Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book

Rovshan G. Sadygov, Daniel Cociorva, John R. Yates

Research output: Contribution to journalReview article

299 Scopus citations


Database searching is an essential element of large-scale proteomics. Because these methods are widely used, it is important to understand the rationale of the algorithms. Most algorithms are based on concepts first developed in SEQUEST and PeptideSearch. Four basic approaches are used to determine a match between a spectrum and sequence: Descriptive, interpretative, stochastic and probability–based matching. We review the basic concepts used by most search algorithms, the computational modeling of peptide identification and current challenges and limitations of this approach for protein identification.

Original languageEnglish (US)
Pages (from-to)195-202
Number of pages8
JournalNature Methods
Issue number3
StatePublished - Dec 2004
Externally publishedYes


ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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