Hello Sergio, Thanks for sending this. After taking a look I have another request. The database you searched against seems to not contain any entrapment DECOYS to help independently validate any computed scores or probabilities. Are you able to search this data against a database containing some decoys? You can use the TPP decoy generator to create decoys (we have been using deBruijn randomized sequences), or should I create it and give you the database to search?
Best, -David On Thu, Oct 10, 2024 at 3:52 AM Sergio Ciordia <scior...@cnb.csic.es> wrote: > Thank you David. You are right, I attach in this new link the 3 files you > need: mzML, fasta and pep.xml. > > Link: PEAKS Dataset > <https://drive.google.com/drive/folders/1Q3LF1wRTM62KfS20dfXmToQMY9ji9Dug> > > I hope you can do something. Thanks anyway for your concern. > > Best regards, > Sergio > > -------------------------- > Sergio Ciordia Higuera > Proteomics Facility > National Center for Biotechnology > C\Darwin, 3 > Universidad Autónoma de Madrid > Cantoblanco > 28049 Madrid (Spain) > Phone: +34 91 585 4540 / 4695 > Fax: +34 91 585 4506 > > > El jue, 10 oct 2024 a las 1:34, David Shteynberg (< > dshteynb...@systemsbiology.org>) escribió: > >> Thank you Sergio! Would you mind also sending the mzML data and the >> sequence database that goes along with these search results from PEAKS? >> >> Best, >> -David >> >> On Oct 9, 2024, at 3:58 PM, Sergio Ciordia <scior...@cnb.csic.es> wrote: >> >> Hi David, >> >> Thank you for your quick and honest response. I am sorry to hear that you >> have no funds to continue TPP implementation. I hope this problem will be >> solved. >> Nevertheless, I appreciate your consideration of evaluating a sample >> file. This file contains what the PEAKS team calls ‘Peptide output in >> pepxml’. I hope it is adequate but in any case I don't think there will be >> a problem in getting a suitable data output for TPP if necessary. The other >> format that can be obtained is mzidentML in case it is of interest. >> >> LINK: pepXML PEAKS sample >> <https://drive.google.com/file/d/185t5m7vJPLQAj8vVpcviX_p58DHZfyAB/view?usp=sharing> >> >> Thanks again for your reply. >> >> Best regards, >> Sergio >> >> -------------------------- >> Sergio Ciordia Higuera >> Proteomics Facility >> National Center for Biotechnology >> C\Darwin, 3 >> Universidad Autónoma de Madrid >> Cantoblanco >> 28049 Madrid (Spain) >> Phone: +34 91 585 4540 / 4695 >> Fax: +34 91 585 4506 >> >> >> El jue, 10 oct 2024 a las 0:46, David Shteynberg (< >> dshteynb...@systemsbiology.org>) escribió: >> >>> Hello Sergio, >>> >>> Thank you for your email. As you know PEAKS is not a search engine that >>> we have integrated in the TPP, mainly because we have not had any requests >>> for this feature before your email. It is something that can be done with >>> a bit of work and testing, but unfortunately there is currently no funding >>> for us to continue this work. I wish I had a more satisfying answer to >>> give you, but perhaps, if you can forward your sample pep.xml file, we can >>> do this if more funding becomes available. >>> >>> Best, >>> -David >>> >>> On Oct 9, 2024, at 3:35 PM, Sergio Ciordia <scior...@gmail.com> wrote: >>> >>> Hi, >>> >>> I have been using TPP for some time now mainly to validate with >>> PeptideProphet the results I get with various search engines and to >>> generate a spectral library that I use in various programs. The thing is >>> that in my lab we are now using PEAKS (v12) and the output is really good. >>> I was wondering if it would be possible to include in TPP an analysis >>> pipeline of the PEAKS data from the pep.xml file generated by the program. >>> I know it is a commercial software but the output is very good and I >>> would be very grateful if you could consider including it like Sequest or >>> Mascot. I think it would not be complicated since they already have the >>> pep.xml output, it would only have to be compatible with XInteract to be >>> able to validate peptide-spectrum matches. >>> >>> If necessary I can provide a sample pep.xml file. >>> >>> Thank you very much. >>> >>> Best regards, >>> Sergio >>> >>> -- >>> 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/621aa092-4079-4dc8-963f-92ca8eb7e6acn%40googlegroups.com >>> <https://groups.google.com/d/msgid/spctools-discuss/621aa092-4079-4dc8-963f-92ca8eb7e6acn%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/VptRGKWbkvM/unsubscribe >>> . >>> To unsubscribe from this group and all its topics, 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/26147492-1510-42FC-A601-FB34DCABBC69%40systemsbiology.org >>> <https://groups.google.com/d/msgid/spctools-discuss/26147492-1510-42FC-A601-FB34DCABBC69%40systemsbiology.org?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/CAOgO5W5q3RRYqwOQ_5W3YQmfcYV%2BHNgbNgnMdJL_aV-eyeOH6g%40mail.gmail.com >> <https://groups.google.com/d/msgid/spctools-discuss/CAOgO5W5q3RRYqwOQ_5W3YQmfcYV%2BHNgbNgnMdJL_aV-eyeOH6g%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/VptRGKWbkvM/unsubscribe >> . >> To unsubscribe from this group and all its topics, 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/5E738AA1-A696-4510-8D4C-D509926D065C%40systemsbiology.org >> <https://groups.google.com/d/msgid/spctools-discuss/5E738AA1-A696-4510-8D4C-D509926D065C%40systemsbiology.org?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/CAOgO5W7%2BQqcKvPBMcMTLWR2oahP8Qz%2BQVpyop9dUusFZC4vL0A%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CAOgO5W7%2BQqcKvPBMcMTLWR2oahP8Qz%2BQVpyop9dUusFZC4vL0A%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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