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 because you are subscribed to 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