Is it possible to extract MS/MS info in batch process from the Product Ion Scan?

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Is it possible to extract MS/MS info in batch process from the Product Ion Scan? karin yanagi  2023-04-07 18:33
 

Hi! I have a TTOF experiment with one TOF scan and several Product Ion Scan. I wonder when I select the peak from one of product ion scan by specifing precursor and product ion. Is there any way I can collect all the MSMS tranistion from this segment of time from the product ion scan. Basically I want a set of data with m/z versus intensity for selected time slot. And is there way i can batch export this type of data

 
 
Nick Shulman responded:  2023-04-07 19:09
I am not sure I understand your question.

Skyline is not a good tool for looking at individual spectra. Skyline is good at extracting chromatograms from multiple spectra where the same things was sampled at a repeating time interval.

I am not sure exactly what TTOF (tandem time of flight) is, but it sounds a lot like other forms of MS2.
Skyline does a great job extracting chromatograms from DIA and PRM MS2.
DIA (data independent acquisition) is when you tell the mass spectrometer to cycle through fragmenting a small set of wide m/z windows.
PRM is when you tell the mass spectrometer the m/z of the precursors that you are interested in and the mass spectrometer cycles through fragmenting narrow windows around those m/z values.
The thing that Skyline does not do a good job extracting chromatograms from is DDA where the mass spectrometer decides what to fragment based on what it sees in the MS1 spectrum. With DDA, the same precursor does not end up getting fragmented on any predictable schedule so the chromatograms do not look good.

You might find helpful some of the tutorials in the "Full-Scan Acquisition Data" section on this page:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorials

If you would like a tool for looking at individual spectra in a mass spec data file, there is a program called "SeeMS.exe" which gets installed as part of ProteoWizard:
https://proteowizard.sourceforge.io/

If you would like to convert your mass spec data file into a text file with lists of m/z and intensity values, you could use MSConvert (which also comes with ProteoWizard). You can tell msconvert to convert your file to "mgf" format, which is a simple format for MS2 spectra with lists of m/z and intensity values.

If this did not answer your question, maybe you could send us your data files and/or a screenshot.
Files which are less than 50MB can be attached to this support request. You can upload larger files here:
https://skyline.ms/files.url
-- Nick