Issue 646: Problem to build library from MaxQuant

issues
Status:resolved
Assigned To:matt.chambers42@gmail.com
Type:Defect
Area:Skyline
Priority:3
Milestone:4.3
Opened:2019-04-25 by luzjpaulo
Changed:2019-05-07 by matt.chambers42
Resolved:2019-05-07 by matt.chambers42
Resolution:Fixed
Closed:
2019-04-25 luzjpaulo
Title»Problem to build library from MaxQuant
Assigned ToGuest»Brendan MacLean
Type»Defect
Area»Skyline
Priority»3
Milestone»4.3
When I create a library from a maxquant search skyline seems to fail to recognize the fixed modification. Once my library is built I find several peptides that do not have the fixed modification. When I create a library from mascot everything is fine.
 
 msms.txt
 modifications.xml
 mqpar.xml

2019-05-01 Brendan MacLean
Assigned ToBrendan MacLean»matt.chambers42@gmail.com
Matt, can you have a look?

2019-05-02 matt.chambers42
I think this is a quasi-duplicate of https://skyline.ms/issues/home/issues/details.view?issueId=645

The missing fixed mod (Propionyl N-term) is a variant specificity of one of the variable mods (Propionyl K). But I will confirm that's what's going on.

2019-05-07 matt.chambers42
The problem wasn't what I thought. Fixed peptide terminal mods for MaxQuant simply weren't supported by BiblioSpec before. I've committed a fix which should be in the next Skyline-daily. Fixed protein terminal mods for MaxQuant will still not be supported, so make sure to put the protein terminal mods in the variable mods section (that should have a negligible effect on search space and time).

2019-05-07 matt.chambers42
resolve as Fixed
Statusopen»resolved
Assigned ToGuest»matt.chambers42@gmail.com