title: Proteogenomics in microbiology: taking the right turn at the junction of genomics and proteomics.
abstract: High-accuracy and high-throughput proteomic methods have completely changed the way we can identify and characterize proteins. MS-based proteomics can now provide a unique supplement to genomic data and add a new level of information to the interpretation of genomic sequences. Proteomics-driven genome annotation has become especially relevant in microbiology where genomes are sequenced on a daily basis and limitations of an in silico driven annotation process are well recognized. In this review paper, we outline different strategies on how one can design a proteogenomic experiment, for example on genome-sequenced (synonymous proteogenomics) versus unsequenced organisms (ortho-proteogenomics) or with the aid of other "omic" data such as RNA-seq. We touch upon many challenges that are encountered during a typical proteogenomic study, mostly concerning bioinformatics methods and downstream data analysis, but also related to creation and use of sequence databases. A large list of proteogenomic case studies of different microorganisms is provided to illustrate the mapping of MS/MS-derived peptide spectra to genomic DNA sequences. These investigations have led to accurate determination of translational initiation sites, pointed out eventual read-throughs or programmed frameshifts, detected signal peptide processing or other protein maturation events, removed questionable annotation assignments, and provided evidence for predicted hypothetical proteins.
authors.affiliation: Department of Clinical Science, The Gade Research Group for Infection and Immunity, University of Bergen, Norway.
authors.forename: Veronika
authors.initials: V
authors.lastname: Kucharova
authors.forename: Harald G
authors.initials: HG
authors.lastname: Wiker
mesh_terms: D019295:Computational Biology / Q000379:methods*; D023281:Genomics / Q000379:methods*; D008828:Microbiological Techniques / Q000379:methods*; D040901:Proteomics / Q000379:methods*
keywords: Genome annotation; MS/MS; Microbiology; Synonymous proteogenomics