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.