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Topic: Extracting MS2 peaks from PASEF DIA data (Read 431 times) previous topic - next topic

Extracting MS2 peaks from PASEF DIA data

I'm sorry if this was previously addressed, but I just started using MS-DIAL (4.9) and would like to extract the fragment ion (MS2) peaks from PASEF-DIA data. I converted my files to IBF and started a new project where the files were aligned. The MS1 peak alignment looks fairly good, but I'm not sure which report to export to get a record of the fragment ion peaks. Thank you for your help.

Re: Extracting MS2 peaks from PASEF DIA data

Reply #1
Hi,
I have basically the same issue, I recently posted it
After file conversion and alignment, that works fine, I cannot extract MS/MS features, so basically I get 0 hits since MS/MS is totally absent.
@Hiroshi Tsugawa could you help us?
Kind regards

 

Re: Extracting MS2 peaks from PASEF DIA data

Reply #2
I have a related question.. Hypothetically, say an LC feature (with CCS = -1) of mz = 250.0100 and RT of 3.5 gives rise to two separate ion-mobility features with CCS of 150 and 170, and the feature with CCS of 150 has a different fragmentation pattern than the feature with CCS of 170.

  • Feature 1 (LC): mz = 250.0100, RT = 3.5 min, CCS = -1
  • Feature 2 (IM #1): mz = 250.0100, RT = 3.5 min, CCS = 150
  • Feature 3 (IM #2): mz = 250.0100, RT = 3.5 min, CCS = 170

Is the MS2 spectrum that is displayed of the fragmentation for the LC peak (as in, is the spectrum the same for all three features), or does MSDIAL read the PASEF frames in the file and can distinguish the spectra between the two IM features with different mobilities? I hope I explained that well... @Hiroshi Tsugawa

PS - I do not have experience with dia-PASEF data, but dda-PASEF data is not a problem for me to do what you are describing @simionkreimer , but I do sometimes have problems with MSDIAL crashing when working with PASEF data.

Take care,
Triston