TPP:X!Tandem and the TPP
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| Revision as of 18:21, 28 June 2007 Jeng (Talk | contribs) (→What is the K-Score?) ← Previous diff |
Revision as of 18:43, 10 July 2007 Jtasman (Talk | contribs) (→current state) Next diff → |
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| *native Tandem is supposed to work with TPP, but results are quite bad | *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/Project/Published%20Experiments/Tandem%20Pluggable%20Scoring/begin.view? CPAS site]) will work much better | + | *using K-score plugin (included in TPP cygwin distrubtion: '''tandem version Apr-1-2007''' and '''k-score version Mar-27-2007''', also avaliable from [https://proteomics.fhcrc.org/CPAS/Project/Published%20Experiments/Tandem%20Pluggable%20Scoring/begin.view? 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. | * 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. | ||
Revision as of 18:43, 10 July 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?
The k-score is a Tandem score plug-in implementing the COMET score function as described in this Keller et al. manuscript. Effectively the k-score is a dot product (which breaks down to summing up matched peak intensities) after significant intensity manipulation of the query spectrum as described in the manuscript. You can access the k-score plug-in as well as documentation on the general Tandem pluggable scoring API here.
To use the k-score plug-in, these three Tandem parameters should be set as follows:
<note label="scoring, algorithm" type="input">k-score</note> <note label="spectrum, use conditioning" type="input">no</note> <note label="scoring, minimum ion count" type="input">1</note>
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: tandem version Apr-1-2007 and k-score version Mar-27-2007, 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
Please see warnings in "current status" section above.
Tandem2XML is used to convert Tandem results into pepXML. Please see that page for instructions.
