Label-Free Quantitative Differential Expression Proteomics of Formalin-Fixed Paraffin-Embedded Liver Biopsy Samples from a Longitudinal Study of Hepatitis C Patients

摘要

A set of nearly sixty highly-curated and histologically annotated FFPE liver needle biopsy samples was profiled with quantitative label-free differential expression proteomics to a depth of >1,000 proteins with 2 or more peptides to match and 1,700 protein groups in all. Nearly 200 proteins showed differential expression with one or more histological measures of fibrosis according to ANOVA with FDR correction 30 proteins show statistical significance with all histological measures, 2 or more peptides to match, and low technical variance (<25% CV in QC Pool) 27 of these 30 proteins have been measured in a recent deep-coverage assessment of the human plasma proteome, suggesting that translation of 90% of the putative biomarkers for fibrosis to plasma is at least technically feasible using mass spectrometry.