Systematic comparison of the human saliva and plasma proteomes

Weihong Yan, Rolf Apweiler, Brian M. Balgley, Pinmanee Boontheung, Jonathan L. Bundy, Benjamin J. Cargile, Steve Cole, Xueping Fang, Mireya Gonzalez-Begne, Timothy J. Griffin, Fred Hagen, Shen Hu, Lawrence E. Wolinsky, Cheng S. Lee, Daniel Malamud, James E. Melvin, Rajasree Menon, Michael Mueller, Renli Qiao, Nelson L. RhodusJoel R. Sevinsky, David States, James L. Stephenson, Shawn Than, John R. Yates, Weixia Yu, Hongwe Xie, Yongming Xie, Gilbert S. Omenn, Joseph A. Loo, David T. Wong

    Research output: Contribution to journalArticlepeer-review


    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.

    Original languageEnglish (US)
    Pages (from-to)116-134
    Number of pages19
    JournalProteomics - Clinical Applications
    Issue number1
    StatePublished - 2009


    • Biomarkers
    • Body fluid
    • MS
    • Plasma
    • Saliva

    ASJC Scopus subject areas

    • Clinical Biochemistry


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