The enormous complexity of marine high molecular weight dissolved organic matter (HMW DOM) has largely prevented its analysis at the molecular level. Recent advances in analytical methods for protein analysis have made molecular level analysis of the protein component of HMW DOM feasible. It is hypothesized that structural characterization of dissolved proteins will help reveal clues into the mechanisms that control cycling of dissolved organic matter. Bottom-up or peptide level proteomic methods can provide accurate identification and sequence tags from de novo sequencing, to determine what classes of proteins escape degradation.

Two methods are employed for bottom-up characterization of the proteins using electrospray ionization-mass spectrometry (ESI-MS). Protein identification is achieved by digestion of gel separated proteins, and by beginning with digestion using MuDPIT or shot-gun sequencing methods. De novo sequencing of the peptide tandem mass spectra generated short amino acid sequences (peptide tags) that were used to search databases for protein class and source information. For whole protein analysis the proteins are recovered, and electroextracted from the gels. The intact proteins are analyzed using on-line RP-HPLC-MS.

Trends of conserved sequences for two specific classes of proteins were observed: membrane/envelope proteins and enzymes. Similarity searching of peptide tags produced identification of conserved sequences from several protein homologues originating from many different species, including: long chain fatty acyl CoA synthetase, anthranilate synthase, ribulose bisphosphate carboxylase, tubulin beta chain, adhesin, transport system protease, ATP synthase alpha chain, and luminal binding protein.