From 741f2ea6defe500e4862706e68e903856abe0b89 Mon Sep 17 00:00:00 2001
From: Karen DRUART <karen.druart@pasteur.fr>
Date: Thu, 6 Oct 2022 15:45:15 +0200
Subject: [PATCH] Upload New File
---
.../20210711-msAlignScript.txt | 99 +++++++++++++++++++
1 file changed, 99 insertions(+)
create mode 100644 Bruker-msAlign-exporter/20210711-msAlignScript.txt
diff --git a/Bruker-msAlign-exporter/20210711-msAlignScript.txt b/Bruker-msAlign-exporter/20210711-msAlignScript.txt
new file mode 100644
index 0000000..453b001
--- /dev/null
+++ b/Bruker-msAlign-exporter/20210711-msAlignScript.txt
@@ -0,0 +1,99 @@
+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
--
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