An ultrafast, reliable and economical approach for quantitative salivary proteomic profiling and oral cancer biomarker discovery

ABSTRACT: Clinical biomarkers identified by shotgun proteomics require proteins in body fluids or tissues to be enzymatically digested before being separated and sequenced by Liquid Chromatography-tandem Mass Spectrometry (LC-MS/MS). How well peptide signals can be resolved and detected is largely dependent on the quality of sample preparation. Conventional approaches such as in-gel, in-solution, and filter-based digestion, despite their extensive implementation by the community, become less appealing due to their unsatisfying protein/peptide recovery rate, lengthy sample processing, and/or less cost-effectiveness. Suspension Trapping has recently been demonstrated as an ultrafast approach for proteomics analysis. Here, for the first time, we extend its application to human salivary proteome analyses. In particular, we present a simple self-assembled glass fiber filter device, which can be packed with minimal difficulty, is extremely cost-effective and maintains the same performances as commercial filters. As a proof-of-principle, we analyzed the whole saliva from 8 healthy individuals as well as a cohort of 10 subjects of oral squamous cell carcinoma (OSCC) patients and non-OSCC subjects. Label-free quantification revealed surprisingly low inter-individual variability, and identified several known markers. Our study provides the first evidence of an easy-to-use and nearly cost-free device for clinical proteomics as well as for general proteome sample preparation.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Saliva

DISEASE(S): Oral Squamous Cell Carcinoma

SUBMITTER: Yanbao Yu  

LAB HEAD: Yanbao Yu

PROVIDER: PXD012436 | Pride | 2019-03-12

REPOSITORIES: pride