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.
