Metaproteomics

Proteomics is the study of the suite of proteins present in a microbial culture or community. Because proteins are the molecular engines that directly drive biogeochemical reactions, proteomics provides a key window into the role of microorganisms in mediating environmental and geochemical processes. At this stage of technological development the sensitivity of shotgun proteomics lags behind that of transcriptomics; in general, shotgun proteomics detects fewer proteins and produces fewer counts per protein than transcriptomics. Further, interpretation of proteomics data relies on genomic databases. However, proteomic approaches are advancing rapidly and the throughput in terms of number of samples is competitive with transcriptomics. This chapter provides an overview of the strengths and weaknesses of proteomic approaches to studying microbial communities. We first introduce the field and consider some examples of how proteomics has been used to investigate microbial communities. Next we review the methodologies used to identify proteins. We then take a closer look at one of the main challenges of proteomics - the need for genomic databases for interpretation of the data. Another challenge is that like metagenomic and metatranscriptomics, shotgun metaproteomics data is often generated in terms of relative abundance. Thus, we consider efforts to put proteomics data into absolute quantitative terms. Finally, we briefly review isotope-based proteomic methods for identifying metabolically active groups and linking particular microbes with specific metabolic processes.