Hello Giangiacomo, You can use the Lib2html tool to convert an splib into a webpage with clickable links to library spectra. You can launch this tool from SpectraST Tools -> Convert Libraries to HTML.
Hope this helps, --Luis On Thu, Jan 21, 2021 at 12:09 AM giangiacomo beretta < giangiacomo.berett...@gmail.com> wrote: > 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 < >> giangiacom...@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-discu...@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/7b9079b3-15d0-407f-9510-c01c1b80ab74n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/7b9079b3-15d0-407f-9510-c01c1b80ab74n%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/CACyS9bq%3Dqw0DNUDr_6smK9zqfTJYp_1%3DwyymHAhq%2BaCJPvvykg%40mail.gmail.com.
