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Batch creation of SCIEX methods

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Batch creation of SCIEX methods kerteszv  2024-11-05 13:45
 

SCIEX TOF

I have a set of precursor masses and/or formulas (say n different one), and a set of collision energies (CE) (say m different one). I would like to create n x m individual method files, all with different precursors and CEs. The name should somehow represent the formula/precursor mass and CE, say sample_precursormass_CE.dam

I see that maybe it might be done in a batch using
BuildAnalystFullScanMethod.exe
but I cannot figure out in what format I need to provide the precursor/CE list, and what parameters I have to use with the EXE. I know that I need a file with the precursor and CE values, and a template method file. I was able to do one inside the software, but even if the CSV file has multiple lines, it just created new method for the first line. If you have a tutorial on that or a video, I would appreciate that, too, I could not find it.

If you could send me an example command line , that would be appreciated.

Thank you very much in advance, Vilmos

PS: Bonus: if I could also do the same, PRM methods with given inclusion lists for a Thermo QExactive, that would be phenomenal.
 
 
Nick Shulman responded:  2024-11-05 15:38
I am not sure whether any person currently knows what parameters BuildAnalystFullScanMethod.exe wants.

If you send me your Skyline document, I could tell you what files and parameters Skyline feeds to BuildAnalystFullScanMethod.exe when you do "File > Export > Method".
You might be able to figure out from those files what you would need to do for your batch scenario.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document.

If that .zip file is less than 50MB you can attach it to this support request. You can always upload larger files here:
https://skyline.ms/files.url

After I get your Skyline document I will use the "File > Export > Method" menu item and let you know what files and parameters Skyline is sending to BuildAnalystFullScanMethod.exe.

You might be able to figure out what BuildAnalystFullScanMethod.exe wants by looking at its source code which is here:
https://github.com/ProteoWizard/pwiz/tree/master/pwiz_tools/Skyline/Executables/BuildMethod/BuildAnalystFullScanMethod
-- Nick
 
kerteszv responded:  2024-11-06 08:19
Nick, thank you. Looking at the code I managed to created .dam files in batch.

Solution, for others, Product ion scan:
1. In the folder that contains BuildAnalystFullScanMethod.exe, make a CSV file, say Sample.csv, with 1 line, for example:
100,1087.49894,20,name,80,40

100 is the precursor mass, 80 is DP and 40 is CE. I did not go after "1087.49894,20,name". Seems like they are "product ion mass, retention time, label".

2. Make a template method file that has dummy precursor, DP and CE values, and set other parameters as what you want to see in the created file. LC synch, length, m/z range, etc. Copy the DAM file into the work folder of the EXE

3. Run the method creator
BuildAnalystFullScanMethod.exe -o NewMethod.dam Template.dam Sample.csv

This will make NewMethod.dam that has a precursor of 100, DP of 80 and CE of 40.

4. If you need multiple, just use a batch file (like 1.bat) with a contents of
BuildAnalystFullScanMethod.exe -o NewMethod1.dam Template.dam Sample1.csv
BuildAnalystFullScanMethod.exe -o NewMethod2.dam Template.dam Sample2.csv
BuildAnalystFullScanMethod.exe -o NewMethod3.dam Template.dam Sample3.csv

where the CSV files contain different parameters.

Note: maybe there is an easier solution. I could not find it. This works.

Thanks Nick again!
Vilmos