TPP:X!Tandem and the TPP
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| ==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...
