Serum amyloid A (SAA) concentration in plasma increases markedly following infl ammation or infection, with the liver being the principal site of its synthesis. SAA was fi rst reported to be associated with both human and animal HDLs in the late 1970s ( 1 ), but is also associated with other lipoprotein fractions ( 2 , 3 ). Further studies showed that HDL particles isolated from endotoxin-treated mice contain up to two SAAs per apoA-I molecule ( 4 ). When SAA containing HDL was reinjected into mice it was cleared from the plasma more rapidly than apoA-I ( 5 ‐ 8 ). However, isolation of SAA and its reconstitution with HDL to create SAA-enriched particles gives particles that on reinjection are more slowly cleared from plasma compared with native SAA containing HDL ( 5 ). HDL particles isolated from patients with myocardial infarction also contain SAA and are small ( 9 ), with a density similar to that of HDL 3 ( 10 ), but with a diameter resembling HDL 2 . The lipid content of these particles is reduced and enriched in triglyceride compared with HDL from healthy people ( 10 ‐ 12 ). During acute infl ammatory stress the principal protein bound to HDL 3 is SAA ( 13 ), not apoA-I, showing a reversal in the protein composition from normal HDL. SAA increases the binding affi nity of HDL to macrophages but reduces HDL binding to hepatocytes ( 14 ), suggesting that SAA directs HDL to preferentially remove cholesterol from sites of infl ammation ( 15 ), possibly through the formation of pre β HDL ( 16 ). HDL cholesteryl ester uptake from reconstituted HDL via SR-B1 is inhibited by the presence of SAA on the particles ( 17 ), but the effl ux of free cholesterol is enhanced through both SR-B1 ( 18 ) and ABCA1 ( 18 , 19 ) to SAA-containing HDL particles. Early studies of the HDL particle focused mainly on changes in the lipid and protein content as well as the structure, size, and clearance of the particles from plasma. Extensive investigations into identifying HDL ’ s protein cargo have suggested that the HDL proteome can be highly variable among individuals and altered in response to acute cardiac events ( 20 ). These studies suggest a need for accurate quantitative methods to carefully assess individual risk factors with regard to heart disease and HDL function. More recent work has begun to quantify the changes in the protein cargo of HDL under both normal conditions and infl ammatory stress. Mass spectrometry is the principal tool used for these studies, employing one of two methods. The fi rst method analyzes intact protein mixtures, called top-down proteomics ( 21 ‐ 23 ), and often involves electron transfer dissociation or electron capture dissociation to obtain amino acid sequence information that helps confi rm protein identifi cation. In the second, more commonly used method called bottom-up proteomics ( 24 ‐ 30 ), protein mixtures are digested with a single protease, usually trypsin. Protein identifi cation is based on accurate mass analysis of peptides combined with MS/MS peptide sequencing.