Multiple-reaction monitoring-mass spectrometric assays can accurately measure the relative protein abundance in complex mixtures

BACKGROUND: Mass spectrometric assays could poten-tially replace protein immunoassays in many applica-tions. Previous studies have demonstrated the utility of liquid chromatography–multiple-reaction monitoring– mass spectrometry (LC-MRM/MS) for thequantification of proteins in biological samples, and many examples of the accuracy of these approaches to quantify supple-mented analytes have been reported. However, a direct comparison ofmultiplexed assays that use LC-MRM/MS with established immunoassays to measure endogenous proteins has not been reported. METHODS: We purified HDL from the plasma of 30 hu-man donors and used label-free shotgun proteomics approaches to analyze each sample.We then developed 2 different isotope-dilution LC-MRM/MS 6-plex as