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Bruker-msAlign-exporter/20220413-DA53-msAlign-QC-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 / 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 and AutoMSn directly rather than relying on users?
+' How do we "rescue" MS/MS scans for which no precursor charge is reported?
+' 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 IntensityMultiplier = 10 
+Const MZTolerance         = 0.001 
+Const ZCeiling		  = 100
+Const PkCountCeiling      = 1000
+Dim   ZDistn(100)
+Dim   PkCountDistn(1000)
+Dim   PathAndFile, objFSO, msalignFile, qcFile, NoZCount
+Dim   ZMinimum, ZQuartile1, ZMedian, ZQuartile3, ZMaximum, ZMode
+Dim   PkCountMinimum, PkCountQuartile1, PkCountMedian, PkCountQuartile3, PkCountMaximum
+
+'***** 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  
+Analysis.Save
+ 
+'***** Set up our output file for writing 
+Set objFSO = CreateObject("Scripting.FileSystemObject")  
+PathAndFile = Left(Analysis.Path, Len(Analysis.Path)-2) & ".msalign"
+Set msalignFile = objFSO.CreateTextFile(PathAndFile)  
+PathAndFile = Left(Analysis.Path, Len(Analysis.Path)-2) & ".qc.tsv"
+Set qcFile = objFSO.CreateTextFile(PathAndFile)  
+  
+For Looper = 0 to ZCeiling
+    ZDistn(Looper) = 0
+Next
+For Looper = 0 to PkCountCeiling
+    PkCountDistn(Looper) = 0
+Next
+ 
+For Each ThisCompound In Analysis.Compounds
+    Dim MS1Spec, MS2Spec, MSMSType, MS1ScanNumber, MS2ScanNumber
+    Dim PrecursorMass, PrecursorCharge, PrecursorMZ, PrecursorIntensity, PrecursorRT
+    Dim StartPos, StopPos, ThisPeak, PeakCounter 
+ 
+    Set MS1Spec = ThisCompound(1) 
+    Set MS2Spec = ThisCompound(2) 
+ 
+'***** Determine the dissociation type (based on whether or not component Name contains the string "ETD"). 
+    If InStr(ThisCompound.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(ThisCompound.Precursor) Then 
+       PrecursorMZ = ThisCompound.Precursor 
+    Else 
+       '***** Otherwise grab the mass from the string naming this component 
+       StartPos = InStr(ThisCompound.Name,"(") + 1 
+       StopPos = InStr(ThisCompound.Name,")") 
+       PrecursorMZ = Mid(ThisCompound.Name,StartPos,StopPos-StartPos) 
+    End If 
+
+    If IsNumeric(ThisCompound.RetentionTime) Then
+       PrecursorRT = ThisCompound.RetentionTime
+    Else
+       PrecursorRT = 0
+    End If 
+
+    If IsNumeric(ThisCompound.Intensity) Then
+       PrecursorIntensity = ThisCompound.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
+       ZDistn(0) = ZDistn(0) + 1
+       ' If we couldn't determine the precursor charge we call it a +1 in the msalign file.
+       PrecursorCharge = 1
+       PrecursorMass = PrecursorMZ - Proton 
+    Else
+       ' Record this precursor charge in the array of precursor charge frequences
+       ZDistn(PrecursorCharge) = ZDistn(PrecursorCharge) + 1
+       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 
+
+    ' Add the number of MS/MS peaks for this spectrum to the Peak Count distribution
+    PkCountDistn(MS2Spec.MSPeakList.Count) = PkCountDistn(MS2Spec.MSPeakList.Count)+1
+ 
+'***** Now write this compound header to the msAlign file 
+    msalignFile.WriteLine("BEGIN IONS")  
+    msalignFile.WriteLine("ID=" & ThisCompound.CompoundNumber)
+    msalignFile.WriteLine("FRACTION_ID=1")
+    msalignFile.WriteLine("FILE_NAME=" & Analysis.Name)
+    msalignFile.WriteLine("SCANS=" & MS2ScanNumber)
+    msalignFile.WriteLine("RETENTION_TIME=" & PrecursorRT)
+    ' Naturally the following will require update when something beyond MS/MS is being used.
+    msalignFile.WriteLine("LEVEL=2")
+    msalignFile.WriteLine("ACTIVATION=" & MSMSType)
+    msalignFile.WriteLine("MS_ONE_ID=" & ThisCompound.CompoundNumber)
+    msalignFile.WriteLine("MS_ONE_SCAN=" & MS1ScanNumber)
+    msalignFile.WriteLine("PRECURSOR_MZ=" & PrecursorMZ)  
+    msalignFile.WriteLine("PRECURSOR_CHARGE=" & PrecursorCharge) 
+    msalignFile.WriteLine("PRECURSOR_MASS=" & PrecursorMass)
+    ' TopFD writes floating point precursor intensities, but Bruker gives us integers
+    msalignFile.WriteLine("PRECURSOR_INTENSITY=" & PrecursorIntensity & ".00")
+
+'***** Now write the compound MS/MS peaks to the msAlign file 
+    For Each ThisPeak in MS2Spec.MSPeakList 
+       msalignFile.Write(Round(ThisPeak.ChargeState * (ThisPeak.m_over_z - Proton),4))
+       msalignFile.Write(" ") 
+       msalignFile.Write(Round(ThisPeak.Intensity * IntensityMultiplier,2)) 
+       msalignFile.Write(" ") 
+       msalignFile.WriteLine(ThisPeak.ChargeState) 
+    Next 
+ 
+    msalignFile.WriteLine("END IONS" & vbCrLf)  
+      
+'***** We're done with this Compound.  Continue to the next one.
