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.
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.
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 BioWorks software package by Thermo 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, corrected z-ion calculation (z-radical) for ETD spectra, and linking to Mike Hoopmann's MSToolkit to support multiple input formats such as compressed ms2 and mzXML (via TPP's RAMP parser). The core algorithms in SEQUEST have also been reimplemented in the Crux program which is available for download from the Noble lab link below.
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Links
- Thermo Scientific BioWorks
- Sage-N Research's SEQUEST Sorcerer
- SEQUEST info at Scripps
- Wikipedia page
- Crux page, publication
- UW sequest.params page
- UW sequest commands page
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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.