Hello Vidya, I have added the support of Morpheus into the TPP codebase. Please let me know which OS (windows or linux) you are processing on so I can provide you with an executable that you should be able to use.
Thanks, -David On Mon, Jun 25, 2018 at 1:09 PM, Vidya Venkatraman <[email protected]> wrote: > 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 <David.Shteynberg@ > systemsbiology.org> 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...@ >>>>>>>>> googlegroups.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/to >> pic/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. > 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 the Google Groups "spctools-discuss" group. 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