Systematic comparison of the human saliva and plasma proteomes

Abstract

The proteome of human salivary fluid has the potential to open new doors for disease biomarker discovery. A recent study to comprehensively identify and catalog the human ductal salivary proteome led to the compilation of 1166 proteins. The protein complexity of both saliva and plasma is large, suggesting that a comparison of these two proteomes will provide valuable insight into their physiological significance and an understanding of the unique and overlapping disease diagnostic potential that each fluid provides. To create a more comprehensive catalog of human salivary proteins, we have first compiled an extensive list of proteins from whole saliva (WS) identified through MS experiments. The WS list is thereafter combined with the proteins identified from the ductal parotid, and submandibular and sublingual (parotid/SMSL) salivas. In parallel, a core dataset of the human plasma proteome with 3020 protein identifications was recently released. A total of 1939 nonredundant salivary proteins were compiled from a total of 19 474 unique peptide sequences identified from whole and ductal salivas; 740 out of the total 1939 salivary proteins were identified in both whole and ductal saliva. A total of 597 of the salivary proteins have been observed in plasma. Gene ontology (GO) analysis showed similarities in the distributions of the saliva and plasma proteomes with regard to cellular localization, biological processes, and molecular function, but revealed differences which may be related to the different physiological functions of saliva and plasma. The comprehensive catalog of the salivary proteome and its comparison to the plasma proteome provides insights useful for future study, such as exploration of potential biomarkers for disease diagnostics.

Comparative Human Salivary and Plasma Proteomes

“…Using a three-dimensional peptide fractionation strategy, the Minnesota lab compiled a list of 2340 proteins in whole saliva (with 60%, or 1395 proteins, identified at the 2-peptide or greater level) (Bandhakavi et al, 2009). Compared with the previously published WS proteome (Yan et al, 2009) (and supplemented by additional data from our lab), the data from the Minnesota group (Bandhakavi et al, 2009) added approximately 497 new WS protein identifications. (It is not clear, however, why 472 proteins in the previously reported WS protein list were not found in the Minnesota dataset.)…”

“…As before (Yan et al, 2009), we compared the WS proteome with the ductal parotid/SM/SL saliva proteome. Similarly, to examine the common nature of saliva and blood, we compared the saliva proteins with the plasma proteome.…”

“…Protein identifications from ductal saliva, i.e., parotid/SMSL, were the result of the NIDCR-supported consortium (Denny et al, 2008). The whole-saliva (WS) proteome was contributed by datasets from four research groups: the University of Minnesota, Research Triangle Institute, Calibrant Biosystems/University of Maryland, and the University of California, Los Angeles (UCLA) (Yan et al, 2009). This initial WS dataset was then augmented with a recent study by Griffin's lab (Bandhakavi et al, 2009) and newly acquired WS data from our lab.…”

“…The initial salivary proteome datasets were recently compiled and have been described previously (Yan et al, 2009). Protein identifications from ductal saliva, i.e., parotid/SMSL, were the result of the NIDCR-supported consortium (Denny et al, 2008).…”

Salivary B-type natriuretic peptide: a new method for heart failure diagnosis and follow-up

“…By contrast, saliva sampling is noninvasive, is not complicated by clotting, is easier to handle and process, and bears no risk of contracting blood-borne infections. Roughly 27% of the whole-saliva proteins are found in plasma, but nearly 40% of the proteins that have been suggested to be candidate markers for diseases such as cancer, cardiovascular disease, and stroke could be found in whole saliva [25].…”