MS1 filtering by DDA on FAIMS-Lumos: Rugged Extracted ion chromatograms alejandro.cohen  2022-08-16
 

Long story short: We recently got a Lumos with Faims source, and I run our BSA samples we run as QCs using CV of 40, 60 and 80 in DDA mode. I created a skyline document using the Import DDA Peptide Search, using the .raw files and CRAP Fasta file (Contains BSA) and Fragger (I tried Amanda too). I get the expected proteins and peptides, but the XICs appear rugged, which I suspect corresponds to the traces for the different CVs.
I tried the Ion Mobility library correction (as suggested in previous post), but this doesn't seem to fix the issue. Basically, I'd like Skyline to filter the CV with the best signal for each precursor. Could this be done? Attached my skyline file.

Cheers

Alejandro

 
 
Brian Pratt responded:  2022-08-16

Hi Alejandro,

It looks like you probably just need to reimport the data now that you have an ion mobility library set.

If that doesn't help, I'd like to see one of your raw files as well.

Thanks for using the Skyline support board,

Brian Pratt

 
alejandro.cohen responded:  2022-08-16

Brian,

As suggested in previous post, I did reimport the data, but this doesn't seem to work.

I'll attach one of the .raw files.

Cheers

Alejandro

 
alejandro.cohen responded:  2022-08-16

Brian,

As suggested in previous post, I did reimport the data, but this doesn't seem to work.

The .raw file exceeds the limit, is there a server (OneDrive, etc) that I could use to share the file?

Cheers

Alejandro

 
Brian Pratt responded:  2022-08-16

You can upload it to http://skyline.ms/files.url, or anything else that's convenient for you.

Best regards,

Brian

 
alejandro.cohen responded:  2022-08-16

Done, uploaded

 
Brian Pratt responded:  2022-08-16

It looks like the problem is just that you had the Ion Mobility "Window Type" set to None. Set that to anything with other than None with a nonzero value and it should work fine.

 
alejandro.cohen responded:  2022-08-16

Worked, fantastic!!!

Thanks Brian