DDA MS1 filtering analysis from TIMS-TOF DDA-PASSF data

DDA MS1 filtering analysis from TIMS-TOF DDA-PASSF data bioc1213  2023-07-05 02:11

I am struggling to process the DDA-PASEF data from TIMS tof using DDA-MS1 filter method as per the tutorials. Is there something I need to be doing before starting the analysis, eg. settings etc?
its been almost more than 1 hr and I see the same info as shown in the attachment.


Matt Chambers responded:  2023-07-07 10:06

You are trying to search DDA-PASEF data following the DDA MS1 tutorial? That's not going to work without some prep work I think. To do DDA search on timsTOF data you need to do some scan summing to sum all the mobility scans for each precursor and sometimes across frames as well. The DDA search wizard can't do that for you yet, but AFAIK Bruker has a tool that can produce an MGF like that. You can also use the combineIonMobilitySpectra flag and scanSumming filter in msconvert on the DDA-PASEF data to get something close to the Bruker MGF. Those outputs should work with at least one of the search engines in the wizard and BiblioSpec should be able to import the results from that. You might have to put the MGF in a separate folder so that when BiblioSpec imports it doesn't find both the .d and MGF (because then it will prefer the .d because it's a vendor file).

The MSFragger search engine however should be able to deal with DDA PASEF data natively, and if you search it outside Skyline with FragPipe that should work, but the internal MSFragger search has some bugs with DDA PASEF. I'll fix those since that would be the easiest way to do DDA PASEF in Skyline.