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Choosing an Optimal Database for Protein Identification from Tandem Mass Spectrometry Data

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Proteome Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1549))

Abstract

Database searching is the preferred method for protein identification from digital spectra of mass to charge ratios (m/z) detected for protein samples through mass spectrometers. The search database is one of the major influencing factors in discovering proteins present in the sample and thus in deriving biological conclusions. In most cases the choice of search database is arbitrary. Here we describe common search databases used in proteomic studies and their impact on final list of identified proteins. We also elaborate upon factors like composition and size of the search database that can influence the protein identification process. In conclusion, we suggest that choice of the database depends on the type of inferences to be derived from proteomics data. However, making additional efforts to build a compact and concise database for a targeted question should generally be rewarding in achieving confident protein identifications.

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Authors and Affiliations

  1. G.N. Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Mathura Road, Delhi, 110025, India

    Dhirendra Kumar, Amit Kumar Yadav & Debasis Dash

Authors
  1. Dhirendra Kumar
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  2. Amit Kumar Yadav
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  3. Debasis Dash
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Correspondence to Debasis Dash .

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Editors and Affiliations

  1. Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia

    Shivakumar Keerthikumar

  2. Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia

    Suresh Mathivanan

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Kumar, D., Yadav, A.K., Dash, D. (2017). Choosing an Optimal Database for Protein Identification from Tandem Mass Spectrometry Data. In: Keerthikumar, S., Mathivanan, S. (eds) Proteome Bioinformatics. Methods in Molecular Biology, vol 1549. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6740-7_3

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  • DOI: https://doi.org/10.1007/978-1-4939-6740-7_3

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6738-4

  • Online ISBN: 978-1-4939-6740-7

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