Hello Chih-Chiang, iProphet will convert all Isoleucines reported to Leucines for comparison purposes. Have you observed an error in your analyses?
-David On Tue, Jun 12, 2018 at 9:06 AM, Chih-Chiang Tsou <chihchiang.t...@gmail.com > wrote: > Dear TPP developers, > > I have a question regarding how iProphet handles ambiguous I/L IDs from > different search engine. I am using X!Tandem, Comet, and MSGF+ and combine > the results using iProphet, and noticed that the three search engines have > different rules ranking I/L hits. > So how does iProphet handle such case if different search engines give > different I/L variant as top ranking PSM? Does iProphet threat different > I/L variant peptide as different IDs and therefore penalizing the final > probability score, or iProphet considers them as the same ID? > > Thanks, > Chih-Chiang > > > > > -- > 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 https://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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
