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Anatomy and evolution of database search engines : a central component of mass spectrometry based proteomic workflows

(2020) MASS SPECTROMETRY REVIEWS. 39(3). p.292-306
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Abstract
Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass spectrometry, have provided scientists with more than 30 published search engines, each with its own properties. In this review, we present the common paradigm behind the different implementations, and its limitations for modern mass spectrometry datasets. We also detail how the search engines attempt to alleviate these limitations, and provide an overview of the different software frameworks available to the researcher. Finally, we highlight alternative approaches for the identification of proteomic mass spectrometry datasets, either as a replacement for, or as a complement to, sequence database search engines.
Keywords
bioinformatics, proteomics, search engine, PEPTIDE IDENTIFICATION, PROTEIN IDENTIFICATION, SHOTGUN PROTEOMICS, SEQUENCE DATABASE, IMPROVING SENSITIVITY, METAPROTEOMICS DATA, IDENTIFY PEPTIDES, MS/MS SPECTRA, TANDEM, ALGORITHM

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MLA
Verheggen, Kenneth, et al. “Anatomy and Evolution of Database Search Engines : A Central Component of Mass Spectrometry Based Proteomic Workflows.” MASS SPECTROMETRY REVIEWS, vol. 39, no. 3, 2020, pp. 292–306, doi:10.1002/mas.21543.
APA
Verheggen, K., Raeder, H., Berven, F. S., Martens, L., Barsnes, H., & Vaudel, M. (2020). Anatomy and evolution of database search engines : a central component of mass spectrometry based proteomic workflows. MASS SPECTROMETRY REVIEWS, 39(3), 292–306. https://doi.org/10.1002/mas.21543
Chicago author-date
Verheggen, Kenneth, Helge Raeder, Frode S Berven, Lennart Martens, Harald Barsnes, and Marc Vaudel. 2020. “Anatomy and Evolution of Database Search Engines : A Central Component of Mass Spectrometry Based Proteomic Workflows.” MASS SPECTROMETRY REVIEWS 39 (3): 292–306. https://doi.org/10.1002/mas.21543.
Chicago author-date (all authors)
Verheggen, Kenneth, Helge Raeder, Frode S Berven, Lennart Martens, Harald Barsnes, and Marc Vaudel. 2020. “Anatomy and Evolution of Database Search Engines : A Central Component of Mass Spectrometry Based Proteomic Workflows.” MASS SPECTROMETRY REVIEWS 39 (3): 292–306. doi:10.1002/mas.21543.
Vancouver
1.
Verheggen K, Raeder H, Berven FS, Martens L, Barsnes H, Vaudel M. Anatomy and evolution of database search engines : a central component of mass spectrometry based proteomic workflows. MASS SPECTROMETRY REVIEWS. 2020;39(3):292–306.
IEEE
[1]
K. Verheggen, H. Raeder, F. S. Berven, L. Martens, H. Barsnes, and M. Vaudel, “Anatomy and evolution of database search engines : a central component of mass spectrometry based proteomic workflows,” MASS SPECTROMETRY REVIEWS, vol. 39, no. 3, pp. 292–306, 2020.
@article{8546734,
  abstract     = {{Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass spectrometry, have provided scientists with more than 30 published search engines, each with its own properties. In this review, we present the common paradigm behind the different implementations, and its limitations for modern mass spectrometry datasets. We also detail how the search engines attempt to alleviate these limitations, and provide an overview of the different software frameworks available to the researcher. Finally, we highlight alternative approaches for the identification of proteomic mass spectrometry datasets, either as a replacement for, or as a complement to, sequence database search engines.}},
  author       = {{Verheggen, Kenneth and Raeder, Helge and Berven, Frode S and Martens, Lennart and Barsnes, Harald and Vaudel, Marc}},
  issn         = {{0277-7037}},
  journal      = {{MASS SPECTROMETRY REVIEWS}},
  keywords     = {{bioinformatics,proteomics,search engine,PEPTIDE IDENTIFICATION,PROTEIN IDENTIFICATION,SHOTGUN PROTEOMICS,SEQUENCE DATABASE,IMPROVING SENSITIVITY,METAPROTEOMICS DATA,IDENTIFY PEPTIDES,MS/MS SPECTRA,TANDEM,ALGORITHM}},
  language     = {{eng}},
  number       = {{3}},
  pages        = {{292--306}},
  title        = {{Anatomy and evolution of database search engines : a central component of mass spectrometry based proteomic workflows}},
  url          = {{http://dx.doi.org/10.1002/mas.21543}},
  volume       = {{39}},
  year         = {{2020}},
}

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