Hello Janel, Thank you for trying out PTMProphet. An internal check in the code verifies that the mod mass during the search matches the mod mass at the time of running PTMProphet. Can you verify the 114 on K is in fact the mass you used at search time? Can you look at that specific spectrum in the pepxml file and all check modification listed for that search_hit?
Thanks, David On Fri, Aug 9, 2019, 4:14 PM Janel <[email protected]> wrote: > 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 > <https://groups.google.com/d/msgid/spctools-discuss/1939b026-8131-4d7d-8a8d-76271a18fceb%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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/CAGJJY%3D-Lr6JTpYKZerF%3D7PFjNYj2DAm4q%2BLM%2BnDA-_aCi9SM6A%40mail.gmail.com.
