A functional annotation of subproteomes in human plasma

Abstract

The data collected by Human Proteome Organization's Plasma Proteome Pilot project phase was analyzed by members of our working group. Accordingly, a functional annotation of the human plasma proteome was carried out. Here, we report the findings of our analyses. First, bioinformatic analyses were undertaken to determine the likely sources of plasma proteins and to develop a protein interaction network of proteins identified in this project. Second, annotation of these proteins was performed in the context of functional subproteomes involved in the coagulation pathway, the mononuclear phagocytic system, the inflammation pathway, the cardiovascular system, and the liver; as well as the subset of proteins associated with DNA binding activities. Our analyses contributed to the Plasma Proteome Database (http://www.plasmaproteomedatabase.org), an annotated database of plasma proteins identified by HPPP as well as from other published studies. In addition, we address several methodological considerations including the selective enrichment of post-translationally modified proteins by the use of multi-lectin chromatography as well as the use of peptidomic techniques to characterize the low molecular weight proteins in plasma. Furthermore, we have performed additional analyses of peptide identification data to annotate cleavage of signal peptides, sites of intra-membrane proteolysis and post-translational modifications. The HPPP-organized, multi-laboratory effort, as described herein, resulted in much synergy and was essential to the success of this project.

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly‐available database

“…Rai et al [56] report the cross-laboratory evaluation of eight submitted datasets, of which five were judged appropriate for comparison of plasma results and four for serum results. Intra-laboratory CV varied from 15 to 43%.…”

“…Ping et al [56] emphasize use of peptide identification results from MS/MS to reveal cleavage of signal peptides, proteolysis within hydrophobic stretches in transmembrane protein sites, and PTMs. Using 2446 of the 3020 PPP from IPI that matched to EnsEMBL gene products, they highlight subproteomes comprised of glycoproteins, low M r proteins and peptides, DNA binding proteins, and coagulation pathway, cardiovascular, liver, inflammation, and mononuclear phagocyte proteins.…”

Atherosclerosis

“…Providing a foundation for study interpretation, the Human Proteome Organization initiated a Plasma Proteome Project. The pilot phase identified 345 cardiovascular disease-related proteins in human plasma (63,64). These catalogs determine additional novel proteins that might associate with cardiovascular disease in future proteomic discovery experiments.…”

Cardiovascular Proteomics

“…The combination of more sophisticated methods to deplete highly abundant proteins, with the use of capillary electrophoresis to detect low molecular weight proteins, might yield more proteomic biomarker candidates with time. The number of detectable proteins in plasma has risen dramatically from 40 proteins in 1975 (28) to over 3,000 in recent studies (29). Albumin depletion techniques have been used relatively successfully to improve the yield of lower molecular weight species in the plasma (30,31).…”