New Proteomic Windows into the Marine Nitrogen Cycle

Nitrogen assimilation by marine microbes is one of the largest fluxes in the global N cycle. Most N in microbial cells resides in proteins, making quantitative understanding of how microbes use nitrogen anabolically – to build which proteins under which circumstances, and for which metabolic purposes – central to marine N biogeochemistry. Proteomics, the mass spectrometry-based identification and quantification of proteins and their properties (such as chemical modifications, isotopic compositions, noncanonical translation, and subcellular localizations), is a key tool in generating this molecular-level picture of microbial N utilization. We present novel quantitative and isotope-labeling proteomics methodologies, as well advances in de novo peptide sequencing and database searching for metaproteomics. These enable broad-coverage, high-precision protein expression quantification in both laboratory and field samples, as well as tracking of biosynthetic incorporation of N into specific protein components of cellular metabolism. With examples from isolated marine microbes, planktonic virus-host systems, and field studies, we illustrate how these techniques afford new insights into marine nitrogen biogeochemistry.