Hi David, Can you show us how to set CLEVEL threshold in TPP pipeline? >From your link provided, the default CLEVEL is set to 0, so when the model estimated error-rates is different from DECOY-estimated error-rates, shall I set the CLEVEL to 1? Another silly question is, is there anyway to quantitatively estimate how much the model estimated error-rates differ from DECOY-estimated error-rates? other than comparing them in the plots......
SunSun On Saturday, February 21, 2015 at 3:39:45 AM UTC+8, David Shteynberg wrote: > > 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] > <javascript:>> 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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.
