20210711-msAlignScript.txt

Dim Chrom, Spec, RT,deconSpec, bUseSNAP, Filename, RTtempEnd, objMasses, objMassList, currentSpectrum 
 
'***************************************************************************************** 
'***************************************************************************************** 
bUseSNAP = True 
Const RTStart = 1
Const RTEnd = 95
Const LowMass = 5000  'Mass Range for peak picking (SNAP) 
Const HighMass = 60000  'Mass Range for peak picking (SNAP) 
Const WindowSize = 1  'Window size for spectrum averages (min) 
Const Extension = ".csv" 
Const Header = "RT / min,MW,Intensity" 
'***************************************************************************************** 
'***************************************************************************************** 
 
 
 
Filename = GetExportFileName(Extension) 
Delete_File (FileName) 
 
Set objMasses = CreateObject("Scripting.FileSystemObject")   
Set objMassList = objMasses.OpenTextFile(FileName, 8, True) 
objMassList.WriteLine(Analysis.Name) 
objMassList.WriteLine(Header) 
 
  
Call ResetPeakfinder() 
Analysis.compounds.clear 
For RT = RTStart To RTEnd Step WindowSize 
  
RTtempEnd = RT+WindowSize 
 
Analysis.ClearChromatogramRangeSelections 
  
Analysis.AddChromatogramRangeSelection RT, RTtempEnd 
 
Analysis.Chromatograms(1).AverageMassSpectrum False, True  
currentSpectrum = Analysis.Spectra.Count 
Set spec = Analysis.Spectra(currentSpectrum) 
spec.deconvolute 
Set deconSpec = spec.childspectra(1) 
Call SetMethodParametersPeakfinder() 
deconSpec.masslistfind LowMass,HighMass 
Call ResetPeakfinder() 
Call WriteToCSV(deconSpec, RT, RTtempEnd) 
 
Next 
Analysis.Save 
Form.Close 
 
 
 
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 WriteToCSV(spectrum, RT, RTtempEnd) 
 
Dim  Peaks, Peak, delim 
delim = "," 
  
  
Set Peaks = spectrum.MSPeakList 
For Each Peak In Peaks 
'WScript.Echo(Peak.m_over_z) 
objMassList.WriteLine(RT & "-" & RTtempEnd & delim & Peak.m_over_z & delim & Peak.Intensity) 
Next 
 
 
End Function 
 
Function GetExportFileName(sExtension)  
    Dim aFileNames      
    aFileNames = split(Analysis.Name,".d",-1,1)  
      
    GetExportFileName = Analysis.Path & "\" & aFileNames(0) & sExtension  
End Function  
 
Sub Delete_File (FileName)      
  
Dim fso      
Set fso = CreateObject("Scripting.FileSystemObject")        
If fso.FileExists(FileName) Then 
fso.DeleteFile(FileName)          
End If             
  
End Sub