Issue 827: X! Tandem point mutations not understood by BlibBuild

issues
Status:open
Assigned To:Matt Chambers
Type:Defect
Area:BiblioSpec
Priority:2
Milestone:23.1
Opened:2021-07-28 by Brendan MacLean
Changed:2023-01-16 by Brendan MacLean
Resolved:
Resolution:
Closed:
2021-07-28 Brendan MacLean
Title»X! Tandem point mutations not understood by BlibBuild
Assigned To»Kaipo
Type»Defect
Area»BiblioSpec
Priority»2
Milestone»21.2
This was reported on the support board:

https://skyline.ms/announcements/home/support/thread.view?rowId=52111

The key XML element that BlibBuild is failing to make sense of is:

<aa type="S" at="24" modified="44.00846" pm="M" />

As an initial fix, I think we need to just change the peptide to replace the S at 24 to M.

A more complete fix would preserve the point mutation information somehow in a way that would allow Skyline to make a correct protein assignment based on the original peptide sequence.

2022-03-08 Kaipo Tamura
Milestone21.2»22.1

2023-01-12 Kaipo Tamura
Tried to fix here: https://github.com/ProteoWizard/pwiz/pull/1702
but the user said the fix did not work for them and was unable to provide an example file.

2023-01-16 Brendan MacLean
Assigned ToKaipo Tamura»Matt Chambers
Milestone22.1»23.1
With Kaipo leaving, it seems like it will be up to Matt to fix this or resolve Not Repro if he can't get more information from the user.