Hi, Florian, The TPP currently support mascot, comet, tandem, and sequest results. I have tried myrimatch and MSGFP+, both went through OK but it come with the WARNING message that you have mentioned. I guess the message simply means the TPP peptideprophet model have not been tested thoroughly on MSGFP+ results at this point. However, you always need a filtering strategy to process your search results, and there is really no "golden standard" to do that. You can arbitrarily choose a score threshold, or use peptideprophet or IDpicker for the filtering. My suggestion is to use a decoy database concatenated to your target database, and use FDR to assess if your filtering strategy is good or not. I have tried TPP on both MSGFP+ and myrimatch against decoy-targeted database, from what I have seen, they work comparably to Comet and Tandem. Just for discussion. and I hope others can give more insides into this topic.
SunSun On Monday, February 16, 2015 at 6:58:15 PM UTC+8, Florian wrote: > > MSGFPlus is announced as a supported search engine here > <http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP#Working_with_supported_search_engines>. > > However, when I run PeptideProphet on MSGFPlus output, I get the following > warning: > > WARNING!! The discriminant function for MSGFPL is not yet complete. It is >> presented here to help facilitate trial and discussion. Reliance on this >> code for publishable scientific results is not recommended. >> > > So, what's true, now? > -- 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.
