title: Achieving in-depth proteomics profiling by mass spectrometry.
abstract: Proteomics addresses the important goal of determining the chemistry and composition of proteins in biological samples. Mass-spectrometry-based strategies have been highly successful in identifying and profiling proteins in complex mixtures; however, although depth of sampling continues to improve, a general recognition exists that no study has yet achieved complete protein coverage in any tissue, cell type, subcellular component, or fluid. The development of new approaches for comprehensively surveying highly complex protein mixtures, distinguishing protein isoforms, quantifying changes in protein abundance between different samples, and mapping post-translational modifications are areas of active research. These will be needed to achieve the "systems-wide" protein profiling goals of defining molecular responses to cell perturbations and obtaining biomarker information for disease detection, prognosis, and responses to therapy. We review recent progress in approaching these problems and present examples of successful applications and the outlook for the future.
authors.affiliation: Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA. natalie.ahn@colorado.edu
authors.forename: Natalie G
authors.initials: NG
authors.lastname: Ahn
authors.forename: John B
authors.initials: JB
authors.lastname: Shabb
authors.forename: William M
authors.initials: WM
authors.lastname: Old
authors.forename: Katheryn A
authors.initials: KA
authors.lastname: Resing
mesh_terms: D000818:Animals; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D040081:Protein Array Analysis / Q000379:methods*; D020543:Proteome / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods
chemical_list: D020543:Proteome