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Database Searching in Mass Spectrometry Based Proteomics

[ Vol. 7 , Issue. 2 ]

Author(s):

Attila Kertesz-Farkas, Beata Reiz, Michael P. Myers and Sandor Pongor   Pages 221 - 230 ( 10 )

Abstract:


Bottom-up proteomics (mass spectrometry analysis of peptides obtained by proteolysis and separated by liquid chromatography, (LC-MS/MS)) is one of the most frequently used techniques for identifying and characterizing proteins in biological samples. A key element of the analysis is database searching when the mass spectra of the peptides are compared with a database of theoretically computed (or experimental) peptide spectra. Here we discuss the main computational approaches to spectrum database searching and the statistical analysis of the results.

Keywords:

Database search, Mass spectrometry, Protein identification, Proteomics, mass spectrum, Liquid chromatography, pattern recognition, genome annotation, 3D structure analysis), fragment

Affiliation:

Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, 34012 Trieste, Italy.



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