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 (< [email protected]>) 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 <[email protected]> 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 (< > [email protected]>) 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 <[email protected]> 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 [email protected]. >> 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 >> [email protected]. >> 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 [email protected]. > 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 > [email protected]. > 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. 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