Proteotyping: Proteomic characterization, classification and identification of microorganisms--A prospectus
Review article, 2015

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.



microbial systematics

mass spectrometry


Roger Karlsson

University of Gothenburg

Nanoxis Consulting AB

Lucia Gonzales-Siles

University of Gothenburg

Fredrik Boulund

University of Gothenburg

Chalmers, Mathematical Sciences, Mathematical Statistics

Liselott Svensson-Stadler

University of Gothenburg

Susann Skovbjerg

University of Gothenburg

Anders Karlsson

Nanoxis Consulting AB

Max Davidsson

Nanoxis Consulting AB

Stefan Hulth

University of Gothenburg

Erik Kristiansson

University of Gothenburg

Chalmers, Mathematical Sciences, Mathematical Statistics

Edward R.B. Moore

University of Gothenburg

Systematic and Applied Microbiology

0723-2020 (ISSN)

Vol. 38 4 246-257

Driving Forces

Sustainable development

Subject Categories

Biomedical Laboratory Science/Technology

Microbiology in the medical area

Areas of Advance

Life Science Engineering (2010-2018)



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3/2/2022 6