TPP:Sequest and the TPP

From SPCTools

What is Sequest?

Sequest is a commercial, closed-source search engine, originally developed in 1993 by Jimmy Eng at the J. Yates lab, University of Washington. Thermo Electron Corporation now holds the license and resells it as part of the Bioworks system.

Using Sequest and the TPP

This page is intended to give instructions for various ways of working with Sequest and the TPP. For example, someone could write instructions for working with the GUI, with Bioworks, on the command-line, etc.

0.0 fragment ion tolerance description

A fragment ion tolerance of 0.0 in the historical versions of SEQUEST corresponds to a tolerance of ~0.5 Da due to the unit mass binning that SEQUEST applies to the input spectra. This could possibly be different in more recent versions of Bioworks SEQUEST.

SEQUEST classically has rounded peaks to the nearest integer m/z for internal processing. Because of this rounding, rounded theoretical fragment ions are compared against rounded acquired peaks. Therefore this rounding imparts an inherent fragment tolerance to the calculation. When the fragment ion tolerance is set to 0.0, peaks are compared against each other within a single rounded m/z bin. The actual tolerance in this case will vary depending on the rounding but could be as extreme as just under 1 Da. When a non-zero value is specified for the fragment ion tolerance, the peak comparison possibly spans more than a single m/z bin. As the fragment ion tolerance only affects the preliminary score and has no affect whatsoever on the final cross correlation score in SEQUEST, differences in this fragment ion tolerance setting actually has minimal effect on the resulting identifications.

More details in this ABRF post: http://www.abrf.org/index.cfm/list.msg/55764?listName=abrf&expand=55764&brSort=thread&LF=1&urlStr=#55764