Abstract
Protein identification from tandem mass spectra is one of the most versatile and widely used proteomics workflows, able to identify proteins, characterize post-translational modifications, and provide semi-quantitative measurements of relative protein abundance. This manuscript describes the concepts, prerequisites, and methods required to analyze a tandem mass spectrometry dataset in order to identify its proteins, by using a tandem mass spectrometry search engine to search protein sequence databases. The discussion includes instructions for extraction, preparation, and formatting of spectral datafiles; selection of appropriate search parameter settings; and basic interpretation of the results.
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Acknowledgments
The preparation of this manuscript was supported, in part, by CPTI Grant R01 CA126189.
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Edwards, N.J. (2011). Protein Identification from Tandem Mass Spectra by Database Searching. In: Wu, C., Chen, C. (eds) Bioinformatics for Comparative Proteomics. Methods in Molecular Biology, vol 694. Humana Press. https://doi.org/10.1007/978-1-60761-977-2_9
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DOI: https://doi.org/10.1007/978-1-60761-977-2_9
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