MEPS 332:281-289 (2007)  -  doi:10.3354/meps332281

Marine proteomics

Brook L. Nunn1,2, Aaron T. Timperman3,*

1Medicinal Chemistry Department, University of Washington, Box 355350, Seattle, Washington 98155, USA
2Marine Chemistry Department, University of Otago, Box 46, Dunedin, New Zealand
3C. Eugene Bennett Department of Chemistry, West Virginia University, Prospect St, Morgantown, West Virginia 26509-6045, USA
*Corresponding author. Email:

ABSTRACT: A wealth of information is recorded in a protein’s primary sequence, which can be used to determine its biological function and origin, and provide clues to the mechanisms of degradation. In contrast to DNA, proteins and their amino acid constituents have demonstrated a wide-spread presence outside the cell, preserved in the environment. In marine samples, proteins are present as mixtures from numerous sources in a salty, complex matrix at low concentrations. As a result of these factors, studies of this nitrogen-based component in the oceans have previously been limited to bulk elemental and amino acid analyses; these analyses were incapable of providing details regarding protein sequence, function and source information. Advances in biological mass spectrometry now allow for the analysis and characterization of the protein component from the marine environment. Proteomic mass spectrometry is a high-throughput analysis of protein mixtures that does not require any prior knowledge of the original protein structures in the mixture, making it an ideal technique for marine studies. Potential marine applications of proteomics include: analyzing organisms cultured under different nutrient conditions to examine cellular expression and adaptation, profiling the marine dissolved and particulate organic matter pools to determine source information and understand long-term carbon preservation, and verifying genomic findings with proteomic analyses to determine which genes are translated and to what extent the protein is expressed. Although some major advances in marine studies and mass spectrometry have been made, there remains a significant amount of methods development and community education before the full potential of proteomics is reached.

KEY WORDS: Seawater · Protein · Mass spectrometry · Genomics · Dissolved organic matter · DOM · Particulate organic matter · POM

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