Yes, now we are on the same page! On Thu, Oct 10, 2024, 2:44 PM Sergio Ciordia <[email protected]> wrote:
> Hi David, > > I have anticipated your answer and I think this is what you asked for. I > have used TPP to generate the DECOY database using these settings: > > [image: image.png] > > I have searched PEAKS again and uploaded the new file ‘ > PEAKS_target_decoy.pep.xml’ and the decoy database to the shared folder. > > Link: PEAKS Dataset > <https://drive.google.com/drive/folders/1Q3LF1wRTM62KfS20dfXmToQMY9ji9Dug> > > See what you think of the output. > > Best, > 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 22:47, Sergio Ciordia (<[email protected]>) > escribió: > >> OK, I think I understand you now. I think what you are asking me to do is >> to create a database containing the target and decoy entries and repeat the >> search. Then in the output that PEAKS gives us, we could locate the >> ‘unknown’ decoy. Is this what you need?. >> >> 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 22:33, 'David Shteynberg' via spctools-discuss >> (<[email protected]>) escribió: >> >>> I think we have a bit of misunderstanding here. I am not looking for >>> decoys that are "known" to PEAKS, I want to include entrapment decoys that >>> are "unknown" to PEAKS and known to us as true negatives. Then we can >>> utilized the true negatives to estimate error rates. The true negative >>> entrapment decoys should not be revealed to the search algorithm, just like >>> the false positives among the target sequences are not known to the >>> algorithm, but represent the error we are trying to control. >>> >>> I hope this makes sense. >>> >>> -David >>> >>> On Thu, Oct 10, 2024 at 10:48 AM Sergio Ciordia <[email protected]> >>> wrote: >>> >>>> Hi David, >>>> >>>> There are several commercial softwares such as PEAKS or Proteome >>>> Discoverer that you upload the target database directly and they internally >>>> generate the Target-Decoy database. The problem is that when you launch the >>>> search and get the output, the software usually removes the decoy entries >>>> from the final results and that's why they don't appear in the list. >>>> >>>> I understand then that we would need the same ‘pep.xml’ file but >>>> containing all the target and decoy entries. Is that what you need?. >>>> >>>> Best, >>>> 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 19:40, 'David Shteynberg' via >>>> spctools-discuss (<[email protected]>) escribió: >>>> >>>>> 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 <[email protected]> >>>>> 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 (< >>>>>> [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> >>>>>>>> . >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> 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