title: Top Down proteomics: facts and perspectives.
abstract: The rise of the "Top Down" method in the field of mass spectrometry-based proteomics has ushered in a new age of promise and challenge for the characterization and identification of proteins. Injecting intact proteins into the mass spectrometer allows for better characterization of post-translational modifications and avoids several of the serious "inference" problems associated with peptide-based proteomics. However, successful implementation of a Top Down approach to endogenous or other biologically relevant samples often requires the use of one or more forms of separation prior to mass spectrometric analysis, which have only begun to mature for whole protein MS. Recent advances in instrumentation have been used in conjunction with new ion fragmentation using photons and electrons that allow for better (and often complete) protein characterization on cases simply not tractable even just a few years ago. Finally, the use of native electrospray mass spectrometry has shown great promise for the identification and characterization of whole protein complexes in the 100 kDa to 1 MDa regime, with prospects for complete compositional analysis for endogenous protein assemblies a viable goal over the coming few years.
authors.affiliation: Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, United States.
authors.forename: Adam D
authors.initials: AD
authors.lastname: Catherman
authors.affiliation: Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, United States.
authors.forename: Owen S
authors.initials: OS
authors.lastname: Skinner
authors.affiliation: Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, United States. Electronic address: n-kelleher@northwestern.edu.
authors.forename: Neil L
authors.initials: NL
authors.lastname: Kelleher
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002853:Chromatography, Liquid / Q000295:instrumentation / Q000379:methods; D004586:Electrophoresis / Q000295:instrumentation / Q000379:methods; D004867:Equipment Design; D006801:Humans; D013058:Mass Spectrometry / Q000295:instrumentation / Q000379:methods; D008969:Molecular Sequence Data; D011506:Proteins / Q000032:analysis* / Q000378:metabolism; D040901:Proteomics / Q000295:instrumentation* / Q000379:methods*
chemical_list: D011506:Proteins