Ah, ok, I see that mspire takes Thermo .srf files, which I believe are the newer Sequest search result files (http://mspire.rubyforge.org/tutorial/search_precision/prophet.html). Since this method hasn't been validated by us, you'll want to be sure that the scan numbers in the mzXML files still refer to the scan numbers in the mspire-converted pep.xml. So in your method you *are* doing a search step, and are still using Sequest.
You might want to give X!Tandem a try! Natalie On Fri, Jul 17, 2009 at 10:10 AM, Natalie Tasman<[email protected]> wrote: > Ok. Just to let you know, you will need to do *some* search step in > order to make use of the TPP. mspire is a completely independent > project and is not supported by the TPP (although looking at their > website, it seems that they try to be compatible at least in formats). > So I think you're missing the peptide ID phase, which is the info > that .pep.xml files should contain. Feel free to educate me about > about mspire if I'm wrong. > > > > On Fri, Jul 17, 2009 at 6:54 AM, Ali<[email protected]> wrote: >> >> 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 -~----------~----~----~----~------~----~------~--~---
