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Proteomics pp 261–288Cite as

Shotgun Protein Identification and Quantification by Mass Spectrometry

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Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 564))

Summary

Shotgun proteomics is based on identification and quantification of peptides from digested proteins using tandem mass spectrometry. In this chapter, we discuss computational methods to analyze tandem mass spectra of peptides, including database searching, de novo peptide sequencing, hybrid approaches, library searching, and unrestricted modification search. A special focus is given to database searching programs since they are most widely used. The process of inferring proteins from identified peptides is then discussed. We also provide description of key steps in the quantitative analysis of mass spectrometry proteomics data.

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Authors and Affiliations

  1. Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA

    Bingwen Lu, Tao Xu, Sung Kyu Park & John R. Yates III

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  1. Bingwen Lu
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  2. Tao Xu
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    Lu, B., Xu, T., Park, S.K., Yates, J.R. (2009). Shotgun Protein Identification and Quantification by Mass Spectrometry. In: Reinders, J., Sickmann, A. (eds) Proteomics. Methods in Molecular Biology™, vol 564. Humana Press. https://doi.org/10.1007/978-1-60761-157-8_15

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