I just shared a box folder with you which contains mzML, fasta and the pepxml file.
https://cedars.app.box.com/folder/50657299852 Regards Vidya On Mon, Jun 25, 2018 at 9:41 AM, David Shteynberg < [email protected]> wrote: > 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 < > [email protected]> 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/Pra >> tik/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 < >>> [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. >> 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 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 a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit https://groups.google.com/d/ > topic/spctools-discuss/qdmov2KGlJE/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > [email protected]. > To post to this group, send email to [email protected]. > 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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