As you become more familiar with LabKey proteomics tools and Sequest, you may wish to override the default Sequest parameters to hone your search more finely. Note that the Sequest 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. Below are the override values to use if sequest is the search engine:

<?xml version="1.0" encoding="UTF-8"?>
<bioml>
 <!-- Override default parameters here. -->
<note label="spectrum, parent monoisotopic mass error plus" type="input">2.1</note>
 <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. Sequest requires a symetric value so bothe plus and minus must be set to the same value.
  • 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 the residue and weight difference for quantitation.
  • Specifies that quantitation is to be performed (using XPRESS).  

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