrossLinker/src/Exec/CrossLinkerDetection.java

@@ -17,6 +17,7 @@
 import MSUmpire.SpectralProcessingModule.ScanIsotopePeakDetectionThread;
 import MSUmpire.SpectralProcessingModule.ScanPeakGroup;
 import MSUmpire.Utility.ConsoleLogger;
+import crosslinker.Linker;
 import java.io.BufferedReader;
 import java.io.FileNotFoundException;
 import java.io.FileReader;
@@ -63,6 +64,7 @@ public static void main(String[] args) throws IOException, InterruptedException,
         Logger logger = Logger.getRootLogger();
 
         InstrumentParameter parameter = null;
+        Linker linker=new Linker();
         parameter = new InstrumentParameter(InstrumentParameter.InstrumentType.Orbitrap);
         parameter.MS1PPM = 20;
         parameter.MS2PPM = 600f;
@@ -256,6 +258,14 @@ public static void main(String[] args) throws IOException, InterruptedException,
                         parameter.MS2Pairing = Boolean.parseBoolean(value);
                         break;
                     }
+                    case "CXL.CoreMass":{
+                        linker.Core=Float.parseFloat(value);
+                        break;
+                    }
+                    case "CXL.ArmMass":{
+                        linker.Arm=Float.parseFloat(value);
+                        break;
+                    }                            
 
 //</editor-fold>//</editor-fold>                   
                 }
@@ -329,7 +339,7 @@ public static void main(String[] args) throws IOException, InterruptedException,
         }
 
         //Initialize crosslinker peak pair finder
-        CrosslinkerPepFinder finder = new CrosslinkerPepFinder(lCMSPeakBase, medianIntensity);
+        CrosslinkerPepFinder finder = new CrosslinkerPepFinder(lCMSPeakBase, medianIntensity, linker);
 
         //Find all peak pairs
         finder.FindAllPairPeaks(NoCPUs);

CrossLinker/src/Exec/cxl.params

@@ -19,3 +19,7 @@ SE.MassDefectFilter=true
 SE.DetectSameChargePairOnly=true
 SE.MS2Pairing=true
 SE.MS2PairTopN=5
+
+#CXL linker
+CXL.CoreMass = 112.0995
+CXL.ArmMass = 68

CrossLinker/src/crosslinker/CrossLinkerHandler.java

@@ -23,6 +23,7 @@ public class CrossLinkerHandler {
 
     public HashMap<String, MALDI_Spot> ResultMap = new HashMap<>();
     public ArrayList<CrossLinkerPep> CrossLinkingPeps = new ArrayList<>();
+    public Linker linker;
 
     private void ReadFile(File folder) throws IOException {
         File[] listOfFiles = folder.listFiles();
@@ -40,15 +41,15 @@ private void ReadFile(File folder) throws IOException {
                         Scan.MsLevel = 2;
                         Scan.MGFTitle = Scan.MGFTitle.split("_")[Scan.MGFTitle.split("_").length - 2];
                         Scan.Normalization();
-                        CrossLinkerScanResult scanresult = new CrossLinkerScanResult(Scan);
+                        CrossLinkerScanResult scanresult = new CrossLinkerScanResult(Scan,linker);
                         Results.add(scanresult);
                     }
                 } else if (files.toLowerCase().endsWith(".pkl")) {
                     PKLScanParser pkl = new PKLScanParser(folder + "/" + files);
                     pkl.scan.MsLevel = 1;
                     pkl.scan.MGFTitle = pkl.scan.MGFTitle.split("_")[pkl.scan.MGFTitle.split("_").length - 2];
                     pkl.scan.Normalization();
-                    CrossLinkerScanResult scanresult = new CrossLinkerScanResult(pkl.scan);
+                    CrossLinkerScanResult scanresult = new CrossLinkerScanResult(pkl.scan,linker);
                     Results.add(scanresult);
                 }
             } else {