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Modern Proteomics – Sample Preparation, Analysis and Practical Applications

Volume 919 of the series Advances in Experimental Medicine and Biology pp 147-156

Date:

Database Search Engines: Paradigms, Challenges and Solutions

  • Kenneth VerheggenAffiliated withDepartment of Medical Protein Research, VIBDepartment of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University
  • , Lennart MartensAffiliated withDepartment of Medical Protein Research, VIBDepartment of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University
  • , Frode S. BervenAffiliated withProteomics Unit, Department of Biomedicine, University of BergenKG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of BergenNorwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital
  • , Harald BarsnesAffiliated withProteomics Unit, Department of Biomedicine, University of Bergen Email author 
  • , Marc VaudelAffiliated withProteomics Unit, Department of Biomedicine, University of Bergen

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Abstract

The first step in identifying proteins from mass spectrometry based shotgun proteomics data is to infer peptides from tandem mass spectra, a task generally achieved using database search engines. In this chapter, the basic principles of database search engines are introduced with a focus on open source software, and the use of database search engines is demonstrated using the freely available SearchGUI interface. This chapter also discusses how to tackle general issues related to sequence database searching and shows how to minimize their impact.

Keywords

Peptide identification Search engines Shotgun proteomics Sequence database searching