A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva

Sricharan Bandhakavi, Matthew D. Stone, Getiria Onsongo, Susan K. Van Riper, Timothy J. Griffin

Research output: Contribution to journalArticle

112 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)5590-5600
Number of pages11
JournalJournal of Proteome Research
Volume8
Issue number12
DOIs
StatePublished - Dec 4 2009

Fingerprint

Proteome
Fractionation
Saliva
Peptides
Proteins
Salivary Proteins and Peptides
Proteomics
Libraries
Fluids
Liquid chromatography
Cations
Blood Proteins
Health
Isoelectric Focusing
Reverse-Phase Chromatography
Monitoring

Keywords

  • 3D-peptide fractionation
  • Dynamic range compression
  • Hexapeptide libraries
  • Saliva
  • Shotgun proteomics

Cite this

A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva. / Bandhakavi, Sricharan; Stone, Matthew D.; Onsongo, Getiria; Van Riper, Susan K.; Griffin, Timothy J.

In: Journal of Proteome Research, Vol. 8, No. 12, 04.12.2009, p. 5590-5600.

Research output: Contribution to journalArticle

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