I am not sure I know a tool called "ProptideProphet" ;) Perhaps you tried to run PeptideProphet but it generated no results for you? When you run "Analyze Peptides" in the TPP interface, it should create a file called interact.pep.xml by default, that will contain probabilities among other information. Did you run "Analyzed Peptides"? Were there any messages reported by the analysis?
On Wed, Jan 20, 2021 at 1:30 AM giangiacomo beretta < giangiacomo.berett...@gmail.com> wrote: > Hi David! It works nicely, thank you ! > > Now I am experiencing another issue of mine :) > > I run ProptideProphet on the XML fiel generated by XTandem. I need this > file presuming that PP will add probabilities to the identified peptides as > this is requested by SpectraST to generate the corresponding spectral > library (this is actually my final goal). > > However, when I try to do it, SpectraST reports: WARNING -- PEPXML IMPORT: > Importing a .pep.xml file with no probabilities. PeptideProphet probably > needs to be run on .pep.xml first. > > Maybe probabilities are used for data processing but not appendend to the > XML output file? > > Thanks a lot in advance! > > G > > Il giorno martedì 19 gennaio 2021 alle 20:53:57 UTC+1 David Shteynberg ha > scritto: > >> Dear Giangiacomo, >> >> Thanks for trying the TPP and reporting the problem. TPP uses the >> proteowizard's msconvert tools for this step. You can remedy the problem >> by either upgrading to a newer version of proteowizard's msconvert tool or >> use --ignoreUnknownInstrumentError option with your current version. On >> the generate mzML page you can specify this option in the "Enter >> additional options to pass directly to the command-line" text box, just >> enter the text --ignoreUnknownInstrumentError >> >> Hope it works! >> >> Cheers, >> -David >> >> >> On Tue, Jan 19, 2021 at 8:10 AM giangiacomo beretta < >> giangiacom...@gmail.com> wrote: >> >>> Hi, when I try to convert raw files, the conversion tool stops >>> immediately reporting the following error: >>> >>> Reader_Thermo::fillInMetadata] unable to parse instrument model; please >>> report this error to the ProteoWizard developers with this information: >>> model(Orbitrap Eclipse) name(Orbitrap Eclipse); if want to convert the file >>> anyway, use the ignoreUnknownInstrumentError flag >>> >>> It appears that the system is not recognizing the instrument model that >>> produced the raw files. Is there any option to overcome this issue? >>> >>> Actually I have converted the same files with ProteoWizard without >>> troubles. >>> >>> Thanks in advance! >>> >>> G >>> >>> -- >>> 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-discu...@googlegroups.com. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/spctools-discuss/2134bb9e-bb7e-4f52-9afc-bf59b75f21aen%40googlegroups.com >>> <https://groups.google.com/d/msgid/spctools-discuss/2134bb9e-bb7e-4f52-9afc-bf59b75f21aen%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 spctools-discuss+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/95da30b4-f9d1-49cc-896e-fe734ba0cac4n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/95da30b4-f9d1-49cc-896e-fe734ba0cac4n%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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D9HEf8jtFUOh0yE1n3bT_%2BFz3VKvqd48oJkaHjJHgDMVg%40mail.gmail.com.
