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

Nature Methods volume 1, pages 195–202 (2004)Cite this article

Abstract

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.

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Figure 1: Overview of the protein identification process.
Figure 2: Simplified representation of an MS/MS spectrum for the peptid e IYEVEGMR.

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Acknowledgements

The authors would like to acknowledge funding from the US National Institutes of Health (R01 MH067880, DK067598-01, ES012021 and RR11823-09).

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Authors and Affiliations

  1. Department of Cell Biology, The Scripps Research Institute, La Jolla, 92037, California, USA

    Rovshan G Sadygov, Daniel Cociorva & John R Yates III

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  1. Rovshan G Sadygov
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  2. Daniel Cociorva
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  3. John R Yates III
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Correspondence to John R Yates III.

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Competing interests

J.R.Y. is an inventor on the SEQUEST patent owned by the University of Washington and licenced by the University to a commercial company.

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Sadygov, R., Cociorva, D. & Yates, J. Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book. Nat Methods 1, 195–202 (2004). https://doi.org/10.1038/nmeth725

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