Exploring peptide capture by anti-protein antibodies for LC-MS-based biomarker determination

Immunocapture LC-MS/MS is a promising technique to ensure high sensitivity and selectivity of low-abundant protein biomarkers. For this purpose, the use of monoclonal antibodies (mAb) is especially attractive as they are renewable reagents that can be standardized. In this article we investigated the possibility of using mAbs developed against intact proteins (anti-protein antibodies) to capture proteotypic epitope peptides. Three mAbs were tested, and all selectively extracted proteotypic epitope peptides from a complex sample. Compared to intact protein extraction, this concept which we call peptide capture by anti-protein antibodies provided cleaner extracts, which further improved the sensitivity. Analysis of three patient samples demonstrated that p can be used for the determination of different endogenous protein levels.