TPP:X!Tandem and the TPP
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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. The pluggable scoring framework and this specific score plug-in was implemented by Brendan MacLean of LabKey Software working with the McIntosh group at the Fred Hutch Cancer Research Center.
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>
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, important for the quantitation tools, when searching mzXML files directly:
<note type="input" label="output, spectra">yes</note>
This parameter is not k-score specific but applies to native Tandem as well.
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 performance appears worse than other search engines in datasets that we've tested
- 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) performs better in a few datasets that we've tested
- 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.
X!Tandem default modifications
Tandem applies default variable modifications to every search:
If a peptide has an N-terminal Q or E, it will spontaneously eliminate -17 Da (-NH3) or -18 (-OH) respectively, to form an N-terminal pyrolidone carboxylic acid. If the N-terminal residue is C and it has been modified by iodoacetimide, it also has an analogous reaction (-17, -NH3). Because they are rather special (they always occur to some degree), they are the only potential modifications that are built into X! Tandem.
