SEQUEST
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SEQUEST is a popular tandem mass spectrometry data analysis program. Sequest identifies collections of tandem mass spectra to peptide sequences that have been generated from databases of protein sequences.
This tool is most useful in the context of shotgun proteomics. Starting with a complex mixture of proteins, this strategy typically employs trypsin to digest proteins. These peptides are separated by liquid chromatography en route to a tandem mass spectrometer. The mass spectrometer then isolates ions of a particular peptide, subjects them to collision-induced dissociation, and records the produced fragments in a tandem mass spectrum. This process, repeated for several hours, will produce thousands of tandem mass spectra. Identifying such a data collection requires automation, and Sequest was the first software to fill that need.
Sequest identifies each tandem mass spectrum individually. The software evaluates protein sequences from a database to compute the list of peptides that could result from each. The peptide's intact mass is known from the mass spectrum, and Sequest uses this information to determine the set of candidate peptides sequences that could meaningfully be compared to the spectrum by including only those which are near the mass of the observed peptide ion. For each candidate peptide, Sequest projects a theoretical tandem mass spectrum, and Sequest compares these theoretical spectra to the observed tandem mass spectrum by the use of cross correlation. The candidate sequence with the best matching theoretical tandem mass spectrum is reported as the best identification for this spectrum.
Matrix Science produces an algorithm called "Mascot" that performs this operation through a statistical evaluation of matches between observed and projected peptide fragments rather than cross correlation.
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