title: A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva.
abstract: Comprehensive identification of proteins in whole human saliva is critical for appreciating its full diagnostic potential. However, this is challenged by the large dynamic range of protein abundance within the fluid. To address this problem, we used an analysis platform that coupled hexapeptide libraries for dynamic range compression (DRC) with three-dimensional (3D) peptide fractionation. Our approach identified 2340 proteins in whole saliva and represents the largest saliva proteomic dataset generated using a single analysis platform. Three-dimensional peptide fractionation involving sequential steps of preparative isoelectric focusing (IEF), strong cation exchange, and capillary reversed-phase liquid chromatography was essential for maximizing gains from DRC. Compared to saliva not treated with hexapeptide libraries, DRC substantially increased identified proteins across physicochemical and functional categories. Approximately 20% of total salivary proteins are also seen in plasma, and proteins in both fluids show comparable functional diversity and disease-linkage. However, for a subset of diseases, saliva has higher apparent diagnostic potential. These results expand the potential for whole saliva in health monitoring/diagnostics and provide a general platform for improving proteomic coverage of complex biological samples.
authors.affiliation: Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street SE, Minneapolis, Minnesota 55455, USA.
authors.forename: Sricharan
authors.initials: S
authors.lastname: Bandhakavi
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Stone
authors.forename: Getiria
authors.initials: G
authors.lastname: Onsongo
authors.forename: Susan K
authors.initials: SK
authors.lastname: Van Riper
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Griffin
mesh_terms: D001798:Blood Proteins / Q000032:analysis; D030562:Databases, Protein; D006801:Humans; D025202:Molecular Diagnostic Techniques; D019151:Peptide Library; D011506:Proteins / Q000032:analysis; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods; D012463:Saliva / Q000737:chemistry*
chemical_list: D001798:Blood Proteins; D019151:Peptide Library; D011506:Proteins; D020543:Proteome