Thanks @Eric Deutsch <[email protected]> , @Phillip Wilmarth <[email protected]> and @Jimmy Eng <[email protected]> I will now do the spectral search using the Spectrast within the TPP toolsuite
On Tue, Jun 9, 2020 at 8:11 PM 'Eric Deutsch' via spctools-discuss < [email protected]> wrote: > Sounds like an XY Problem here. > > > > If it’s spectral clustering you want to do, and within the TPP, perhaps > consider SpectraST: > > > http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST#Spectral_Archive_.28Unidentified_Spectral_Library.29_Building > > > > You won’t need to fool around with DTA files and 8-track tapes. > > Although the examples show mzXML files at the URL above, you should use > mzML files, of course. > > > > Regards, > > Eric > > > > > > > > *From:* [email protected] < > [email protected]> *On Behalf Of *Phillip Wilmarth > *Sent:* Tuesday, June 9, 2020 8:44 AM > *To:* spctools-discuss <[email protected]> > *Subject:* Re: [spctools-discuss] Re: C:/TPP/bin/runsearch' is not > recognized as an internal or external command > > > > 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]> 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 > > > > > > > > > > > > -- > 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/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 > <https://groups.google.com/d/msgid/spctools-discuss/61d01c4a-750a-41b3-b3ec-679278771a8fo%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/0ffa822e836b492cb8176340eaf05db8%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/0ffa822e836b492cb8176340eaf05db8%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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