Differential and non‐labeling quantitative peptidomics reveals the circulating peptide biomarkers for the disease in the blood

Abstract

The low‐molecular‐weight proteome, peptidome, is a source of potential biomarkers for the disease. However, almost all detected peptides in previous reports are fragments originating from highly abundant plasma proteins. In addition, the major plasma proteins in blood mask the presence of circulating peptide biomarkers indicative of the disease state, making the discovery of such biomarkers challenging. Here we have established the methodology for differential and quantitative serum peptidome profiling that is efficient in the discovery of these biomarkers. By using non‐labeling and quantitative 2D‐LC‐MALDI‐TOF MS, all of the MS spectra from 1,152 fractions per sample were analyzed using a total of about 170 serum samples consisting of healthy individuals and patients with liver disease, i.e., chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Upon such analysis, we were able to identify circulating peptides useful as diagnostic biomarkers, including a glycosylated fragment and cellular proteins that are present at low concentrations in serum. These results indicate that circulating peptides at low abundance, particularly those of a cellular origin, are potential biomarkers for the virus‐related chronic liver disease and may contribute to molecular diagnostics and early intervention of virus‐related hepatocellular carcinoma.