Issue 365: Make peptide matching to background proteome more flexible

issues
Status:closed
Assigned To:Guest
Type:Defect
Area:Skyline
Priority:3
Milestone:3.7
Opened:2014-11-19 by Brendan MacLean
Changed:2017-06-08 by Brendan MacLean
Resolved:2017-06-08 by Brendan MacLean
Resolution:Fixed
Closed:2017-06-08 by Brendan MacLean
2014-11-19 Brendan MacLean
Title»Make peptide matching to background proteome more flexible
Assigned To»Nick Shulman
Notify»Jarrett Egertson
Type»Defect
Area»Skyline
Priority»3
Milestone»3.1
As Jarrett mentioned, and just came up again in the most recent webinar, background proteome matching for peptide sequences works for semi-tryptic peptide that were cleaved at the N-terminus, but not at the C-terminus. We should fix this. Nick, you also mentioned maybe having an algorithm that could match any peptide sequence regardless of how it was cleaved. This too has also been requested. People would like to be able to have the ability to associate peptides with no specific enzyme cleavage associated with there source proteins.

But, if the latter is too difficult, at least we should fix the semi-tryptic C-terminal peptides issue.

2014-11-27 Brendan MacLean
This came up again on the DIA tutorial webinar. And another, similar case was just reported on the support board:

https://skyline.gs.washington.edu/labkey/announcements/home/support/thread.view?rowId=17568

In this case, the protein N-terminal Methionine is lost on an otherwise tryptically cleaved peptide.

2017-06-08 Brendan MacLean
resolve as Fixed
Statusopen»resolved
Assigned ToNick Shulman»Brendan MacLean
Milestone3.1»3.7
Nick fixed this with more flexible matching.

2017-06-08 Brendan MacLean
close
Statusresolved»closed
Assigned ToBrendan MacLean»Guest