Amino acid analysis of peptides using isobaric-tagged isotope dilution LC-MS/MS

Protein quantification using stable isotope dilution mass spectrometry requires the quantification of specific peptides unique to the protein of interest. Since these peptides are used as calibration standards, accurate and precise measurement of these target peptides is critical. This peptide measurement has typically been made by amino acid analysis (AAA) using absorbance or fluorescence detection methods. This approach can be limited to only a few amino acids, is often not traceable to high-quality reference standards, and not uncommonly has coefficients of variation (CVs) that exceed 10%. We report here an isobaric-tagged isotope dilution mass spectrometry method for AAA that provides excellent sensitivity, specificity, and precision; utilizes a broad range of amino acids; and uses U.S. National Institute of Standards and Technology (NIST) amino acid standards for an accuracy base. The average CV for the method applied to three different peptides with measurements on 7 different days was 3.57% (range 2.72-4.20%). We applied this method to the quantification of three NIST standard peptides and hemagglutinin, an influenza virus surface protein.