Can PeptideProphet be used with any algorithm?

[Amit Kumar Yadav]

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

[David Shteynberg]

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

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[Amit Kumar Yadav]

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 <dshteynb...@systemsbiology.org>
wrote:

[Amit Kumar Yadav]

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 <amit007thech...@gmail.com>