Advances in tandem mass spectrometry (tandem MS) and sequencing have enabled the field of community proteomics, which seeks to identify expressed proteins, their sequence variability, and the physiological responses of organisms to variable environmental conditions. Bottom-up tandem MS-based community proteomic approaches generate fragmentation spectra from peptides. Fragmentation spectra are then searched against genomic or metagenomic databases to deduce the amino acid sequences of peptides, providing positive identifications for proteins. Marine community proteomic studies have verified the importance of nutrient transport, energy generation, and carbon fixation functions in bacteria and archaea and revealed spatial and temporal shifts in the expressed functions of communities. Here, we discuss sample collection, preparation, and processing methods for planktonic tandem MS-based community proteomics.
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