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!

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.

Not really maintaining Topograph any longer.