title: Bioinformatics tools to identify and quantify proteins using mass spectrometry data.
abstract: Proteomics tries to understand biological function of an organism by studying its protein expressions. Mass spectrometry is used in the field of shotgun proteomics, and it generates mass spectra that are used to identify and quantify proteins in biological samples. In this chapter, we discuss the bioinformatics algorithms to analyze mass spectrometry data. After briefly describing how mass spectrometry generates data, we illustrate the bioinformatics algorithms and software for protein identification such as de novo approach and database-searching approach. We also discuss the bioinformatics algorithms and software to quantify proteins and detect the differential proteins using isotope-coded affinity tags and label-free mass spectrometry data.
authors.affiliation: Stanford Genome Technology Center, Biochemistry Department, Stanford University, Stanford, California, USA. Electronic address: clairesr@stanford.edu.
authors.forename: So Young
authors.initials: SY
authors.lastname: Ryu
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D019295:Computational Biology; D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods*; D011506:Proteins / Q000032:analysis / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D011506:Proteins
keywords: Bioinformatics; Mass spectrometry; Protein identification; Protein quantification; Proteomics; Software