Hi Javan, MSConvert can create MS2 format peak lists from RAW files. MS2 format is kind of a file of concatenated DTA files. It is not too hard to convert from one to the other. I have probably have a Python script somewhere that makes MS2 files from folders of DTA files. I am not sure if I have one that goes the other direction. Cheers, Phil
see: McDonald, W.H., Tabb, D.L., Sadygov, R.G., MacCoss, M.J., Venable, J., Graumann, J., Johnson, J.R., Cociorva, D. and Yates III, J.R., 2004. MS1, MS2, and SQT—three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. *Rapid Communications in Mass Spectrometry*, *18*(18), pp.2162-2168. On Tuesday, June 9, 2020 at 1:42:28 AM UTC-7, Javan Okendo wrote: > > Thanks all for your help. I now understand why this can't work. The reason > I wanted to use SEQUEST was because the program I wanted to use only takes > .DTA file format for spectral clustering and I have looked around there is > not software which can give me these .DTA file formats. > > On Tue, Jun 9, 2020 at 3:52 AM Phillip Wilmarth <[email protected] > <javascript:>> wrote: > >> Hi Javan, >> Many (many) years ago Thermo had a command line executable SEQUEST that >> BioWorks called to run SEQUEST. Thermo put it inside hidden folders and >> there were license key issues. You could not copy the EXE to another >> machine and have it run. That scheme may have persisted for some of the >> earliest Proteome Discoverer releases. >> >> I do not think that there is still a SEQUEST.EXE associated with Proteome >> Discoverer. Something made running SEQUEST from the command line break >> (ancient memory cells are recalling something more...). Maybe it was a >> transition to C# from C++ and command line parsing issues. I never could >> get it to work. I gave up trying to run SEQUEST when Comet came out. >> >> You can get a 60-day demo version of Proteome Discoverer from Thermo. I >> do not know if you can create things like pepxml files from PD so that you >> could post-process the SEQUEST searches with TPP. PD is internally all >> SQLite3 relational database tables (something like 80 of them). It is >> either not a very good design for the database tables or just really hard >> to try and figure out (or both). You can snoop on the SQLite DB with >> various tools, but a proper schema description would be helpful. Table >> names and field names are not real transparent. >> Cheers, >> Phil >> >> >> On Monday, June 8, 2020 at 3:51:50 PM UTC-7, Jimmy Eng wrote: >>> >>> Javan, >>> >>> You're not going to be able to run SEQUEST through the TPP unless you've >>> purchased the software from Thermo and have it installed on the same >>> computer that's running the TPP. It doesn't come with the TPP itself. And >>> support for the SEQUEST pipeline option should probably be removed from the >>> UI unless anyone can confirm that it actually still works. >>> >>> On Monday, June 8, 2020 at 1:56:45 PM UTC-7, JAVAN OKENDO wrote: >>>> >>>> >>>> I am getting the above mentioned error when running SEQUEST on TPP. I >>>> did install the TPP correctly and when I try to run the program it gives >>>> an >>>> error. See the screenshot with the error details >>>> >>>> >>>> >>>> >>>> >>>> [image: Screenshot from 2020-06-08 22-50-26.png] >>>> >>>> -- >> 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] <javascript:>. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/a9275fb5-b5cd-4f9c-8f97-36789faaeee7o%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/a9275fb5-b5cd-4f9c-8f97-36789faaeee7o%40googlegroups.com?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/61d01c4a-750a-41b3-b3ec-679278771a8fo%40googlegroups.com.
