The Human Plasma Proteome

By Leigh Anderson, M. Polanski, R. Pieper, T. Gatlin, R. Tirumalai, Thomas P. Conrads, Timothy D. Veenstra, J. Adkins, J. Pounds, R. Fagan and 1 more. Molecular & Cellular Proteomics, 2004

697 citations recorded by the source corpus.

We have merged four different views of the human plasma proteome, based on different methodologies, into a single nonredundant 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 two-dimensional electrophoresis and mass spectroscopy (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-mass plasma components followed by MS identification. Of 1,175 nonredundant gene products, 195 were included in more than one of the four input datasets. Only 46 appeared in all four. Predictions of signal sequence and transmembrane domain occurrence, as well as Genome Ontology annotation assignments, allowed characterization of the nonredundant list and comparison of the data sources. The “nonproteomic” literature (468 input proteins) is strongly biased toward 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.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/96db18cb06164570e4a1d0eb1020e6091b9839e9

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In Molecular Biology

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Citations in the corpus

• The Size of the Human Proteome: The Width and Depth (2016, background): “Information on possible protein sequence variability is represented as the number of AS variants, nsSNPs/SAPs, and PTMs per gene.”
• Quantitative Mass Spectrometric Multiple Reaction Monitoring Assays for Major Plasma Proteins* (2006, methodology): “Although we do not yet know the frequency of high efficiency peptides among the tryptic products of each protein, we believe that numerous additional plasma proteins can be measured down to 1 g/ml using MRMs and estimate that 50–100 proteins may be added to our list as we extend this effort to addit”