I am using Linux. Do i need to compile it again? Regards
On Tue, Jul 10, 2018 at 12:07 PM, David Shteynberg < [email protected]> wrote: > 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 < >> [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_D >>>>>>>> emo2009/ >>>>>>>> >>>>>>>> ... 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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