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 < > [email protected] <javascript:>> 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] <javascript:>. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> 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.
