title: Database Search Engines: Paradigms, Challenges and Solutions.
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.
authors.affiliation: Department of Medical Protein Research, VIB, Ghent, Belgium.|Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Verheggen
authors.affiliation: Department of Medical Protein Research, VIB, Ghent, Belgium.|Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.affiliation: Proteomics Unit, Department of Biomedicine, University of Bergen, Jonas Liesvei 91, N-5009, Bergen, Norway.|KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway.|Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway.
authors.forename: Frode S
authors.initials: FS
authors.lastname: Berven
authors.affiliation: Proteomics Unit, Department of Biomedicine, University of Bergen, Jonas Liesvei 91, N-5009, Bergen, Norway. harald.barsnes@biomed.uib.no.
authors.forename: Harald
authors.initials: H
authors.lastname: Barsnes
authors.affiliation: Proteomics Unit, Department of Biomedicine, University of Bergen, Jonas Liesvei 91, N-5009, Bergen, Norway.
authors.forename: Marc
authors.initials: M
authors.lastname: Vaudel
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D030562:Databases, Protein; D057166:High-Throughput Screening Assays; D006801:Humans; D011506:Proteins / Q000032:analysis*; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D057386:Search Engine; D012984:Software; D053719:Tandem Mass Spectrometry; D014584:User-Computer Interface
chemical_list: D011506:Proteins; D020543:Proteome
keywords: Peptide identification; Search engines; Sequence database searching; Shotgun proteomics