Self-Assembled STrap for Global Proteomics and Salivary Biomarker Discovery

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.
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 lowcost-effectiveness. Suspension trapping has
recently been demonstrated as an ultrafast approach for proteomic
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 performance 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 interindividual
variability and several known markers. Our study provides the first
evidence of an easy-to-use and low-cost device for clinical proteomics
as well as for general proteomic sample preparation.