+Next
+'***** Now complete writing the msalign file
+msalignFile.Close  
+
+'***** QC METRIC COMPUTATION
+
+'***** Compute quartiles for Precursor Z, skipping unknown precursor charges
+ZMinimum = -1
+ZQuartile1 = -1
+ZMedian = -1
+ZQuartile3 = -1
+ZMaximum = -1
+ZMode  = -1
+
+PositiveBinSum = 0
+BiggestBinFreq = 0
+For Looper = 1 to ZCeiling
+    If ZDistn(Looper) > 0 Then
+       PositiveBinSum = PositiveBinSum + ZDistn(Looper)
+       If ZMinimum = -1 Then
+          ZMinimum = Looper
+       End If
+       If ZDistn(Looper) > BiggestBinFreq Then
+          BiggestBinFreq=ZDistn(Looper)
+	  ZMode = Looper
+       End If
+       ZMaximum = Looper
+    End If
+Next
+
+' What target number of spectra must be taken into account to find the first, second, and third quartiles?
+Q1BinSum = PositiveBinSum / 4
+Q2BinSum = PositiveBinSum / 2
+Q3BinSum = Q1BinSum + Q2BinSum
+PositiveBinSum = 0
+For Looper = 1 to ZCeiling
+    PositiveBinSum = PositiveBinSum + ZDistn(Looper)
+    If ZQuartile1 = -1 AND PositiveBinSum >= Q1BinSum Then
+       ZQuartile1 = Looper
+    End IF
+    If ZMedian = -1 AND PositiveBinSum >= Q2BinSum Then
+       ZMedian = Looper
+    End IF
+    If ZQuartile3 = -1 AND PositiveBinSum >= Q3BinSum Then
+       ZQuartile3 = Looper
+    End IF
+Next
+
+'***** Compute quartiles for MS/MS Peak Count
+PkCountMinimum = -1
+PkCountQuartile1 = -1
+PkCountMedian = -1
+PkCountQuartile3 = -1
+PkCountMaximum = -1
+PkCountMode  = -1
+
+PositiveBinSum = 0
+BiggestBinFreq = 0
+For Looper = 0 to PkCountCeiling
+    If PkCountDistn(Looper) > 0 Then
+       PositiveBinSum = PositiveBinSum + PkCountDistn(Looper)
+       If PkCountMinimum = -1 Then
+          PkCountMinimum = Looper
+       End If
+       If PkCountDistn(Looper) > BiggestBinFreq Then
+          BiggestBinFreq=PkCountDistn(Looper)
+	  PkCountMode = Looper
+       End If
+       PkCountMaximum = Looper
+    End If
+Next
+
+' What target number of spectra must be taken into account to find the first, second, and third quartiles?
+Q1BinSum = PositiveBinSum / 4
+Q2BinSum = PositiveBinSum / 2
+Q3BinSum = Q1BinSum + Q2BinSum
+PositiveBinSum = 0
+For Looper = 0 to PkCountCeiling
+    PositiveBinSum = PositiveBinSum + PkCountDistn(Looper)
+    If PkCountQuartile1 = -1 AND PositiveBinSum >= Q1BinSum Then
+       PkCountQuartile1 = Looper
+    End IF
+    If PkCountMedian = -1 AND PositiveBinSum >= Q2BinSum Then
+       PkCountMedian = Looper
+    End IF
+    If PkCountQuartile3 = -1 AND PositiveBinSum >= Q3BinSum Then
+       PkCountQuartile3 = Looper
+    End IF
+Next
+
+qcFile.WriteLine("AllSpectraCount" & vbTab & Analysis.SpectraCount)
+qcFile.WriteLine("AutoMSnCompoundCount" & vbTab & Analysis.Compounds.Count)
+qcFile.WriteLine("CompoundsLackingZ" & vbTab & ZDistn(0))
+qcFile.WriteLine()
+
+qcFile.WriteLine("ZMinimum" & vbTab & ZMinimum)
+qcFile.WriteLine("ZQuartile1" & vbTab & ZQuartile1)
+qcFile.WriteLine("ZMedian" & vbTab & ZMedian)
+qcFile.WriteLine("ZQuartile3" & vbTab & ZQuartile3)
+qcFile.WriteLine("ZMaximum" & vbTab & ZMaximum)
+qcFile.WriteLine("ZMode" & vbTab & ZMode)
+
+qcFile.WriteLine()
+qcFile.WriteLine("MS2PkCountMinimum" & vbTab & PkCountMinimum)
+qcFile.WriteLine("MS2PkCountQuartile1" & vbTab & PkCountQuartile1)
+qcFile.WriteLine("MS2PkCountMedian" & vbTab & PkCountMedian)
+qcFile.WriteLine("MS2PkCountQuartile3" & vbTab & PkCountQuartile3)
+qcFile.WriteLine("MS2PkCountMaximum" & vbTab & PkCountMaximum)
+qcFile.WriteLine("MS2PkCountMode" & vbTab & PkCountMode)
+
+qcFile.WriteLine()
+qcFile.WriteLine("CompoundZ" & vbTab & "Frequency")
+For Looper = 0 to ZMaximum
+    qcFile.WriteLine(Looper & vbTab & ZDistn(Looper))
+Next
+
+qcFile.WriteLine()
+qcFile.WriteLine("MS2PkCount" & vbTab & "Frequency")
+For Looper = 0 to PkCountMaximum
+    qcFile.WriteLine(Looper & vbTab & PkCountDistn(Looper))
+Next
+
+qcFile.Close
+MsgBox ("Wrote .msalign and .qc.tsv file successfully.")
+Form.Close