How to query Thermo AIF MS2 data?

[yguitton]

Hi,

Is there a specific way to query an LC-MS file with All Ion Fragmentation (AIF) MS2 with massQL?
If yes can you give me an example?

Or should i use query like that one even if my MSMS are taken from an AIF experiment and not a DDA? QUERY scaninfo(MS2DATA) WHERE MS2PROD=226.18:TOLERANCEPPM=5

Thanks

[mwang87]

Hi Yann, sorry for the delay!

Yes, DIA should be no problem.

QUERY scaninfo(MS2DATA) WHERE MS2PROD=226.18:TOLERANCEPPM=5

should totally be fine, and so you'll find AIF scans that have that product peak since MSe will look like MS2 in the mzML files.