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> >>>>>>> . >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> You received this message 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