Modifying Sequest Settings in LabKey Server

Sequest settings are based on the sequest.params file (See your Sequest documentation). For many applications, the Sequest 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 Sequest parameters for the pipeline, which will set the defaults for every search protocol defined for data files in the pipeline (see Set the LabKey Pipeline Root).
• You can override the default Sequest parameters for an individual search protocol (see Search and Process MS/MS Data).

Sequest takes parameters specified in XML format. In LabKey Server, the default parameters are defined in a file named sequest_default.input.xml, at the pipeline root. When you create a new search protocol for a given data file or set of files, you can override the default parameters. Each search protocol has a corresponding Sequest Sequest analysis definition file, and any parameters that you override are stored in the file, named sequest.xml by default.

Note: If you are modifying a sequest.xml file by hand, you don't need to copy parameter values from the sequest_default_input.xml file. The parameters definitions in these files are merged by LabKey Server at runtime.

Using X!Tandem Syntax for Sequest Parameters

You don't have to be knowledgeable about XML to modify Sequest parameters in LabKey Server. You only need to find the parameter that you need to change, determine the value want to set it to, and paste the correct line into the Sequest XML section when you create your MS2 search protocol.

When possible the Sequest parameters will use the same tags already defined for X!Tandem. Most X!Tandem tags are defined in the X!Tandem documentation, available here:

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

As you'll see in the X!Tandem documentation, the general format for a parameter is as follows:

   <note type="input" label="GROUP, NAME">VALUE</note>

For example, in the following entry, the parameter group is residue, and the parameter name is modification mass. The value given for the modification mass is 227.2 daltons at cysteine residues.

   <note type="residue, modification mass">227.2@C</note>

LabKey Server provides additional parameters for Sequest where X!Tandem does not have an equivlent parameter, for working with the data pipeline and for performing quantitation, described in the following sections.

The Sequest parameters the you see in a standard sequest.params file are defined here: