dc.contributor.author | Kucharova, Veronika | en_US |
dc.contributor.author | Wiker, Harald G. | en_US |
dc.date.accessioned | 2015-03-17T13:15:53Z | |
dc.date.available | 2015-03-17T13:15:53Z | |
dc.date.issued | 2014-12 | eng |
dc.identifier.issn | 1615-9861 | |
dc.identifier.uri | https://hdl.handle.net/1956/9547 | |
dc.description.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. | en_US |
dc.language.iso | eng | eng |
dc.publisher | WILEY-VCH Verlag | eng |
dc.rights | Attribution-NonCommercial CC BY-NC | eng |
dc.rights.uri | http://creativecommons.org/licenses/by-nc/4.0/ | eng |
dc.title | Proteogenomics in Microbiology: Taking the Right Turn at the Junction of Genomics and Proteomics | en_US |
dc.type | Peer reviewed | |
dc.type | Journal article | |
dc.date.updated | 2015-03-04T12:14:32Z | en_US |
dc.description.version | publishedVersion | en_US |
dc.rights.holder | Copyright 2014 The Authors. PROTEOMICS Published by WILEY-VCH Verlag GmbH & Co. KGaA This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. | |
dc.identifier.doi | https://doi.org/10.1002/pmic.201400168 | |
dc.identifier.cristin | 1160136 | |
dc.source.journal | Proteomics | |
dc.source.40 | 14 | |
dc.source.14 | 23-24 | |
dc.source.pagenumber | 2360-2675 | |