Pan-proteomics, a concept for unifying quantitative proteome measurements when comparing closely-related bacterial strains

ABSTRACT

The comparison of proteomes between genetically heterogeneous bacterial strains may offer valuable insights into physiological diversity and function, particularly where such variation aids in the survival and virulence of clinically-relevant strains. However, reports of such comparisons frequently fail to account for underlying genetic variance. As a consequence, the current knowledge regarding bacterial physiological diversity at the protein level may be incomplete or inaccurate. To address this, greater consideration must be given to the impact of genetic heterogeneity on proteome comparisons. This may be possible through the use of pan-proteomics, an analytical concept that permits the ability to qualitatively and quantitatively compare the proteomes of genetically heterogeneous organisms. Limited examples of this emerging technology highlight currently unmet analytical challenges. In this article we define pan-proteomics, where its value lies in microbiology, and discuss the technical considerations critical to its successful execution and potential future application.

KEYWORDS:

• Pan-proteomics
• Microbiology
• Bioinformatics
• Bacterial strains
• Comparative proteomics
• Genetic heterogeneity
• Clinical microbiology

Acknowledgements

The authors acknowledge the use of the following open source software: GIMP 2 (www.gimp.org); the r project for statistical computing (www.r-project.org); and, Cyctoscape (http://www.cytoscape.org). Further acknowledgment is provided to Dr Marcus Hastie from the Protein Discovery Centre, QIMR Berghofer Medical Research Institute, for running the 2D DIGE experiment.

Financial and competing interests disclosure

JA Broadbent was supported by funding from the Queensland University of Technology Institute of Health and Biomedical Innovation Early Career Researcher Grant. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.