TPP:X!Tandem and the TPP
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| <note label="spectrum, use conditioning" type="input">no</note> | <note label="spectrum, use conditioning" type="input">no</note> | ||
| <note label="scoring, minimum ion count" type="input">1</note> | <note label="scoring, minimum ion count" type="input">1</note> | ||
| + | |||
| + | Additionally, also set the following Tandem parameter which allows Tandem2XML (a Tandem to pepXML converter) to correctly assign scan numbers to the pepXML scan attributes when searching mzXML files directly: | ||
| <note type="input" label="output, spectra">yes</note> | <note type="input" label="output, spectra">yes</note> | ||
Revision as of 17:26, 24 September 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 four 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>
Additionally, also set the following Tandem parameter which allows Tandem2XML (a Tandem to pepXML converter) to correctly assign scan numbers to the pepXML scan attributes when searching mzXML files directly:
<note type="input" label="output, spectra">yes</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.
