I was able to make a first stab attempt at it and I was successful after minor modification to the way spectrum_names are encoded in spectrum_query tags in the morpheus pepXML files. After running a simple sed to replace the names with something that wouldn't overlap with anoth file when combined by using the each run's basename I was able to generate results.
My PeptideProphet processed analysis for these two searches can be downloaded here: https://www.dropbox.com/s/f5r8j5yj2p2r3b8/morpheus_interact.tgz Here are my sed commands, but I hope this could be fixed within morpheus. sed -i 's/controllerType=0 controllerNumber=1 scan=[0-9]*/OR20080317_S_SILAC-LH_1-1_01/g' OR20080317_S_SILAC-LH_1-1_01.pep.xml sed -i 's/controllerType=0 controllerNumber=1 scan=[0-9]*/OR20080320_S_SILAC-LH_1-1_11/g' OR20080320_S_SILAC-LH_1-1_11.pep.xml Cheers, -David P.S. I expect to merge this into the SVN codebase sooner than later. On Fri, Feb 7, 2014 at 8:35 AM, Dave Trudgian < [email protected]> wrote: > David, > > That's the same data. I've made PepXML and the other Morpheus output > available at: > > https://proteomics.swmed.edu/data/morpheus_tpp/ > > DT > > > On Thursday, February 6, 2014 5:36:35 PM UTC-6, David Shteynberg wrote: > >> I was referring to this data: >> >> http://tools.proteomecenter.org/wiki/index.php?title=TPP_Tutorial_v2 >> >> However, this is not high res MS/MS either. This would be a good >> starting point. The decoys and targets don't have to separate by score >> alone, PeptideProphet should be able to model the plots you show in either >> case. >> >> Cheers, >> -David >> >> >> On Thu, Feb 6, 2014 at 3:13 PM, Dave Trudgian <david.t...@ >> utsouthwestern.edu> wrote: >> >>> Hi David, >>> >>> Am happy to generate some pepXMLs from the tutorial data, but assuming >>> you mean the stuff at: >>> >>> ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/TPP_Demo2009/ >>> >>> ... I'm not sure that's the best to work with for Morpheus. It's CID >>> Ion-trap MS/MS, which is not Morpheus' target. Morpheus doesn't work as >>> well as other algorithms on low-res MS/MS so I'm not sure if anyone would >>> want to use it like that. >>> >>> I grabbed two of the result sets from the Coon lab site - Yeast analysis >>> with FT HCD or IT CID. The distributions of Morpheus scores are very >>> different. The CID data doesn't even look like target and decoy matches are >>> separable, so I think high-res MS/MS is a must. See attached. >>> >>> DT >>> >>> >>> On Thursday, February 6, 2014 3:44:08 PM UTC-6, David Shteynberg wrote: >>> >>>> I was dabbling in this, but running into some issues with morpheus >>>> slowing my machine to a point where I was unable to do any other work so I >>>> moved to another project. However, I am certainly still interested in >>>> this, but I know that pepXML coming out of morpheus may need some work. If >>>> you'd be willing to generate some pepXML's from the tutorial data and work >>>> with me to correct the pepXML issues I should be able to model the results >>>> quite quickly with PeptideProphet. Please let me know if that sounds good >>>> to you. >>>> >>>> Cheers, >>>> -David >>>> >>>> >>>> On Thu, Feb 6, 2014 at 12:08 PM, Eric Deutsch < >>>> [email protected]> wrote: >>>> >>>>> Hi Dave, at ISB we are not planning this, so please go ahead and let >>>>> us know how it goes! >>>>> >>>>> >>>>> >>>>> Regards, >>>>> >>>>> Eric >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> *From:* [email protected] [mailto:spctools...@googlegrou >>>>> ps.com] *On Behalf Of *Dave Trudgian >>>>> >>>>> *Sent:* Thursday, February 06, 2014 12:02 PM >>>>> *To:* [email protected] >>>>> >>>>> *Subject:* [spctools-discuss] Re: support for Morpheus search >>>>> algorithm in TPP >>>>> >>>>> >>>>> >>>>> Craig, just wondering if you or anyone else is working on this? If not >>>>> I was thinking I would have a go at putting in a Morpheus model for >>>>> PeptideProphet towards the end of next week. >>>>> >>>>> >>>>> >>>>> Dave Trudgian >>>>> >>>>> On Saturday, November 30, 2013 4:37:30 PM UTC-6, Craig Wenger wrote: >>>>> >>>>> Is there a mechanism for adding support for a new search algorithm to >>>>> the various TPP tools? A few users have requested TPP compatibility for >>>>> the >>>>> Morpheus <http://morpheus-ms.sourceforge.net/> search algorithm. It >>>>> already outputs pepXML. >>>>> >>>>> >>>>> >>>>> -Craig >>>>> >>>>> >>>>> >>>>> -- >>>>> 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/groups/opt_out. >>>>> >>>>> -- >>>>> 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/groups/opt_out. >>>>> >>>> >>>> -- >>> 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/groups/opt_out. >>> >> >> -- > 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/groups/opt_out. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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