The best thing to do is to investigate the model plots to make sure that the results look accurate. In my experience, MSGF+ tends to be somewhat overaggressive and will assign peptides to some spectra that are clearly incorrect. This is usually corrected or eliminated if the results are combined with those of a second search engine (e.g. Comet) and processed with iProphet.
On Thursday, February 19, 2015 at 2:49:16 AM UTC-8, Florian wrote: > > Hej. > Thanks for the comment. I analyzed my data with MSGF+ and the result looks > fine. I am just concerned that if I want to publish data which were > analyzed combining MSGF+ and TPP, I will get problems. So, could the TPP > developers please comment on the warning? Is it planned to thoroughly test > the MSGF+ any time soon? > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
