X!Tandem is an open-source search engine that matches tandem mass spectra with peptide sequences. LabKey Server uses X!Tandem to search an mzXML file against a FASTA database and displays the results in the MS2 viewer for analysis.

Modifying X!Tandem Settings in LabKey Server

For many applications, the X!Tandem default settings used by LabKey Server are likely to be adequate, so you may not need to change them. If you do wish to override some of the default settings, you can do so in one of two ways:

• You can modify the default X!Tandem parameters for the pipeline, which will set the defaults for every search protocol defined for data files in the pipeline (see Set Up the LabKey Pipeline Root).
• You can override the default X!Tandem parameters for an individual search protocol (see Search and Process MS/MS Data).

Note: When you create a new search protocol for a given data file or set of files, you can override the default parameters. In LabKey Server, the default parameters are defined in a file named default_input.xml file, at the pipeline root. You can modify the default parameters for the pipeline during the pipeline setup process, or you can accept the installed defaults. If you are modifying search protocol parameters for a specific protocol, the parameter definitions in the XML block on the search page are merged with the defaults at runtime.

If you're just getting started with LabKey Server, the installed search engine defaults should be sufficient to meet your needs until you're more familiar with the system.

X!Tandem Search Parameters

See the section entitled "Search Parameter Syntax" under Search and Process MS2 Data for general information on parameter syntax. Most X!Tandem parameters are defined in the X!Tandem documentation, available here:

http://www.thegpm.org/TANDEM/api/index.html

LabKey Server provides additional parameters for X!Tandem for working with the data pipeline and for performing quantitation. For further details, please see: Configure Common Parameters.

Selecting a Scoring Technique

X!Tandem supports pluggable scoring implementations. You can choose a scoring implementation with this parameter:

<note label="scoring, algorithm" type="input">k-score</note>

Examples of Commonly Modified Parameters

As you become more familiar with LabKey Server and X!Tandem, you may wish to override the default X!Tandem parameters to hone your search more finely. Note that the X!Tandem default values provide good results for most purposes, so it's not necessary to override them unless you have a specific purpose for doing so.

The get started tutorial overrides some of the default X!Tandem parameters to demonstrate how to change certain ones. The override values are stored with the tutorial's ready-made search protocol, and appear as follows:

<?xml version="1.0" encoding="UTF-8"?>
<bioml>
 <!-- Override default parameters here. -->
 <note label="spectrum, parent monoisotopic mass error minus" type="input">2.1</note>
 <note label="spectrum, fragment mass type" type="input">average</note>
 <note label="residue, modification mass" type="input">227.2@C</note>
 <note label="residue, potential modification mass" type="input">16.0@M,9.0@C</note>
 <note label="pipeline quantitation, residue label mass" type="input">9.0@C</note>
 <note label="pipeline quantitation, algorithm" type="input">xpress</note>
</bioml>

Taking each parameter in turn:

• spectrum, parent monoisotopic mass error minus: The default is 2.0; 2.1 is specified here to allow for the mass spectrometer being off by two peaks in its pick of the precursor parent peak in the first MS phase.
• spectrum, fragment mass type: The default value is "monoisotopic"; "average" specifies that a weighted average is used to calculate the masses of the fragment ions in a tandem mass spectrum.
• residue, modification mass: A comma-separated list of fixed modifications.
• residue, potential modification mass: A comma-separated list of variable modification.
• pipeline quantitation, residue label mass: Specifies that quantitation is to be performed.
• pipeline quantitation, algorithm: Specifies that XPRESS should be used for quantitation.