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Proteotyping: Proteomic characterization, classification and identification of microorganisms - A prospectus

Review article
Authors R. Karlsson
Lucia Gonzales-Siles
Fredrik Boulund
Liselott Svensson-Stadler
Susann Skovbjerg
A. Karlsson
M. Davidson
Stefan Hulth
Erik Kristiansson
Edward R.B. Moore
Published in Systematic and Applied Microbiology
Volume 38
Issue 4
Pages 246-257
ISSN 0723-2020
Publication year 2015
Published at Department of Mathematical Sciences
Department of Chemistry and Molecular Biology
Institute of Biomedicine, Department of Infectious Medicine
Pages 246-257
Language en
Links dx.doi.org/10.1016/j.syapm.2015.03....
Keywords Proteotyping, Proteomics, Mass spectrometry, Microbial systematics, SPECTROMETRY-BASED PROTEOMICS, TANDEM MASS-SPECTROMETRY, ASSISTED-LASER-DESORPTION/IONIZATION, OUTER-MEMBRANE PROTEOME, TOP-DOWN, POSTTRANSLATIONAL MODIFICATIONS, 2-DIMENSIONAL ELECTROPHORESIS, BACTERIAL SYSTEMATICS, BIOLOGICAL QUESTIONS, IDENTIFYING PROTEINS, Biotechnology & Applied Microbiology, Microbiology
Subject categories Microbiology

Abstract

Modern microbial systematics requires a range of methodologies for the comprehensive characterization, classification and identification of microorganisms. While whole-genome sequences provide the ultimate reference for defining microbial phylogeny and taxonomy, selected biomarker-based strategies continue to provide the means for the bulk of microbial systematic studies. Proteomics, the study of the expression of genes, as well as the structure and function of the resulting proteins, offers indirect measures of genome sequence data. Recent developments in applications of proteomics for analyzing microorganisms have paralleled the growing microbial genome sequence database, as well as the evolution of mass spectrometry (MS) instrumentation and bioinformatics. MALDI-TOF MS, which generates proteomic mass patterns for 'fingerprint'-based characterizations, has provided a marked breakthrough for microbial identification. However, MALDI-TOF MS is limited in the number of targets that can be detected for strain characterization. Advanced methods of tandem mass spectrometry, in which proteins and peptides generated from proteins, are characterized and identified, using LC-MS/MS, provide the ability to detect hundreds or thousands of expressed microbial strain markers for high-resolution characterizations and identifications. Model studies demonstrate the application of proteomics-based analyses for bacterial species- and strain-level detection and identification and for characterization of environmentally relevant, metabolically diverse bacteria. Proteomics-based approaches represent an emerging complement to traditional methods of characterizing microorganisms, enabling the elucidation of the expressed biomarkers of genome sequence information, which can be applied to 'proteotyping' applications of microorganisms at all taxonomic levels. (C) 2015 Elsevier GmbH. All rights reserved.

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