Issue 398: Investigate Mascot score threshold

issues
Status:closed
Assigned To:Guest
Type:Todo
Area:BiblioSpec
Priority:3
Milestone:3.1
Opened:2015-02-11 by Kaipo
Changed:2017-09-21 by Kaipo
Resolved:2017-09-21 by Kaipo
Resolution:Fixed
Closed:2017-09-21 by Kaipo
2015-02-11 Kaipo
Title»Investigate Mascot score threshold
Assigned To»kaipot@u.washington.edu
Type»Todo
Area»BiblioSpec
Priority»3
Milestone»3.1
In BiblioSpec, we switched from using the identity threshold to the homology threshold based on this information from John Cottrell at Matrix Science:

"Mascot has two score thresholds - the identity threshold and the homology threshold. We recommend using the homology threshold in almost all cases because it will give best sensitivity for a given FDR, and the Protein family summary reports expect values based on the homology threshold. I suspect Skyline is using expect values based on the identity threshold. You can confirm this by switching to the older, Select summary report and seeing whether the lists of peptides then match up"

Following this change, a user requested the use of the identity threshold: https://skyline.gs.washington.edu/labkey/announcements/home/support/thread.view?rowId=18891

We should determine if/how to support use of the old identity threshold.

2017-09-21 Kaipo
resolve as Fixed
Statusopen»resolved
Pretty sure we did this. No one has complained in 2.5 years.

2017-09-21 Kaipo
close
Statusresolved»closed
Assigned Tokaipot@u.washington.edu»Guest