A Non-Redundant List of Proteins Present in Plasma

In a recent paper, we examined the properties of a "consensus" human plasma proteome created by merging four different datasets, based on different methodologies, into a single non-redundant list of 1175 distinct gene products. The methodologies used were 1) literature search for proteins reported to occur in plasma or serum; 2) multidimensional chromatography of proteins followed by 2-D electrophoresis and MS identification of resolved proteins; 3) tryptic digestion and multidimensional chromatography of peptides followed by MS identification, and 4) tryptic digestion and multidimensional chromatography of peptides from low-molecular weight plasma components followed by MS identification. Of 1175 non-redundant gene products, 195 were included in more than one of the four input data sets. Only 46 appeared in all four. Predictions of signal sequence and transmembrane domain occurrence, as well as Genome Ontology (GO) annotation assignments, allowed characterization of the non-redundant list and comparison of the data sources. The “nonproteomic” literature (468 input proteins) is strongly biased towards signal sequence-containing extracellular proteins, while the three proteomics methods showed a much higher representation of cellular proteins, including nuclear, cytoplasmic and kinesin complex proteins. Cytokines and protein hormones were almost completely absent from the proteomics data (presumably due to low abundance), while categories like DNA-binding proteins were almost entirely absent from the literature data (perhaps unexpected and therefore not sought). Most major categories of proteins in the human proteome are represented in plasma, with the distribution at successively deeper layers shifting from mostly extracellular to a distribution more like the whole (primarily cellular) proteome. The resulting nonredundant list confirms the presence of a number of interesting candidate marker proteins in plasma and serum., and provides a starting point for development of specific assays for panel validation (e.g., using SISCAPA technology).

The Human Plasma Proteome: A Non-Redundant List Developed by Combination of Four Separate Sources. Anderson, N.L., Polanski, M., Pieper, R., Gatlin, T., Tirumalai, R.S., Conrads, T.P., Veenstra, T.D., Adkins, J.N., Pounds, J.G, Fagan, R., and Lobley, A., Molecular & Cellular Proteomics, in press (2004).