Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissues

We developed 6,927 quantitative multiple reaction monitoring mass spectrometry (MRM-MS) assays that measure 2,187 unique proteins in 20 mouse organs and tissues to enable system-level analysis of protein expression in mice. Targets for assay development were selected by untargeted MS analysis, and corresponding stable isotope-labelled standards were synthesized in-house. Development experiments determined the lower limit of quantitation, linear range, and repeatability of each assay. Subsequently, the developed assays were formatted into panels tailored to each organ or tissue type and were used to measure normal protein concentrations in samples from three mouse strains; C57BL/6NCrl, NOD/SCID, and BALB/cAnNCrl. In total 5,149 measurements were obtained corresponding to 1,691 unique proteins, and results included sex- and strain-specific profiles in protein abundances. Collectively, these assays are the largest group of quantitative MRM-MS assays established and implemented in mice to date, and enable accurate quantitation of mouse proteins for molecular phenotyping. Furthermore, the measured concentration data provide important biological information for experimental design involving mouse models.