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] <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 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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