Hi Natalie I used sequest. I've sort of given up on that. I now convert my .raw files directly to .pep.xml files using mspire. Its not much of a pipeline anymore but it does the job.
Regards Ali On Jul 15, 9:19 pm, Natalie Tasman <[email protected]> wrote: > Hi Ali, > > Greg made some good comments on your post regarding the Sequest search > engine. I'm curious as to what search engine you're using. The TPP > includes X!Tandem, which is generally significantly faster than Sequest, and > is multi-threaded (and free, so you can even consider running it across a > cluster-- something we're hoping to make easier in the future). Note, > though, all search engines, including X!Tandem, are affected by the search > parameters that you use. So a semi-tryptic search will generally always > take longer than a full-tryptic search but increase the search space (which > is good), so it's always going to be a trade-off. We include some default > X!Tandem parameter files; as you get more experience, you might want to play > with modifying some of the parameters to optimize your search. > > Natalie > > On Fri, Jul 10, 2009 at 6:59 AM, Greg Bowersock <[email protected]> wrote: > > Sequest is not very fast. The only way to really speed up sequest is to > > give it more processors, provided you are using sequest in a way that will > > allow you to use the extra processors. There are many factors that affect > > the speed of processing though, with the two largest being the type of > > digestion and the size of the database. The number of modifications also > > plays a role in the amount of time, so as you can see there isn't any one > > way to really speed up sequest. Also, 10 hours isn't all that bad, try doing > > a no-enzyme search on a decent sized database, that can take days on 1-2 > > processors. > > > On Fri, Jul 10, 2009 at 4:42 AM, Ali <[email protected]> wrote: > > >> Hi everyone > > >> I am doing some databse search with mzXML files generated from > >> Thermo .raw files against my database. I have a duo core 2GB RAM > >> machine. I understand that TPP does not use multi-threading but one > >> mzXML file seems to take 10 hours to process!! Is there anyway I can > >> speed up this process? > > >> Regards > > >> Ali --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
