Proteotyping bacteria: Characterization, differentiation and identification of pneumococcus and other species within the Mitis Group of the genus Streptococcus by tandem mass spectrometry proteomics

PLoS One. 2018 Dec 10;13(12):e0208804. doi: 10.1371/journal.pone.0208804. eCollection 2018.


A range of methodologies may be used for analyzing bacteria, depending on the purpose and the level of resolution needed. The capability for recognition of species distinctions within the complex spectrum of bacterial diversity is necessary for progress in microbiological research. In clinical settings, accurate, rapid and cost-effective methods are essential for early and efficient treatment of infections. Characterization and identification of microorganisms, using, bottom-up proteomics, or "proteotyping", relies on recognition of species-unique or associated peptides, by tandem mass spectrometry analyses, dependent upon an accurate and comprehensive foundation of genome sequence data, allowing for differentiation of species, at amino acid-level resolution. In this study, the high resolution and accuracy of MS/MS-based proteotyping was demonstrated, through analyses of the three phylogenetically and taxonomically most closely-related species of the Mitis Group of the genus Streptococcus: i.e., the pathogenic species, Streptococcus pneumoniae (pneumococcus), and the commensal species, Streptococcus pseudopneumoniae and Streptococcus mitis. To achieve high accuracy, a genome sequence database used for matching peptides was created and carefully curated. Here, MS-based, bottom-up proteotyping was observed and confirmed to attain the level of resolution necessary for differentiating and identifying the most-closely related bacterial species, as demonstrated by analyses of species of the Streptococcus Mitis Group, even when S. pneumoniae were mixed with S. pseudopneumoniae and S. mitis, by matching and identifying more than 200 unique peptides for each species.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / metabolism*
  • Bacterial Typing Techniques*
  • Proteome / metabolism*
  • Proteomics*
  • Streptococcus pneumoniae / classification*
  • Streptococcus pneumoniae / metabolism*
  • Tandem Mass Spectrometry*


  • Bacterial Proteins
  • Proteome

Grants and funding

This research was supported by the European Commission 7th Framework Programme: “Tailored-Treatment”, project no. 602860; and the Swedish Västra Götaland regional funding: project nos. ALFGBG-437221 and ALFGBG-720761. R.K. acknowledges support from the Swedish Västra Götaland Region, FoU grant number VGFOUREG-665141 and Lab Medicine Project number 51060-6258. F.S.-S. and D.J.-L. acknowledge support from the Swedish Västra Götaland Region, Lab Medicine Project number 51060-6268. F.S.-S. and D.J.-L. were supported by stipends for Basic and Advanced Research from the CCUG, through the Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg. The CCUG is supported by the Department of Clinical Microbiology, Sahlgrenska University Hospital. Authors AK and RK are employed by Nanoxis Consulting AB. Nanoxis Consulting AB. provided support in the form of salaries for authors [AK, RK], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.