Support of MSGF+ may not be full. There exist known issues with the way MSGF+ encodes some modifications in pep.xml that may not be correct. Also, high-scoring DECOY have been observed in MSGF+ analysis. The users are encouraged to be vigilant in comparing model estimated error-rates to the DECOY-estimated error-rates to make sure the two agree and set CLEVEL parameter accordingly see: http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_Asked_Questions#What_is_CLEVEL_and_when_do_I_use_it.3F
On Fri, Feb 20, 2015 at 7:59 AM, Jason Winget <[email protected]> wrote: > 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. > -- 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.
