Database Search Engines: Paradigms, Challenges and Solutions

  • Kenneth Verheggen
  • Lennart Martens
  • Frode S. Berven
  • Harald Barsnes
  • Marc Vaudel
Chapter

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 

Abbreviations

PSM

Peptide Spectrum Match

PTM

Post-Translational Modification

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Kenneth Verheggen
    • 1
    • 2
  • Lennart Martens
    • 1
    • 2
  • Frode S. Berven
    • 3
    • 4
    • 5
  • Harald Barsnes
    • 3
  • Marc Vaudel
    • 3
  1. 1.Department of Medical Protein ResearchVIBGhentBelgium
  2. 2.Department of Biochemistry, Faculty of Medicine and Health SciencesGhent UniversityGhentBelgium
  3. 3.Proteomics Unit, Department of BiomedicineUniversity of BergenBergenNorway
  4. 4.KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical MedicineUniversity of BergenBergenNorway
  5. 5.Norwegian Multiple Sclerosis Competence Centre, Department of NeurologyHaukeland University HospitalBergenNorway

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