Abstract: As described herein, a robust generalizable method to accurately and sensitively quantitate proteins in tissues and fluids from human patients in a direct manner, not reliant on antibody reagents has been developed. This provides new and robust methods that are useful as biochemical outcome measures in human clinical trials. The methods where mouse tissues fully labeled with stable isotopes are mixed with the human tissue of interest, and the mixture subjected to high throughput proteomics methods are provided. The method detects multiple protein peptides showing 100% conservation between human and mouse, and establishes test and control proteins for quantitation of surrogate biomarkers. This assay method provides a high degree of reliability and sensitivity, as well as generalizability, compared to more traditional antibody-based assays. The specific peptide pairs and methods of quantitation are also described.