Hello Vidya, Currently, there is no support for Morpheus in the TPP. If you are able to place you search results in a shared drive and send me a link for testing, I should be able to add the Morpheus support back in.
Thanks, -Davod On Sat, Jun 23, 2018 at 3:25 PM, Vidya Venkatraman <vidya.venk...@gmail.com> wrote: > Hi David, > > I am using TPP v5.1.0 and when i try to run xinteract on the Morpheus > pep.xml, I get the following error that engine Morpheus not recognized. Any > ideas if I am missing something? > > xinteract (TPP v5.1.0 Syzygy, Build 201806211802-exported (Linux-x86_64)) > > running: "/hpc/apps/TPP/5.1.0/bin/InteractParser > 'interact.morpheus.pep.xml' '2017-12-4_ABRF_200_DDA1.pep.xml' -L'7'" > file 1: 2017-12-4_ABRF_200_DDA1.pep.xml > processed altogether 72135 results > command completed in 9 sec > > running: "/hpc/apps/TPP/5.1.0/bin/DatabaseParser > 'interact.morpheus.pep.xml'" > command completed in 1 sec > > running: "/hpc/apps/TPP/5.1.0/bin/RefreshParser > 'interact.morpheus.pep.xml' '/common/venkatramanv/Data/ > Pratik/Thermo/DDA/raw/PRG2016_DECOY.fasta'" > > - Searching the tree... > - Linking duplicate entries... > - Printing results... > > command completed in 15 sec > > running: "/hpc/apps/TPP/5.1.0/bin/PeptideProphetParser > 'interact.morpheus.pep.xml' ACCMASS RT NONPARAM DECOYPROBS DECOY=DECOY_" > using Accurate Mass Bins > using RT > Using Decoy Label "DECOY_". > Decoy Probabilities will be reported. > Using non-parametric distributions > (Morpheus) > error: engine Morpheus not recognized > > command "/hpc/apps/TPP/5.1.0/bin/PeptideProphetParser > 'interact.morpheus.pep.xml' ACCMASS RT NONPARAM DECOYPROBS DECOY=DECOY_" > exited with non-zero exit code: 256 > QUIT - the job is incomplete > > Thanks > Vidya > > On Friday, February 7, 2014 at 12:22:54 PM UTC-8, David Shteynberg wrote: >> >> 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 < >> david.t...@utsouthwestern.edu> 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 < >>>>>> edeu...@systemsbiology.org> wrote: >>>>>> >>>>>>> Hi Dave, at ISB we are not planning this, so please go ahead and let >>>>>>> us know how it goes! >>>>>>> >>>>>>> >>>>>>> >>>>>>> Regards, >>>>>>> >>>>>>> Eric >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> *From:* spctools...@googlegroups.com [mailto:spctools...@googlegrou >>>>>>> ps.com] *On Behalf Of *Dave Trudgian >>>>>>> >>>>>>> *Sent:* Thursday, February 06, 2014 12:02 PM >>>>>>> *To:* spctools...@googlegroups.com >>>>>>> >>>>>>> *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 spctools-discu...@googlegroups.com. >>>>>>> To post to this group, send email to spctools...@googlegroups.com. >>>>>>> >>>>>>> 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 spctools-discu...@googlegroups.com. >>>>>>> To post to this group, send email to spctools...@googlegroups.com. >>>>>>> >>>>>>> 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 spctools-discu...@googlegroups.com. >>>>> To post to this group, send email to spctools...@googlegroups.com. >>>>> 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 spctools-discu...@googlegroups.com. >>> To post to this group, send email to spctools...@googlegroups.com. >>> 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 spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at https://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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