title: Mass spectrometry of peptides and proteins.
abstract: This tutorial article introduces mass spectrometry (MS) for peptide fragmentation and protein identification. The current approaches being used for protein identification include top-down and bottom-up sequencing. Top-down sequencing, a relatively new approach that involves fragmenting intact proteins directly, is briefly introduced. Bottom-up sequencing, a traditional approach that fragments peptides in the gas phase after protein digestion, is discussed in more detail. The most widely used ion activation and dissociation process, gas-phase collision-activated dissociation (CAD), is discussed from a practical point of view. Infrared multiphoton dissociation (IRMPD) and electron capture dissociation (ECD) are introduced as two alternative dissociation methods. For spectral interpretation, the common fragment ion types in peptide fragmentation and their structures are introduced; the influence of instrumental methods on the fragmentation pathways and final spectra are discussed. A discussion is also provided on the complications in sample preparation for MS analysis. The final section of this article provides a brief review of recent research efforts on different algorithmic approaches being developed to improve protein identification searches.
authors.affiliation: Department of Chemistry, University of Arizona, Tucson, AZ, 85721-0041, USA. vwysocki@email.arizona.edu
authors.forename: Vicki H
authors.initials: VH
authors.lastname: Wysocki
authors.forename: Katheryn A
authors.initials: KA
authors.lastname: Resing
authors.forename: Qingfen
authors.initials: Q
authors.lastname: Zhang
authors.forename: Guilong
authors.initials: G
authors.lastname: Cheng
mesh_terms: D000465:Algorithms; D000818:Animals; D030562:Databases, Protein; D004583:Electrons; D006801:Humans; D007477:Ions; D007700:Kinetics; D013058:Mass Spectrometry / Q000379:methods*; D008956:Models, Chemical; D010455:Peptides / Q000737:chemistry*; D017785:Photons; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D021241:Spectrometry, Mass, Electrospray Ionization; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D007477:Ions; D010455:Peptides; D011506:Proteins