Hi, I wanted to know if i need to report only the peptide scores or scores with p-and/e-value.
On Dec 2, 12:18 pm, Amit Kumar Yadav <[email protected]> wrote: > I have never used TPP before, though i have known about it. > I am not using any software on a regular basis. I just use them for > benchmarking my own algorithm. > > Now, I am trying out the PETUNIA gui. > The executables for file format conversions look easier to me. > Never used the pepXML format as well. > > So, I will have to read on the pepXML format first. > > Do i need to provide scores for :-- > (1). Peptide spectrum match (PSM scores for peptide-centric > identification) OR > (2). Protein scores derived on PSMs above? (We don't have protein > centric scores-our protein assignments are based on at least one high > scoring PSM) > > Looking forward to using peptideprophet. > > On Dec 2, 12:52 am, David Shteynberg <[email protected]> > wrote: > > > > > Hi, > > > If your search algorithm or scoring can be reported in pepXML format > > we can extend the TPP quite easily to integrate your algorithm. > > Please send such a pepXML file and the search scores that are > > appropriate and we will work with you to resolve any pepXML issues you > > might have and retool the TPP to process your data. > > > -David > > > On Tue, Dec 1, 2009 at 2:46 AM, Amit Kumar Yadav > > > <[email protected]> wrote: > > > Hi, > > > > Can we use Peptide Prophet with any algorithm for which we have the > > > APIs? > > > > We have developed a new scoring algorithm. Can we use Peptide Prophet > > > with it? > > > If yes, how? What do we need to do so as to incorporate it. > > > > Please give details. > > > > Thanks in advance- > > > AKY > > > > -- > > > > You received this message because you are subscribed to the Google Groups > > > "spctools-discuss" group. > > > To post to this group, send email to [email protected]. > > > To unsubscribe from this group, send email to > > > [email protected]. > > > For more options, visit this group > > > athttp://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
