This article is available online at http://www.jlr.org Acetyl-CoA carboxylase (ACC) is the rate-controlling enzyme in the fatty acid biosynthetic pathway, and catalyzes the formation of malonyl-CoA from acetyl-CoA plus bicarbonate. Malonyl-CoA is not only substrate for fatty acid synthase (FAS) but is also a potent inhibitor of carnitine palmitoyl transferase 1 ( 1 ), the rate-limiting enzyme of fatty acid  -oxidation. Therefore, malonyl-CoA is a key molecule that controls fatty acid metabolism in the body. In addition, recent studies have shown that the level of hypothalamic malonyl-CoA is dynamically regulated by fasting and feeding and that it alters subsequent feeding behavior ( 2 ).To determine ACC activity in tissues, an invasive tissue biopsy is necessary. However, whole body synthesis of fatty acid may be evaluated by the quantifi cation of serum malonyl-CoA metabolites. This concept originates from our previous studies, which showed that serum concentrations of the immediate products of the rate-controlling enzymes in cholesterol and bile acid biosynthetic pathways refl ected the activities of the rate-controlling enzymes and whole body cholesterol and bile acid biosynthesis ( 3 ). Furthermore, patients with malonyl-CoA decarboxylase (MCD) defi ciency, who must have increased tissue malonyl-CoA concentrations, are characterized by markedly elevated urinary malonic acid (MA), called "malonic aciduria" ( 4 ). This phenomenon suggests that malonyl-CoA is easily hydrolyzed into MA by an unidentifi ed tissue thioesterase(s). Therefore, we thought that serum MA concentrations might well refl ect total body FAS.Abstract We describe a new sensitive and specifi c method for the quantifi cation of serum malonate (malonic acid, MA), which could be a new biomarker for de novo lipogenesis (fatty acid synthesis). This method is based upon a stable isotope-dilution technique using LC-MS/MS. MA from 50 l of serum was derivatized into di-(1-methyl-3-piperidinyl)malonate (DMP-MA) and quantifi ed by LC-MS/MS using the positive electrospray ionization mode. The detection limit of the DMP-MA was approximately 4.8 fmol (500 fg) (signal-to-noise ratio = 10), which was more than 100 times more sensitive compared with that of MA by LC-MS/MS using the negative electrospray ionization mode. The relative standard deviations between sample preparations and measurements made using the present method were 4.4% and 3.2%, respectively, by one-way ANOVA. Recovery experiments were performed using 50 l aliquots of normal human serum spiked with 9.6 pmol (1 ng) to 28.8 pmol (3 ng) of MA and were validated by orthogonal regression analysis. The results showed that the estimated amount within a 95% confi dence limit was 14.1 ± 1.1 pmol, which was in complete agreement with the observed X 0 = 15.0 ± 0.6 pmol, with a mean recovery of 96.0%. This method provides reliable and reproducible results for the quantifi cation of MA in human serum. Abbreviations: ACC, acetyl-CoA carboxylase; DMP-MA, Di-(1-methyl-3-piperidinyl)malonate; FAS, fatty aci...