Microbiology and proteomics, getting the best of both worlds!
Article first published online: 19 JUN 2012
© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd
Special Issue: Baeza
Volume 15, Issue 1, pages 12–23, January 2013
How to Cite
Armengaud, J. (2013), Microbiology and proteomics, getting the best of both worlds!. Environmental Microbiology, 15: 12–23. doi: 10.1111/j.1462-2920.2012.02811.x
- Issue published online: 3 JAN 2013
- Article first published online: 19 JUN 2012
- Received 27 April, 2012; revised 18 May, 2012; accepted 22 May, 2012.
High-throughput identification of proteins with the latest generation of hybrid high-resolution mass spectrometers is opening new perspectives in microbiology. I present, here, an overview of tandem mass spectrometry technology and bioinformatics for shotgun proteomics that make 2D-PAGE approaches obsolete. Non-labelling quantitative approaches have become more popular than labelling techniques on most proteomic platforms because they are easier to carry out while their quantitative outcome is rather robust. Parameters for recording mass spectrometry data, however, need to be chosen carefully and statistics to assess the confidence of the results should not be neglected. Interestingly, next-generation sequencing methodologies make any microbial model quickly amenable to proteomics, leading to the documentation of a wide range of organisms from diverse environments. Some recent discoveries made using microbial proteomics have challenged some biological dogma, such as: (i) initiation of the translation does not occur predominantly from ATG codons in some microorganisms, (ii) non-canonical initiation codons are used to regulate the production of specific but important proteins and (iii) a gene may code for multiple polypeptide species, heterogeneous in terms of sequences. Microbial diversity and microbial physiology can now be revisited by means of exhaustive comparative proteomic surveys where thousands of proteins are detected and quantified. Proteogenomics, consisting of better annotating of genomes with the help of proteomic evidence, is paving the way for integrated multi-omic approaches in microbiology. Finally, meta-proteomic tools and approaches are emerging for tackling the high complexity of the microbial world as a whole, opening new perspectives for assessing how microbial communities function.