Unable to view deuterated heavy internal standard in LC chromatogram

General Server Forum (Inactive)
Unable to view deuterated heavy internal standard in LC chromatogram wongk38  2018-02-14 16:53
Status: Closed

The latest Skyline software 4.1 doesn't allow for the viewing of deuterated heavy internal standard when we open up previous Skyline document (v 3.7) containing results.

I've attached some photos to show the differences between the 2 software. Ideally, it would be nice if the updated Skyline version would be able to view the previous results from the older Skyline version.

What would be the best path forward to address this issue?

Many thanks!
jeckels responded:  2018-02-14 17:28
Hi Kent,

I'll forward this to the Skyline team for comment. I know their general intent is to be backwards compatible.

It looks like only one screenshot got attached. Is there a second to show how things look in the other version?

wongk38 responded:  2018-02-14 17:31
Thanks for the Josh for the quick response. I've attached a second screenshot. Not sure why it didn't appear initially.
Brian Pratt UW responded:  2018-02-15 11:49
Hi Kent,

Just wrapping up our off-list conversation for posterity here. Thanks for making your Skyline file available to me.

The issue is that pre-4.1 Skyline would allow any grouping of small molecule precursor ions under a parent molecule, each precursor having its own individual chemical formula that included ionization. As of 4.1, Skyline strictly models precursors as adducts applied to a common neutral molecule, which brings it into line with our proteomic model of neutral peptide with varying modifications and charges. Having this unified molecular model allows more of Skyline's capabilities for quantification etc to be applied to non-peptide molecules.

Unfortunately, Skyline is doing a poor job of finding the commonalities of your precursors and translating that to a neutral molecule with multiple adducts. It's a little better with the current state of the Skyline 4.1 code (patch release coming soon) - I can at least see the chromatograms - but I'm still not happy with the way Skyline is translating your document.

Your document is completely rational, and it's clear that, for example, your first entry, currently described as ions C20H31O5 and C20H27H'4O5, should be understood as neutral molecule C20H32O5 with adducts [M-H] and [M4H2-H], but Skyline isn't getting that right.

I would advise sticking with 3.7 for the moment, while I work to understand what Skyline is doing wrong. Josh is quite correct in saying that we value backward compatibility, and we'll make this right. Sorry for the bother!

Brian Pratt
Skyline Developer Team