Novel mass spectrometric immunoassays (MSIAs) for the isolation and structural characterization of plasma apolipoprotein A-I (apoA-I), apoA-II, and apoE have been developed. The assays combine selective isolation of apolipoprotein species via affinity capture with mass-specific detection using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. In application, plasma (from 50 l of whole blood drawn from individuals, using finger lancet) was addressed with affinity pipette tips derivatized with antibodies toward the specific apolipoprotein. The time required for each assay was ف 15 min, less if assays on multiple individuals were performed in parallel. In a brief study of five individuals, several recently reported apoA-II variants were identified and observed consistently in all individuals. Additionally, the apoE phenotype of E3/ E3 was observed in three of the individuals, and E2/E3 and E3/E4 observed in the remaining two individuals, the latter of whom suffers from Alzheimer's disease. Overall, the MSIA approach offers a rapid, sensitive, and highly accurate means of profiling apolipoproteins from small volumes of plasma. The apolipoproteins represent a significant class of proteins whose functions range from enzyme activation (e.g., LCAT and lipoprotein lipase) to lipid/cholesterol transport and clearance. Although well studied over the past two decades, it has only recently become clear that mutations present within the apolipoproteins may be responsible for, or assist in, the progression of disease. Table 1 gives a brief overview of some diseases correlated with specific mutations present within apolipoproteins. Universally, these mutations are commonly studied on the DNA level using a variety of genotyping assays. For instance, apolipoprotein E (apoE) genotyping usually involves PCR amplification of short subsequences of exons 2 and 3 (containing both polymorphic sites) and analysis of the PCR products by: 1 ) dot blot hybridization with allele-specific oligonucleotide probes (1); 2 ) oligonucleotide ligation assay (2); 3 ) single-stranded conformational polymorphisms (3); or, 4 ) restriction fragment-length polymorphism analysis using restriction enzymes recognizing the sites of polymorphism (4). More advanced approaches involve competitive amplified single mutation detection by selective probe hybridization immunoassay (5) or primer-extension mass spectrometry assays directed at the polymorphic sites within the gene (6). This latter assay brings to the analysis the direct detection of indicators (extended primers containing the base complement of the polymorphism) at exact mass values, thus enabling an assay that is free of artifacts encountered in other assays using, e.g., electrophoretic gel shifts or differential hybridization.As with the nucleic acid mass spectrometry assays, direct mass spectrometric analysis of proteins (or proteolytic fragments) brings an unprecedented degree of analytical accuracy to the analysis of point mutations. However, whereas the polym...