XL Peptides IMS library saves different entry per file

XL Peptides IMS library saves different entry per file Juan C. Rojas E.  2022-09-08 09:08

Hi Skyline Team,

Today I noticed that when I try creating an IMS library for XL-peptides with "Use Results" and multiple files a different value is stored for each precursor for each file. This does not happen for "normal" linear peptides.

I know that multiple Ion mobility values might be stored to represent multiple conformers but I am not sure that is what is identifying here. So I am wondering if this was intended to allow for multiple conformer annotations or is it a glitch for only XL-peptides?

Instrument: timsTOF Pro
Skyline-daily version:

As always, thanks for your time and the great work!
Juan C.

Brian Pratt responded:  2022-09-08 09:13

Hi Juan,

Hard to say what's going on there - I'd be curious to see your data if possible, to see if there's anything unusual about it.


Brian Pratt

Juan C. Rojas E. responded:  2022-09-09 02:15

Hi Brian,

Some time ago I shared with Nick a "BSA_DSBU_PXD027234" Skyline document from a published study that is standing in Panorama in the Data Sharing folder of the MLU-Sinz Lab together with the heavy timsTOF files. The skyline document you'll find it attached to the post, but the raw data you can either get it from ProteomeXchange or from the Panorama site.

I was able to replicate the issue I described before with the DSBU dataset. I also noticed today that every time I click "Use Results" it doubles the size of the list...I guess it is trying to add new entries instead of rewriting (?). However, I don't know why it does that only for the XL-peptides.

Thanks for the attention to this, Brian.
Juan C.

Brian Pratt responded:  2022-09-09 08:19

That doubling effect is a significant insight, I can guess at the nature of the problem from that. I'll have a look at your data and resolve this.



Nick Shulman responded:  2022-09-09 21:37

Thank you for reporting this bug.
This bug will be fixed in the Skyline-Daily that comes out right after Skyline 22.2 is released (probably in a few weeks).
-- Nick