Hi, First off I'll just say that it's my first time using PTM Prophet and I'm excited to see what it can do! I'm running Comet->peptideprophet->ptmprophet in TPP v 5.2.0 and unfortunately, I'm running into a number of these errors:
(example) ERROR: Cannot initialize for sequence: nKVIDGIDPPK[242], unknown mods may exist in spectrum Rep1_wt_010.12231.12231.1 Please specify modification and rerun PTMProphet ... Here's the command I used for PTMProphet: *EXECUTING: cd c:/Users/.../prophet-testing-HBH/Test && c: && C:/TPP/bin/PTMProphetParser STY:79.966,MW:15.995,K:114,n:42.010565 MINPROB=0.5 MAXTHREADS=0 FRAGPPMTOL=500 c:/Users/.../prophet-testing-HBH/Test/interact.ipro.pep.xml interact.ptm.ipro.pep.xml * It looks like PTMProphet isn't reading the mass of the modification correctly, but it isn't all the time (i.e. some of the modifications are analyzed even though they are also the total mass of the aa instead of just the mass change). I also tried using high and low mass accuracy files and changing the FRAGPPMTOL, but still got the same errors. I must be missing something, but I'm not sure what. An option? Something else? Any help would be appreciated! Thanks in advance, Janel -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/1939b026-8131-4d7d-8a8d-76271a18fceb%40googlegroups.com.
