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Peptide identification in “shotgun” proteomics using tandem mass spectrometry: Comparison of search engine algorithms

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Abstract

High-throughput proteomics technologies are gaining popularity in different areas of life sciences. One of the main objectives of proteomics is characterization of the proteins in biological samples using liquid chromatography/mass spectrometry analysis of the corresponding proteolytic peptide mixtures. Both the complexity and the scale of experimental data obtained even from a single experimental run require specialized bioinformatic tools for automated data mining. One of the most important tools is a so-called proteomics search engine used for identification of proteins present in a sample by comparing experimental and theoretical tandem mass spectra. The latter are generated for the proteolytic peptides derived from a protein database. Peptide identifications obtained with the search engine are then scored according to the probability of a correct peptide-spectrum match. The purpose of this work was to perform a comparison of different search algorithms using data acquired for complex protein mixtures, including both annotated protein standards and clinical samples. The comparison was performed for three popular search engines: commercially available Mascot, as well as open-source X!Tandem and OMSSA. It was shown that the search engine OMSSA identifies in general a smaller number of proteins, while X!Tandem and Mascot deliver similar performance. We found no compelling reasons for using the commercial search engine instead of its open source competitor.

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Authors and Affiliations

  1. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninsky pr. 38, bld. 2, Moscow, 119334, Russia

    M. V. Ivanov, L. I. Levitsky, A. A. Lobas, I. A. Tarasova, M. L. Pridatchenko & M. V. Gorshkov

  2. Moscow Institute of Physics and Technology (State University), Institutskii per. 9, Dolgoprudny, Moscow region, 141700, Russia

    M. V. Ivanov, L. I. Levitsky, A. A. Lobas & M. V. Gorshkov

  3. Institute of Biomedical Chemistry, Pogodinskaya street 10, bld. 8, Moscow, 119121, Russia

    V. G. Zgoda & S. A. Moshkovskii

  4. Medical University of Vienna, Spitalgasse 23, Vienna, 1090, Austria

    G. Mitulovic

Authors
  1. M. V. Ivanov
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  2. L. I. Levitsky
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  3. A. A. Lobas
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  4. I. A. Tarasova
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  5. M. L. Pridatchenko
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  6. V. G. Zgoda
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  7. S. A. Moshkovskii
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  8. G. Mitulovic
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  9. M. V. Gorshkov
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Corresponding author

Correspondence to M. V. Gorshkov.

Additional information

Published in Mass-spektrometriya, 2015, Vol. 12, No. 1, pp. 39–45.

The article was translated by the authors.

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Ivanov, M.V., Levitsky, L.I., Lobas, A.A. et al. Peptide identification in “shotgun” proteomics using tandem mass spectrometry: Comparison of search engine algorithms. J Anal Chem 70, 1614–1619 (2015). https://doi.org/10.1134/S1061934815140075

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  • DOI: https://doi.org/10.1134/S1061934815140075

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