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Bruker-msAlign-exporter/20211123-MSAlignOutput_AzoNM.vbs

+SetLocale(1033) ' Localise for US (. instead , accepted as decimal separator for calculations)    
+ 
+Dim comp, spec, i, oPeak, prec, chargeState, PrecursorMZ, PrecursorMass, RTStart, RTEnd, bUseSNAP 
+Dim MSMSSpec, MSMSoutput(), FileName, sExtension, Factor, MSMSType, counter 
+Const Proton = 1.00727647 
+bUseSNAP = True 
+sExtension = ".msalign" 
+counter = 1 
+Const ETDData = "ETD" 
+ 
+'************************************************************************************************** 
+'************************************************************************************************* 
+Factor = 10
+RTStart = 1
+RTEnd = 80
+ 
+'************************************************************************************************* 
+'************************************************************************************************ 
+ 
+FileName = GetExportFileName(sExtension) 
+Dim objFSO, objFile 
+Set objFSO = CreateObject("Scripting.FileSystemObject") 
+Set objFile = objFSO.CreateTextFile(FileName) 
+ 
+ 
+Call SetMethodParametersPeakfinder() 
+Analysis.ClearChromatogramRangeSelections 
+Analysis.AddChromatogramRangeSelection RTStart, RTEnd, 0, 0 
+Analysis.FindAutoMSn 
+On Error Resume Next 
+      
+ 
+ 
+ 
+For Each comp In Analysis.compounds 
+    MSMSType = "CID" 
+    PrecursorMass = 0 
+    chargeState = 0 
+    PrecursorMZ = 0 
+    chargeState = CInt(GetChargeState(comp)) 
+     
+     
+    If IsNumeric(comp.Precursor) Then 
+        PrecursorMZ = Round(comp.precursor, 4) 
+    Else 
+        PrecursorMZ= GetPrecMassFromName(comp) 
+    End If 
+     
+     
+     
+    PrecursorMass = Round(((PrecursorMZ*chargeState) - chargeState),4) 
+ 
+ 
+ 
+    Set MSMSSpec = comp(2) 
+     
+    If IsETD(MSMSSpec) Then 
+        MSMSType = "ETD" 
+    End If 
+ 
+    ReDim MSMSoutput(MSMSSpec.MSPeakList.Count, 2) 
+    for i=1 to MSMSSpec.MSPeakList.Count  
+      Set oPeak = MSMSSpec.MSPeakList(i) 
+      MSMSoutput(i,0) = Round((oPeak.DeconvolutedMolweight - Proton),4) 
+      MSMSoutput(i,1) = Round((oPeak.intensity * Factor),2) 
+      MSMSoutput(i,2) = oPeak.chargestate 
+    Next 
+ 
+ 
+    objFile.WriteLine("BEGIN IONS") 
+    objFile.WriteLine("ID=" & comp.CompoundNumber) 
+    objFile.WriteLine("SCANS=" & GetScanNumbers(MSMSSpec)) 
+    objFile.WriteLine("ACTIVATION=" & MSMSType) 
+    objFile.WriteLine("PRECURSOR_MZ=" & PrecursorMZ) 
+    objFile.WriteLine("PRECURSOR_CHARGE=" & chargeState) 
+    objFile.WriteLine("PRECURSOR_MASS=" & PrecursorMass) 
+ 
+    Dim count, line 
+    For count = 1 To UBound(MSMSOutput) 
+        line =  (MSMSoutput(count,0) & " " & MSMSoutput(count,1) & " " & MSMSoutput(count,2)) 
+        objFile.WriteLine(line) 
+    Next 
+    objFile.WriteLine("END IONS" & vbCrLf) 
+     
+Next 
+ 
+Call ResetPeakfinder() 
+objFile.Close 
+Analysis.Save 
+Form.Close 
+ 
+ 
+'*********************************************************************** 
+Public Function GetChargeState (comp) 
+    GetChargeState = 1 
+    mChargeState = 1 
+    Dim mSpec, mPrec, mPeak, mChargeState, p, y 
+    Set mSpec = comp(1) 
+    If IsNumeric(comp.Precursor) Then        'get the precursor mass. This checks to make sure the compound has an assigned precursor.  (A bug in DA 4.4 means this can be missing) 
+        mPrec = Round(comp.precursor, 4) 
+    Else 
+        mPrec = GetPrecMassFromName(comp)    'if the precursor mass is missing then extract the information from the compound name 
+    End If 
+     
+    for y=1 to mSpec.MSPeakList.Count         'As the charge state for the precursor is not included search through the MS spectrum to find the precursor mass and get the charge state from there 
+          Set mPeak = mSpec.MSPeakList(y) 
+           
+              If Round(mPeak.m_over_z,4) = mPrec Then 
+                  mChargeState = mPeak.ChargeState 
+                  Exit For 
+              End If 
+    Next 
+ 
+    GetChargeState = mChargeState    'return the chrage state (if for some reason the charge state can not be determined (SNAP was not able to deconvolute peak) then return "1" as charge state 
+ 
+End Function 
+ 
+Sub SetMethodParametersPeakfinder()  
+    Dim oPeakFinderParameters  
+    Set oPeakFinderParameters = Analysis.Method.MassListParameters()  
+    If bUseSNAP = True Then  
+        oPeakFinderParameters.DetectionAlgorithm = 2 ' 3 means Sum; 2 means SNAP; 0 means APEX  
+    Else  
+        oPeakFinderParameters.DetectionAlgorithm = 3 ' 3 means Sum; 2 means SNAP; 0 means APEX  
+    End If  
+End Sub   
+ 
+Sub ResetPeakfinder  
+    Dim oPeakFinderParameters  
+    Set oPeakFinderParameters = Analysis.Method.MassListParameters()  
+    oPeakFinderParameters.DetectionAlgorithm = 3 ' 3 means Sum; 2 means SNAP; 0 means APEX  
+End Sub  
+ 
+Function GetExportFileName(sExtension)  
+    Dim aFileNames      
+    aFileNames = split(Analysis.Name,".d",-1,1)  
+      
+    GetExportFileName = Analysis.Path & "\" & aFileNames(0) & sExtension  
+End Function   
+ 
+Function IsETD(comp) 
+    Dim mComp, mCompName 
+    IsETD = False 
+    mCompName = comp.Name 
+    If InStr(mCompName,ETDData) Then 
+        IsETD= True 
+    End If 
+      
+End Function 
+ 
+Function GetScanNumbers(Spectrum) 
+    Dim position, position2, initialScanPos 
+    GetScanNumbers = "" 
+    position = InStr(Spectrum.Name,"#") 
+    position2 = InStrRev(Spectrum.Name,"-") 
+    If position2 >0 Then 
+        initialScanPos = position2-(position+1) 
+        GetScanNumbers = (Mid(Spectrum.Name, position+1, initialScanPos))+1 
+    Else 
+        GetScanNumbers = (Mid(Spectrum.Name, position+1))+1 
+    End If  
+     
+End Function 
+ 
+Function GetPrecMassFromName(comp) 
+    GetPrecMassFromName = 0 
+    Dim compName 
+    compName = comp.Name 
+    Dim count, str, startPos, endPos 
+    startPos = (InStr(compName,"(") + 1) 
+    endPos = InStr(compName,")") 
+    str = Mid(compName,(startPos),(endPos-startPos)) 
+    GetPrecMassFromName = CDbl(str) 
+ 
+End Function