Hi David, sorry for the mistypos! Yes I run PeptideProphet under Analyze Peptides, and no relevant messages were generated :)
However, I forgot to mention that the problem is related to interact.pep.xml processing in SpectraST in its command line version (independent from TPP). I am sorry, I did not notice that TPP includes an option for spectral library generation that works perfectly fine, and this is what I needed..! Just last question, is there any tool for visualisation/inpection of spectra in splib libraries ? Lots of thanks, Giangiacomo Il giorno giovedì 21 gennaio 2021 alle 01:24:47 UTC+1 David Shteynberg ha scritto: > 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 < > [email protected]> 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 < >>> [email protected]> 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 [email protected]. >>>> 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 [email protected]. >> > 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/7b9079b3-15d0-407f-9510-c01c1b80ab74n%40googlegroups.com.
