A great emphasis has been placed on understanding the carbon cycle because the increased input of anthropogenic carbon into the atmosphere could have a dramatic affect on global climate. While there is agreement that atmospheric carbon dioxide and the earth's temperature are increasing, the effects of these changes on the earth's climate are greatly debated. For modelers to accurately predict future changes to global climate, the mechanisms which control carbon cycling must be thoroughly understood. Dissolved organic carbon plays a significant role in carbon cycling, as this reservoir of carbon is nearly equivalent to the atmospheric inorganic carbon in size. One of major challenges faced by marine chemists is the characterization of dissolved organic carbon (DOC) at the molecular level. Due to its complexity, low ambient concentrations, and a complex background matrix, only <30% of oceanic DOC is identifiable at the molecular level using traditional analytical techniques. Many recent advancements in the analytical technology used for protein sequencing and identification have greatly improved our ability to characterize dissolved protein in seawater at the molecular level. We are using ultrafiltration, gel electrophoresis, and tandem mass spectrometry to sequence and characterize dissolved proteins in seawater. Molecular level information will increase our understanding of the sources, transformations, and fates of dissolved proteins in seawater.