Greg, Thanks for your comments. I look forward to seeing the paper on the standards. It's a mixed bag of instruments here, Orbitrap XL, ABI 4800, QTOF Premier, Bruker HCT Plus, Bruker UltraFlex II, and an Agilent QTOF on the way. Since they are distributed between two distinct facilities it's unlikely we'll end up running a structured comparison of the platforms and which data analysis methods suit which instrument best.
Most stuff through our pipeline is from the Orbitrap, and we do seem to get an appreciable improvement in coverage for a given FDR by using OMSSA as well as Mascot and Tandem K-Score. I think I'll try seeing how much crux and Inspect, and Phenyx add, for the Orbitrap data at least, if I get the time. Cheers, DT In message <[email protected]> [email protected] writes: > I haven't done too much with iProphet yet, but I really need to get that > going asap. I've just been swamped with too much to do and then a vacation, > so now I should be able to get caught up. We are working on a paper or two > where we've done multiple search engines and multiple data analysis packages > on data from the UPS1 standard (and possibly UPS2, not sure if that is going > to be included or not), which was run on an LTQ XL, LTQ-XL Orbitrap, and an > LTQ-FT. We originally were going to also use the 4000 Q-Trap, but once we > saw the results we decided that it might be better left unsaid. I haven't > been the one doing the in depth analysis, but I think I remember that the > X!Tandem k-score data was pretty similar to the sequest results. All 3 > search engines have some differences due to their algorithms, so combining > is always a good idea. I haven't done much with OMSAA, I tried it out some > roughly 4-5 years ago, and wasn't that impressed, but it has probably > changed quite a bit for the better since then. > > It starts to become an issue of just how much data is really needed for each > sample, since you can always add another search engine or do something else. > It isn't an easy question to answer, but maybe there will be some agreement > to this soon. > > Greg > > On Tue, Aug 4, 2009 at 11:28 AM, Dave Trudgian <[email protected]> wrote: > > > > > Greg, > > > > Nice to know I'm not the only one. I've tried to structure our pipeline > > in a generic fashion, and separate things out to conf files, but it's by > > no means an example of pristine coding. Fingers crossed it would still > > be of use to someone. > > > > As an aside, I think I noticed on here that you've been using iProphet? > > We're combining Mascot, Tandem K-Score, and OMSSA searches by default, > > and have been intending to add more. I just wondered if you have an idea > > of what additional search engines would be most complimentary? I've not > > gotten round to trying out others myself, except pushing crux (free > > sequest re-implementation) results through the sequest pipeline... and I > > haven't done that enough to really assess how much extra we get vs > > Mascot/Tandem/OMSSA. > > > > DT -- Dr. David Trudgian, Bioinformatician in Proteomics, University of Oxford. Tel: (+44) (01865 2)87807 (CCMP - Mon-Thu) Tel: (+44) (01865 2)75557 (Dunn - Friday ) --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
