Issue 702: Illegal character is phosphopeptide sequence

issues
Status:resolved
Assigned To:Brendan MacLean
Type:Defect
Area:Skyline
Priority:3
Milestone: 
Opened:2019-12-06 by demarco0
Changed:2019-12-09 by Brendan MacLean
Resolved:2019-12-09 by Brendan MacLean
Resolution:Fixed
Closed:
2019-12-06 demarco0
Title»Illegal character is phosphopeptide sequence
Assigned ToGuest»Brendan MacLean
Type»Defect
Area»Skyline
Priority»3
To whom it may concern,

I am trying to import a peptide search from MaxQuant. When I try to import the msms.txt file, I get an error message that reads "Illegal character found in sequence DKLLSVDGLIDAEAS(Phospho (STY))E (line 6).

suspect it has something to do with the way the phosphopeptides are annotated by maxquant, but I cannot figure out what the problem is.

I have attached the files here.

Thank you

A-
 
 modifications.xml
 mqpar.xml
 msms.txt

2019-12-09 Brendan MacLean
resolve as Fixed
Statusopen»resolved
Assigned ToGuest»Brendan MacLean
Please try Skyline-daily, if this is not with Skyline-daily. MaxQuant changed its modification format since we released Skyline 19.1. We think we have this fixed in Skyline-daily which will go out as 19.2 soon.