Generating a mobility library

Generating a mobility library alan mckenzie-coe  2022-06-06 11:40

I’m trying to generate a mobility library, so far I have curated my target peptides and transitions. I have also made the following changes shown in the screenshots attached.

Brian Pratt responded:  2022-06-06 11:52

That error is coming from inside the Agilent DLL, so we’ll have to work with them to figure this out. That probably won’t be possible until after ASMS but if you can upload the raw file and the Skyline document (use Skyline’s File>Share command to create a tidy file) that will help us get a jump on this.

Brian Pratt

alan mckenzie-coe responded:  2022-06-06 12:22

I have attached the files.

alan mckenzie-coe responded:  2022-06-06 12:23

I have attached the files.

Brian Pratt responded:  2022-06-06 12:31

Thanks. We’ll need the raw file too - likely too large to attach, but you can upload to our site.


alan mckenzie-coe responded:  2022-06-30 10:25

I have uploaded the Skyline files and raw data in the zip folder, Generating a mobility library_with_Data_Error

Brian Pratt responded:  2022-06-30 15:46

Excellent, I'll work with this and see what I can find out. At first glance I think the problem may well be on the Skyline side, having to do with how we approach ion mobility library building for ions that don't produce any MSI chromatograms.



Brian Pratt responded:  2022-07-01 09:45

Hi Alan,

OK, that error comes when we ask the Agilent API to convert back to drift time from the CCS value it gave for a particular (DT, mz, charge) observation.

Specifically, it returns CCS=437.31581033776683 for (DT=75.802466126052, mz=286.820459998333, charge=3) but when asked for the DT for (CCS=437.31581033776683, mz=286.820459998333, charge=3) value it errors out.

I'm guessing that drift time is outside the useful range, and indeed there's not much signal for that ion and we're probably just picking up noise.

So, two issues - Agilent really ought to be able to round-trip that calculation, and Skyline probably ought not to try to determine a drift time for such a weak signal. Not much I can do about the first, but we can get smarter about the latter.

In the meantime, you can probably move forward by temporarily removing the charge 3 ions from the document before training the IMS library.

Best regards,