In the companion report (Bederman, I. R., Reszko, A. E., Kasumov, T., David values of (i) lower and upper limits for the precursor enrichment, (ii) the shape of the gradient, and (iii) the fractional synthesis. At each step, the mass isotopomer distributions of the samples were analyzed by ISA and the two-isotopomer method to determine whether each method could correctly (i) detect gradients of precursor enrichment, (ii) estimate the gradient limits, and (iii) estimate the fractional synthesis. The two-isotopomer method did not identify gradients of precursor enrichment and underestimated fractional synthesis by up to 2-fold in the presence of gradients. ISA uses all mass isotopomers, correctly identified imposed gradients of precursor enrichment, and estimated the expected values of fractional synthesis within the constraints of the data.In the companion report (1) (2) of the activities of glycolytic (2-5) and lipogenic enzymes (7-9) (perivenous Ͼ periportal) versus the activity of cytosolic acetyl-CoA synthetase (periportal Ͼ perivenous) (10). Gradients of precursor enrichment were detected using isotopomer spectral analysis (ISA) (11). In addition, we found that fractional lipogenesis calculated by the two-isotopomer method (an algebraic method similar to that described by Chinkes et al. (12)) produces lower estimates of fractional synthesis than those produced by the best fit estimates of ISA. Although the "linear gradient" ISA model (see companion report (1) for model definitions) yielded a better fit than the "Single pool" ISA model, it was not possible to evaluate the effect of gradients on estimates of fractional synthesis. Thus, we could not quantitatively evaluate the performance of the ISA in comparison to the two-isotopomer method, because the true rates of fractional synthesis in the liver dog and rat liver perfusion study were unknown.The goal of the present study was to evaluate the differences in estimates of precursor enrichment and fractional synthesis calculated by the two-isotopomer method and ISA. We used an experimental model where both the gradient in precursor enrichment and the fractional synthesis are known. This was accomplished by in vitro preparations that simulated the zonation of acetyl-CoA enrichment. Lipogenesis from sub-populations of hepatocytes across the liver lobule was simulated, in parallel incubations, by synthesizing a fatty acid using purified fatty acid synthase (13,14) and [U-13 C 3 ]malonyl-CoA of varying enrichment. We used gradients of malonyl-CoA enrichment, because fatty acid synthesis involves the conversion to malonyl-CoA of all acetyl units added to the primer. We used [U-13 C 3 ]propionyl-CoA as a primer to avoid the possibility of contamination of our newly synthesized pentadecanoate with unlabeled pentadecanoate. In the presence of unlabeled malonyl-CoA, the process yields M3 2 [13,14, C 3 ]pentadecanoate. By monitoring the distribution of M3 to M15 isotopomers of pentadecanoate, we simulated in vitro the polymerization of six [13 C]acetyl units