Review
doi: 10.1007/978-3-319-41448-5_6.
Database Search Engines: Paradigms, Challenges and Solutions
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- PMID: 27975215
- DOI: 10.1007/978-3-319-41448-5_6
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Review
Database Search Engines: Paradigms, Challenges and Solutions
Adv Exp Med Biol.
2016.
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.
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