Issue 377: Need to limit the peptides used in calculating PP enrichment to those from short-lived proteins

issues
Status:closed
Assigned To:Guest
Type:Todo
Area:Topograph
Priority:1
Milestone:3.1
Opened:2014-12-10 by Evvie Vincow
Changed:2017-10-18 by Brendan MacLean
Resolved:2017-10-18 by Brendan MacLean
Resolution:Won't Fix
Closed:2017-10-18 by Brendan MacLean
2014-12-10 Evvie Vincow
Title»Need to limit the peptides used in calculating PP enrichment to those from short-lived proteins
Assigned To»Nick Shulman
Type»Todo
Area»Topograph
Priority»1
Milestone»3.1
Nick, artifactual high PP enrichment values for individual peptides are driving the mean enrichment values up. This has always been a problem, but it's now severe because the absolute peptide enrichments in my last two studies are so low. Increasing the required deconvolution score does not solve the problem. If I could limit the peptides by protein half-life, that would help a great deal, because shorter-lived proteins have high absolute peptide enrichments and are less affected by peak picking artifacts.

I really need this feature in order to get accurate results from my two most recent datasets. Ideally I could set an upper and a lower bound on half-life, but I'd settle for just an upper bound. In other words, I'd limit peptides included in the median PP calculation first by decon score and then by protein half-life (user-entered value).

Thanks much!

2014-12-10 Evvie Vincow
Postscript: Ideally I could choose which cohort's half-life to use, but if that's awkward, using the average value (called simply "Half-Life") would definitely be better than not having the feature.

2017-10-18 Brendan MacLean
resolve as Won't Fix
Statusopen»resolved
Assigned ToNick Shulman»Evvie Vincow
Not really maintaining Topograph any longer.

2017-10-18 Brendan MacLean
close
Statusresolved»closed
Assigned ToEvvie Vincow»Guest