|Title||»||Need to limit the peptides used in calculating PP enrichment to those from short-lived proteins|
|Assigned To||»||Nick Shulman|
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).