TPP:X!Tandem and the TPP

From SPCTools

(Difference between revisions)
Jump to: navigation, search
Revision as of 17:58, 22 June 2007
Jtasman (Talk | contribs)
(Using X!Tandem and the TPP)
← Previous diff
Revision as of 18:01, 22 June 2007
Jtasman (Talk | contribs)
(Using X!Tandem and the TPP)
Next diff →
Line 5: Line 5:
==Using X!Tandem and the TPP== ==Using X!Tandem and the TPP==
-This page is intended to give instructions for various ways of working with X!Tandem and the TPP. Currently, we continue to refine the PeptideProphet models for X!Tandem-Kscore. While X!Tandem data will run through the pipeline without error, results are non-optimal. Also, we do not yet support X!Tandem in the GUI.+This page is intended to give instructions for various ways of working with X!Tandem and the TPP. Currently, we continue to refine the PeptideProphet models for X!Tandem-Kscore.
 + 
 +===current state===
 +While X!Tandem data will run through the pipeline without error, results are non-optimal. Also, we do not yet support X!Tandem in the GUI.
 + 
 +*native Tandem is supposed to work with TPP, but results are quite bad
 +*using K-score plugin (included in TPP cygwin distrubtion, also avaliable from [https://proteomics.fhcrc.org/CPAS/announcements/Published%20Experiments/Tandem%20Pluggable%20Scoring/thread.view?rowId=1885 CPAS site] will work much better
 +* proceed at your own risk if they use the more sophisticated Tandem features (e.g. some refinement options) because PeptideProphet may not work with them.
==Running X!Tandem== ==Running X!Tandem==

Revision as of 18:01, 22 June 2007

Contents

What is X!Tandem?

X!Tandem is an open-source (and free) search engine, developed by the GPM.

What is the K-Score?

Using X!Tandem and the TPP

This page is intended to give instructions for various ways of working with X!Tandem and the TPP. Currently, we continue to refine the PeptideProphet models for X!Tandem-Kscore.

current state

While X!Tandem data will run through the pipeline without error, results are non-optimal. Also, we do not yet support X!Tandem in the GUI.

  • native Tandem is supposed to work with TPP, but results are quite bad
  • using K-score plugin (included in TPP cygwin distrubtion, also avaliable from CPAS site will work much better
  • proceed at your own risk if they use the more sophisticated Tandem features (e.g. some refinement options) because PeptideProphet may not work with them.

Running X!Tandem

Someone could contribute info on setting up the params file for Tandem here..

Converting X!Tandem data for the TPP

How to run Tandem2XML, issues with PeptideProphet modeling, etc...

Personal tools