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]> 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.
