Proteotyping: Tandem Mass Spectrometry Shotgun Proteomic Characterization and Typing of Pathogenic Microorganisms
Book chapter, 2016

Proteotyping provides the means to identify and quantify the actual expression patterns of proteins and their associated pathways, which provides a more accurate picture of infectious agents and their pathogenic potential. Proteotyping, as an analytical method, is intimately correlated with genotypic or genomic data and offers an approach for a holistic characterization of microorganisms. Bioinformatics is vital for the analysis of the data generated by shotgun proteomics. This chapter describes the complete bioinformatics workflow necessary for proteotyping. Mass spectrometry (MS)-based shotgun proteomics analyses offer more detailed and comprehensive analyses of microorganisms. Two approaches may be applied: the so-called top-down and bottom-up proteomics. A major driver for the development and use of tandem MS and proteotyping in clinical settings will be the rapidly growing databases of whole genome reference sequences, which will refine microbial phylogeny and provide a foundation for proteomics-based identification.

Proteomics-based identification

Microbial phylogeny

Pathogenic microorganisms

Shotgun proteomic characterization

Wholegenome reference sequences

Bioinformatics workflow


Tandem mass spectrometry


Roger Karlsson

Sahlgrenska University Hospital

Nanoxis Consulting AB

Lucia Gonzales-Siles

University of Gothenburg

Fredrik Boulund

Chalmers, Mathematical Sciences, Mathematical Statistics

Åsa Lindgren

Sahlgrenska University Hospital

University of Gothenburg

Liselott Svensson-Stadler

Sahlgrenska University Hospital

University of Gothenburg

Anders Karlsson

Nanoxis Consulting AB

Erik Kristiansson

Chalmers, Mathematical Sciences, Applied Mathematics and Statistics

Edward R.B. Moore

University of Gothenburg

Sahlgrenska University Hospital

MALDI‐TOF and Tandem MS for Clinical Microbiology

9781118960226 (ISBN)

Subject Categories

Bioinformatics (Computational Biology)

Medical Genetics

Bioinformatics and Systems Biology



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