Environmental proteomics: a paradigm shift in characterizing microbial activities at the molecular level

Abstract

The increase in sequencing capacity led to a new wave of metagenomic projects, enabling and setting the prerequisite for the application of environmental proteomics technologies. This review describes the current status of environmental proteomics. It describes sample preparation as well as the two major technologies applied within this field: two-dimensional electrophoresis-based environmental proteomics and liquid chromatography-mass spectrometry-based environmental proteomics. It also highlights current publications and describes major scientific findings. The review closes with a discussion of critical improvements in the area of integrating experimental mass spectrometry technologies with bioinformatics as well as improved sample handling.

FIG. 1.

Overview of two major environmental proteomic strategies. In one strategy (top left), proteins are separated by 2D-GE followed by MS analysis with either peptide mass mapping or LC-MS approaches. An alternate strategy (top right) involves protein digestion followed by online liquid LC separation and MS characterization. There are dramatic differences in measurement throughput, automation, and depth of protein identification for these two related but distinct approaches, as discussed in the text. IEF, isoelectric focusing; SDS, sodium dodecyl sulfate.