title: Protein identification and expression analysis using mass spectrometry.
abstract: The identification and quantification of the proteins that a whole organism expresses under certain conditions is a main focus of high-throughput proteomics. Advanced proteomics approaches generate new biologically relevant data and potent hypotheses. A practical report of what proteome studies can and cannot accomplish in common laboratory settings is presented here. The review discusses the most popular tandem mass-spectrometry-based methods and focuses on how to produce reliable results. A step-by-step description of proteome experiments is given, including sample preparation, digestion, labeling, liquid chromatography, data processing, database searching and statistical analysis. The difficulties and bottlenecks of proteome analysis are addressed and the requirements for further improvements are discussed. Several diverse high-throughput proteomics-based studies of microorganisms are described.
authors.affiliation: The BIATECH Institute, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA. ekolker@biatech.org
authors.forename: Eugene
authors.initials: E
authors.lastname: Kolker
authors.forename: Roger
authors.initials: R
authors.lastname: Higdon
authors.forename: Jason M
authors.initials: JM
authors.lastname: Hogan
mesh_terms: D000595:Amino Acid Sequence; D003627:Data Interpretation, Statistical; D008969:Molecular Sequence Data; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*
chemical_list: D011506:Proteins