If you are looking to provide a phospho-site localization confidence measure you have two options. One is PTMprophet , the other is Luciphor ( http://luciphor.sourceforge.net/ ). Both work with peptide level results produced by the TPP.
Damian On Sunday, November 3, 2013 9:08:57 AM UTC-5, zion wrote: > > Dear All: > > Recently some reviewers gave me feedback: "The criteria for acceptance of > Mascot peptide assignments and protein identifications need to be provided > for the phosphopeptide analyses.", my question is that if i have used > peptideProphet and proteinProphet, and i got the confident proteins at > protein leve(FDR=1%), how can i provide the peptide assignment criteria? > > Thanks a lot!! > > -Peter > -- 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
