Hi One way to combine search engines outside the MaxQuant environment with good quantification algorithms is the OpenMS package. This might be a sensible way to go if you like to combine multiple search eninges and the TPP search workflow with an alternative open-source quantification engine. I am not saying that it is the best but it might be worth a shot.
Hannes On 2 December 2014 at 00:17, Alejandro <[email protected]> wrote: > Hi Brian, > > Of what I have seen XPRESS does indeed performs better than ASAP with high > resolution data, plus it's incredible fast. Still, there's always the need > for QC. I also use MaxQuant, specially for multiplex isotopic data, but in > general one gets much more IDs using Xtandem (or combination of search > engines with Iprophet, something really helpful) than with Andromeda. > > Cheers, > > Alejandro > > On Monday, December 1, 2014 11:28:51 PM UTC+1, Brian Hampton wrote: >> >> It has been my experience that ASAPRatio is slow (haven't used 4.8 yet) >> and inaccurate even with high mass accuracy data. I've used both chemical >> isotopic labeling and SILAC data sets and you really need to QC the >> results. The output of ASAPRatio is not to be trusted, based on my >> experience with it. I've seen "interesting" hits have a given >> "interesting" ratio and then go back and look at the peak integrations and >> have occasionally found that after performing QC on the data that the ratio >> was reversed from what was originally reported by the algorithm! This >> calls into question the accuracy of the entire dataset quantitation as >> performed by ASAPRatio. >> >> The original Aebersold paper on ASAPRatio is demonstrated on a reduced >> complexity dataset e.g. a pulldown. The P-value was described as a way to >> quickly sort changed from unchanged compared to the background. I am >> suspicious that ASAPRatio is just not that suited to datasets from complex >> samples like cell lysates et. al. which is what I have been using it for >> and I suspect you have as well. >> >> I will begin use of XPRESS and see how that performs. Given the need for >> quantification of proteomic data sets, I hope the TPP team is working on a >> better MS1 quan package than what is currently present in TPP. It would be >> nice to see something more robust like Skyline but better suited to shotgun >> vs targeted quantification. There is a paper describing ISOQUANT which >> looks promising but I believe it was originally written to handle SILAC >> only datasets. Maybe the TPP developers can obtain this from the author >> and adapt it to handle multiple isotope labeling strategies and make it >> available to all their loyal TPP users who have benefited greatly by their >> efforts to date. >> >> Since you have high resolution data, have you tried MaxQuant? >> >> Cheers, >> Brian >> >> Brian Hampton >> Protein Analysis Lab >> Center for Vascular and Inflammatory Diseases >> University of Maryland School of Medicine >> 655 West Baltimore Street BRB 7-018 >> Baltimore MD 21201 >> V: 410-706-8207 >> >> >> On Mon, Dec 1, 2014 at 1:04 PM, Alejandro <[email protected]> wrote: >> >>> A quick update. >>> >>> After running the same files with TPP 4.8, running time with ASAP ratio >>> is quite reduced, to ~1h, but quantitation seems to work better with XPRESS. >>> >>> Alejandro >>> >>> On Wednesday, November 19, 2014 7:29:30 PM UTC+1, Alejandro wrote: >>>> >>>> Hi all, >>>> >>>> I'm analyzing dimethylated data obtained with a QExactive using >>>> XTandem! (have tried both static or variable searches). If the data is >>>> quantified using Xpress, the time it takes is quite normal, ie fast, >>>> minute(s) or so for a 1GB RAW file (ca. 250MB mzXML), however when >>>> activating ASAPratio, the processing takes hundred times more than with >>>> Xpress (which reports a quite disperse distribution of ratios, not seen >>>> with Orbitrap data, thus the reason to see how ASAP performs). After >>>> looking in the list I found a post which discussed somehow this >>>> https://groups.google.com/d/topic/spctools-discuss/Tkko >>>> HpXAh4A/discussion which was related to multithreading. >>>> >>>> When running this analysis the bottleneck seems to come from the >>>> ASAPratio: >>>> >>>> Stucked at: >>>> >>>> running: "C:/Inetpub/tpp-bin/XPressPeptideParser "interactasap.pep.xml" >>>> -m20 -a -nn,8.04437027 -nK,8.04437027 -H -c5" >>>> .................................................. 1k >>>> .................................................. 2k >>>> .................................................. 3k >>>> .................................................. 4k >>>> .................................................. 5k >>>> .................................................. 6k >>>> .................................................. 7k >>>> . >>>> command completed in 22 sec >>>> >>>> running: "C:/Inetpub/tpp-bin/ASAPRatioPeptideParser "interactasap.pep.xml" >>>> -lnK -C -r0.02" >>>> >>>> >>>> The same scenario as the one described in the old post seems to happen >>>> here, only one core and ~50MB usage of RAM, using only >>>> ASAPRatioPeptideParser.exe and this taking several hours to complete. >>>> >>>> Could it be also the mentioned "...redundant disk reads and base64 >>>> decoding due to poor caching of the scans read from mzXML..." the cause? Or >>>> it is just the nature of the data obtained with the Qexactive that makes it >>>> take longer? I haven't checked if something would change by using an old >>>> version of ASAPRatio ~2009 from that post. Though I don't think this would >>>> be compatible with the current parsers. >>>> >>>> Any clues? >>>> >>>> Thanks, >>>> >>>> Alejandro >>>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> To post to this group, send email to [email protected]. >>> Visit this group at http://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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