Protein comprises the largest compartment of organic nitrogen in the ocean, and makes up a major portion of organic carbon in phytoplankton. Protein has long been thought to be highly labile in the environment and rapidly lost during diagenesis. However, the analysis of dissolved and particulate organic matter with NMR has revealed that much of dissolved and particulate marine organic nitrogen is linked by amide bonds, the very bonds that join amino acids in proteins. Throughout the global ocean, total hydrolysable amino acids (THAAs, the building blocks of proteins) can be measured in the water column and sediments, yet their biosynthetic source has remained elusive. Here, analytical techniques were developed combining protein solubilizing buffer extractions, gel electrophoresis, and proteomic mass spectrometry in order to investigate the biogeochemical significance of marine protein from primary production during transport and incorporation in sediments. These techniques enabled the detection and classification of previously unidentified marine sedimentary proteins. Specific proteins were tracked through the water column to continental shelf and deeper basin (3490 m) sediments of the Bering Sea, one of the world's most productive ecosystems. Diatoms were observed to be the principal source of identifiable protein in sediments. In situ shipboard phytoplankton degradation experiments were conducted to follow protein degradation, and it was observed that individual proteins remained identifiable even after 53 days of microbial recycling. These studies show that proteins can be identified from complex environmental matrices, and the methods developed here can be applied to investigate and identify proteins in degraded organic matter from a broad range of sources. The longevity of some fraction of algal proteins indicates that carbon and nitrogen sources can be tracked down the marine water column to sediments in diatom dominated systems as well as other types of phytoplankton. Using proteomic techniques to understand the marine carbon and nitrogen cycles will become increasingly important as climate change influences the timing, location, and phylogeny of those organisms responsible for oceanic primary production.