This CDC invention is a method for identifying and quantifying a group of proteins in a complex mixture by a liquid chromatography-tandem mass spectrometry assay. The technology was developed for influenza although it can be used for a wide variety of protein quantification applications. As specifically developed, conserved peptides from the proteins of influenza (hemagglutinin, neuramidase, matrix 1 and 2, and nucleoprotein) have been synthesized and labeled to be used as internal standards for the quantification of those proteins in a complex (biological or manufactured) matrix. One or more of these peptides can be used to simultaneously detect and quantify the target proteins by establishing mass ratios and calibration curve comparison. This method for quantifying influenza proteins and peptides in samples has potential for improving vaccine production quality control and therefore, the effectiveness and overall cost-efficiency of influenza vaccines.