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 <pwilm...@gmail.com> 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 spctools-discuss+unsubscr...@googlegroups.com. > 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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAGdnHmtNKs4YY7V-NgCOvEfPnNKjaVetOzTvMBqkH5PsN9LUYQ%40mail.gmail.com.
