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Interpretation of Tandem Mass Spectra of Posttranslationally Modified Peptides

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Mass Spectrometry Data Analysis in Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1007))

Abstract

Tandem mass spectrometry provides a sensitive means of analyzing the amino acid sequence of peptides and modified peptides by providing accurate mass measurements of precursor and fragment ions. Modern mass spectrometry instrumentation is capable of rapidly generating many thousands of tandem mass spectra and protein database search engines have been developed to match the experimental data to peptide candidates. In most studies there is a schism between discarding perfectly valid data and including nonsensical peptide identifications—this is currently a major bottleneck in data-analysis and it calls for an understanding of tandem mass spectrometry data. Manual evaluation of the data and perhaps experimental cross-checking of the MS data can save many months of experimental work trying to do biological follow-ups based on erroneous identifications. Especially for posttranslationally modified peptides there is a need for manual validation of the data because search algorithms seldom have been optimized for the identification of modified peptides and because there are many pitfalls for the unwary. This chapter describes some of the issues that should be considered when interpreting and validating tandem mass spectra and gives some useful tables to aid this process.

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Acknowledgments

J. B. gratefully acknowledges financial support from the Carlsberg foundation and the Lundbeck foundation. RM is supported by Fundação para a Ciência e a Tecnologia (FCT) Ciência 2007. R.M. is further supported by FCT grants (PTDC/QUI-BIQ/099457/2008 and PTDC/EIA-EIA/099458/2008).

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark

    Jakob Bunkenborg

  2. Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal

    Rune Matthiesen

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  1. Jakob Bunkenborg
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  2. Rune Matthiesen
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Editors and Affiliations

  1. Inst. Molecular Pathology & Immunology, Universidade do Porto Inst. Molecular Pathology & Immunology, Porto, Portugal

    Rune Matthiesen

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Bunkenborg, J., Matthiesen, R. (2013). Interpretation of Tandem Mass Spectra of Posttranslationally Modified Peptides. In: Matthiesen, R. (eds) Mass Spectrometry Data Analysis in Proteomics. Methods in Molecular Biology, vol 1007. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-392-3_6

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  • DOI: https://doi.org/10.1007/978-1-62703-392-3_6

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-391-6

  • Online ISBN: 978-1-62703-392-3

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