Ok, thanks! Just trying to figure out best practices. Best, Janel ᐧ On Tue, Aug 13, 2019 at 2:45 PM David Shteynberg < [email protected]> wrote:
> Yes, it makes sense to always run iProphet, to combine the results at the > peptide level before your combined them at the protein level with > ProteinProphet. Your best bet is to combine your PeptideProphet analyses > into a single analysis with iProphet and then run ProteinProphet on one > iProphet output. This may not always be possible given available computer > resources. In this case, you can break your data up into several iProphet > analyses and combine these into one ProteinProphet analysis. It doesn't > matter much when you run PTMProphet, but if you run it after iProphet it > might run a bit faster since it will only compute the localization of the > combined results. > > Cheers, > -David > > On Sat, Aug 10, 2019 at 11:28 AM Janel Beckley <[email protected]> > wrote: > >> Hi David, >> I just needed to have the exact mass for the K mod. Now it works without >> errors. Thanks! >> >> I have a couple more questions...about file merging in the TPP. If I want >> to combine a series of MS experiments each with multiple files, I presume I >> should always run iprophet to combine files prior to running >> proteinprophet, right? Also, does it matter if PTMprophet is run before or >> after iprophet? Thanks for all your help! >> >> Best, >> Janel >> ᐧ >> >> On Fri, Aug 9, 2019 at 7:41 PM David Shteynberg < >> [email protected]> wrote: >> >>> 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 a topic in the >>> Google Groups "spctools-discuss" group. >>> To unsubscribe from this topic, visit >>> https://groups.google.com/d/topic/spctools-discuss/NubMtD_ear4/unsubscribe >>> . >>> To unsubscribe from this group and all its topics, 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 >>> <https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D-Lr6JTpYKZerF%3D7PFjNYj2DAm4q%2BLM%2BnDA-_aCi9SM6A%40mail.gmail.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/CAANdTKQdL6SzrsT6z6XqQdDvAsZVwVKr%3DMZ6wZQuY4Qsos8vHg%40mail.gmail.com >> <https://groups.google.com/d/msgid/spctools-discuss/CAANdTKQdL6SzrsT6z6XqQdDvAsZVwVKr%3DMZ6wZQuY4Qsos8vHg%40mail.gmail.com?utm_medium=email&utm_source=footer> >> . >> > -- > You received this message because you are subscribed to a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/spctools-discuss/NubMtD_ear4/unsubscribe > . > To unsubscribe from this group and all its topics, send an email to > [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D-GLLxAaLgfwk7Ww88z4CQ0EsZyZ2j2UE_hJkfu4StauA%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D-GLLxAaLgfwk7Ww88z4CQ0EsZyZ2j2UE_hJkfu4StauA%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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