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Bruker-msAlign-exporter/20220411-DA53-msAlign-exporter.vbs

+'***** Bruker DataAnalysis msAlign Exporter
+' Created by Matt Willetts (Bruker), Kyle A. Brown (U-Wisconsin), and David L. Tabb (Institut Pasteur)
+' This software makes it possible to conduct TopPIC searches on data from Bruker Q-TOF instruments.
+' The SNAP / MaxEnt / AutoMSn code at the very top handles "deconvolution."
+' Everything else crafts an msalign file from the list of Compound objects.
+
+'***** To Do:
+' How can we detect the precursor charge better?  The loop through MS1 peaks seems error-prone.
+' How can we specify the settings for SNAP, MaxEnt, and AutoMSn directly rather than relying on users?
+' How do we "rescue" MS/MS scans for which no precursor charge is reported?
+' Let's improve QC reporting, such as charge state histograms.
+' Do we need to write "FEATURE" files for better TopPIC compatibility?
+
+' Localise for US, using '.' rather than ',' as a decimal separator 
+SetLocale(1033)  
+Const Proton              = 1.00727647   
+Const sExtension          = ".msalign"   
+Const IntensityMultiplier = 10 
+Const MZTolerance         = 0.001 
+Dim   PathAndFile, objFSO, objFile, CompoundCount, NoZCount
+
+'***** Run deconvolution in SNAP / MaxEnt / AutoMSn
+'***** Configure for SNAP peak picking 
+Analysis.Method.MassListParameters.DetectionAlgorithm = 2 
+'***** Just select everything for peak picking 
+Analysis.ClearChromatogramRangeSelections 
+Analysis.AddChromatogramRangeSelection 0, 1000
+Analysis.FindAutoMSn  
+On Error Resume Next  
+ 
+'***** Set up our output file for writing 
+PathAndFile = Left(Analysis.Path, Len(Analysis.Path)-2) & sExtension
+CompoundCount = 0
+NoZCount = 0
+ 
+Set objFSO = CreateObject("Scripting.FileSystemObject")  
+Set objFile = objFSO.CreateTextFile(PathAndFile)  
+  
+For Each comp In Analysis.compounds
+    CompoundCount = CompoundCount + 1
+    Dim MS1Spec, MS2Spec 
+    Dim MSMSType, PrecursorMass, PrecursorCharge, PrecursorMZ, PrecursorIntensity, PrecursorRT, StartPos, StopPos, ThisPeak, MS1ScanNumber, MS2ScanNumber, PeakCounter 
+ 
+    Set MS1Spec = comp(1) 
+    Set MS2Spec = comp(2) 
+ 
+'***** Determine the dissociation type (based on whether or not component Name contains the string "ETD"). 
+    If InStr(comp.Name,"ETD") Then  
+        MSMSType = "ETD" 
+    Else 
+        MSMSType = "CID" 
+    End If 
+ 
+'***** Determine the precursor m/z and mass, since we will need that to determine its charge 
+    If IsNumeric(comp.Precursor) Then 
+       PrecursorMZ = comp.Precursor 
+    Else 
+       '***** Otherwise grab the mass from the string naming this component 
+       StartPos = InStr(comp.Name,"(") + 1 
+       StopPos = InStr(comp.Name,")") 
+       PrecursorMZ = Mid(comp.Name,StartPos,StopPos-StartPos) 
+    End If 
+
+    If IsNumeric(comp.RetentionTime) Then
+       PrecursorRT = comp.RetentionTime
+    Else
+       PrecursorRT = 0
+    End If 
+
+    If IsNumeric(comp.Intensity) Then
+       PrecursorIntensity = comp.Intensity
+    Else
+       PrecursorIntensity = 0
+    End If 
+
+'***** Determine the precursor charge state, keeping track of how many precursors cannot be matched back to the MS scans. 
+    PrecursorCharge = -1 
+ 
+    For Each ThisPeak in MS1Spec.MSPeakList
+       If Abs(ThisPeak.m_over_z - PrecursorMZ)< MZTolerance Then 
+           PrecursorCharge = ThisPeak.ChargeState 
+           Exit For 
+       End If 
+    Next 
+    If PrecursorCharge = -1 Then
+       NoZCount = NoZCount + 1
+       PrecursorCharge = 1
+       PrecursorMass = PrecursorMZ - Proton 
+    Else 
+       PrecursorMass = (PrecursorMZ*PrecursorCharge) - (PrecursorCharge*Proton) 
+    End If 
+ 
+'***** Get the first MS scan number to report for this compound 
+    StartPos = InStr(MS1Spec.Name,"#") 
+    StopPos = InStrRev(MS1Spec.Name,"-") 
+    If StopPos = 0 Then 
+       MS1ScanNumber=Mid(MS1Spec.Name, StartPos+1) 
+    Else 
+       MS1ScanNumber=Mid(MS1Spec.Name, StartPos+1, StopPos-(StartPos+1)) 
+    End If 
+
+
+'***** Get the first MS/MS scan number to report for this compound 
+    StartPos = InStr(MS2Spec.Name,"#") 
+    StopPos = InStrRev(MS2Spec.Name,"-") 
+    If StopPos = 0 Then 
+       MS2ScanNumber=Mid(MS2Spec.Name, StartPos+1) 
+    Else 
+       MS2ScanNumber=Mid(MS2Spec.Name, StartPos+1, StopPos-(StartPos+1)) 
+    End If 
+ 
+'***** Now write this compound header to the msAlign file 
+    objFile.WriteLine("BEGIN IONS")  
+    objFile.WriteLine("ID=" & comp.CompoundNumber)
+    objFile.WriteLine("FRACTION_ID=1")
+    objFile.WriteLine("FILE_NAME=" & Analysis.Name)
+    objFile.WriteLine("SCANS=" & MS2ScanNumber)
+    objFile.WriteLine("RETENTION_TIME=" & PrecursorRT)
+    ' Naturally the following will require update when something beyond MS/MS is being used.
+    objFile.WriteLine("LEVEL=2")
+    objFile.WriteLine("ACTIVATION=" & MSMSType)
+    objFile.WriteLine("MS_ONE_ID=" & comp.CompoundNumber)
+    objFile.WriteLine("MS_ONE_SCAN=" & MS1ScanNumber)
+    objFile.WriteLine("PRECURSOR_MZ=" & PrecursorMZ)  
+    objFile.WriteLine("PRECURSOR_CHARGE=" & PrecursorCharge) 
+    objFile.WriteLine("PRECURSOR_MASS=" & PrecursorMass)
+    ' TopFD writes floating point precursor intensities, but Bruker gives us integers
+    objFile.WriteLine("PRECURSOR_INTENSITY=" & PrecursorIntensity & ".00")
+
+'***** Now write the compound MS/MS peaks to the msAlign file 
+    For Each ThisPeak in MS2Spec.MSPeakList 
+       objFile.Write(Round(ThisPeak.ChargeState * (ThisPeak.m_over_z - Proton),4))
+       objFile.Write(" ") 
+       objFile.Write(Round(ThisPeak.Intensity * IntensityMultiplier,2)) 
+       objFile.Write(" ") 
+       objFile.WriteLine(ThisPeak.ChargeState) 
+    Next 
+ 
+    objFile.WriteLine("END IONS" & vbCrLf)  
+      
+Next  
+  
+objFile.Close  
+Analysis.Save
+MsgBox (CompoundCount & " compounds, " & NoZCount & " without precursor charges!")
+Form.Close