Method for the simultaneous quantitation of apolipoprotein E isoforms using tandem mass spectrometry

Using apolipoprotein E (ApoE) as a model protein, we developed a protein isoform analysis method utilizing stable isotope labeling tandem mass spectrometry (SILT MS). ApoE isoforms are quantitated using the intensities of the b and y ions of the ¹³C-labeled tryptic isoform-specific peptides versus unlabeled tryptic isoform-specific peptides. The ApoE protein isoform analysis using SILT allows for the simultaneous detection and relative quantitation of different ApoE isoforms from the same sample. This method provides a less biased assessment of ApoE isoforms compared to antibody-dependent methods, and may lead to a better understanding of the biological differences between isoforms.