Hi Alex, Greg is correct-- SEQUEST on one processor won't be particularly fast, especially compared to X!Tandem. The TPP is compatible with the other search engines that you mention, but they haven't yet been added to the graphic interface. Please let us know if you're specifically using them and we can post instructions for using the commandline.
-Natalie On Fri, Feb 20, 2009 at 11:43 AM, Greg Bowersock <bowers...@gmail.com> wrote: > Actually, your sequest license is for 1 PC only. If you are using the web > based sequest, you can modify the configuration to use mulitple processors > to speed up your processing. Sequest is quite abit slower than X!Tandem and > Mascot though, so don't expect it to be fast. If you are doing your searches > from inside of BioWorks, then I'm not sure how to use multiple processors. > If you need the information on how to modify the web based sequest > interface, let me know and I can send you the changes. > > Greg > > On Fri, Feb 20, 2009 at 11:17 AM, Alex_PCB <acampos.accou...@gmail.com> > wrote: >> >> I want to combine results from different database search engines >> through TPP and have been using mascot and xtandem so far. Recently, >> we have purchased a Thermo LTQ-FT and the biobrowser license as well. >> I follow the TPP workflow to get data from Thermo raw and search with >> sequest (i.e., convert into mzXML -> extract dta's -> search them >> using command line -> generate .out -> convert into pepxml .....). >> The problem is that one ~10,000-spectra raw file takes about 2 days to >> conclude the search. The same file is searched in less than one hour >> using mascot, xtandem, or even, the Biobrowser. Is this normal speed >> for sequest? Is there anyway to speed up the searches while making the >> files compatible with TPP analysis? Our sequest license is for one >> processor only. >> >> One more thing, I thought i read somewhere that the TPP would be >> compatible with OMSSA and Phenyx as well. Though, the pipeline options >> in the petunia main page are only for mascot, sequest, xtandem and >> spectrast. Is it still under develpment? >> >> Thanks for your help. >> >> Best regards, >> Alex >> >> > > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
