SEQUEST®

SEQUEST is a tandem mass spectrometry database search program originally developed in 1993 in the Yates lab at the University of Washington. It correlates tandem mass spectra of peptides against peptide sequences from a sequence database.

NOTE: UW SEQUEST is no longer being supported. The open source version of this tool is named Comet.

Classical SEQUEST applies a two-stage scoring method for each search. The first stage applies the preliminary score to filter through all candidate peptides in the sequence database. The best scoring candidate peptides are then re-scored using the cross correlation algorithm. The sensitivity of the cross correlation algorithm is enhanced by the correction factor that is applied in its calculation. As of April 2012 in the 2012.01.0 release of UW SEQUEST, the cross correlation score is now the primary score function and is applied to all candidate peptides; the preliminary score is still computed at the end of the search for the top hits for pseudo backwards compatibility.

There currently exists a few variants of SEQUEST. The primary version that most researchers will have acccess to is that which is supplied as part of the Proteome Discoverer (formerly BioWorks) software package by Thermo Fischer Scientific. That version includes enhancements such as a probability-based score as well as a custom interface that Thermo distributes. Sage-N Research has implemented a high throughput version of SEQUEST in their Sorcerer appliance; their version also contains many unique features specific to their tool. The Yates lab at Scripps has a version that was modified to support their ms2/sqt input and output formats. And the University of Washington proteomics community currently uses a version of the tool that we have applied our own enhancements to including E-value statistics, threading, and linking to Mike Hoopmann's MSToolkit for direct support for multiple input formats such as compressed ms2 and mzXML. The core algorithms in SEQUEST have also been reimplemented in the Crux program from the Noble lab.

    Selected SEQUEST publications
  • "An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database". Eng JK, McCormack AL, and Yates JR III. J Am Soc Mass Spectrom 5: 976–989. 1994. link
  • "Direct database searching with MALDI-PSD spectra of peptides". Griffin PR, MacCoss MJ, Eng JK, Blevins RA, Aaronson JS, Yates JR III. Rapid Communications in Mass Spectrometry, 9(15):1546-51. 1995. link
  • "Search of Sequence Databases with Uninterpreted High-Energy Collision-Induced Dissociation Spectra of Peptides". Yates JR III, Eng JK, Clauser KR, and Burlingame AL. J Am Soc Mass Spectrom 7: 1089-1098. 1996. link
  • "A Fast SEQUEST Cross Correlation Algorithm". Eng, JK, Fischer B, Grossmann J, MacCoss MJ. J. Proteome Res., 2008. link

SEQUEST® is a registered trademark of the University of Washington.