Database Search Engines: Paradigms, Challenges and Solutions

Kenneth Verheggen; Lennart Martens; Frode S Berven; Harald Barsnes; Marc Vaudel

doi:10.1007/978-3-319-41448-5_6

Database Search Engines: Paradigms, Challenges and Solutions

Adv Exp Med Biol. 2016:919:147-156. doi: 10.1007/978-3-319-41448-5_6.

Authors

Kenneth Verheggen^{1

2}, Lennart Martens^{1

2}, Frode S Berven^{3

4

5}, Harald Barsnes⁶, Marc Vaudel³

Affiliations

¹ Department of Medical Protein Research, VIB, Ghent, Belgium.
² Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
³ Proteomics Unit, Department of Biomedicine, University of Bergen, Jonas Liesvei 91, N-5009, Bergen, Norway.
⁴ KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway.
⁵ Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway.
⁶ Proteomics Unit, Department of Biomedicine, University of Bergen, Jonas Liesvei 91, N-5009, Bergen, Norway. [email protected].

PMID: 27975215
DOI: 10.1007/978-3-319-41448-5_6

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; Sequence database searching; Shotgun proteomics.

Publication types

Research Support, Non-U.S. Gov't
Review

MeSH terms

Animals
Computational Biology / methods*
Data Mining / methods*
Databases, Protein*
High-Throughput Screening Assays
Humans
Proteins / analysis*
Proteome*
Proteomics / methods*
Search Engine*
Software
Tandem Mass Spectrometry*
User-Computer Interface

Substances

Proteins
Proteome