Annotate unknow full scan compound using NIST GC-MS library

Annotate unknow full scan compound using NIST GC-MS library wanying cao  2024-04-26 09:06

Hi Skyline team, I used to be a Skyline protein mode user but now switched to GC small molecule omics analysis. Current software I am using can only give me a laundry list of RT with precursor mass without any compound name information. I can import transition list and results file to Skyline but cannot annotate these peaks from RT. So I was trying to figure out how can I actually annotate this peaks using Skyline then output a list of compound peak area list.

So I was thinking to use NIST GC-MS library but clearly I have difficult time find the right one (my compounds are all volatile compounds with <350 m/z, but all library I can find is peptide size). So I was wondering can Skyline annotate those undefined Peaks from GC-MS (Agilent)? If yes, how can we actually do it using Skyline? Thank you very much!

Brian Pratt responded:  2024-04-27 10:11

Are you asking if Skyline can identify the compounds? If so, the answer is no, Skyline isn't built for that.

If you do know the compound associated with a chromatogram in Skyline, you can set its name with a right click in the Targets tree, and selecting Modify.

But the most convenient route is to start with a proper spectral library. I'd say keep looking for a usable library - NIST is not the only source for those.

Thanks for using the Skyline support board,

Brian Pratt

wanying cao responded:  2024-04-29 06:34

Got you. Thank you, Brian and Skyline team!