The use of metabolomics in nutrition-related research has made a significant impact on assessing novel biomarkers of dietary intake as well as analyses of intervention studies. Mass spectrometry and proton nuclear magnetic resonance spectroscopy are the two key experimental technologies in the field. NMR spectroscopy could provide information on lipoprotein subclass distribution and lipoprotein particle concentrations, low-molecular-weight metabolites as well as detailed molecular information on serum lipids. It is suggested that besides the measurement of standard lipids, including total cholesterol, LDL cholesterol and HDL cholesterol concentrations, the measurement of specific HDL subclasses might help in evaluation of the risk of cardiovascular events. Increased concentration of large HDL particles has inverse association with the risk of coronary artery disease, while small HDL particles appear to be associated with increased risk. Lipid Oxysophocarpine transfer proteins phospholipid transfer protein and cholesterol ester transfer protein are among factors which modify HDL composition and also affect efficiency of HDL-mediated reverse cholesterol transport. HDL associated enzyme paraoxonase 1 also is an important factor regulating anti-oxidative processes of lipoprotein particles, mainly LDL and HDL. Few studies so far examined cross-sectional association between nutrients and lipoprotein subclasses suggest that alcohol, disaccharides, and n-3 PUFAs are associated with serum lipoprotein subclass distribution. Controlled trials have focused on n3 PUFAs, mainly using supplements. Most studies investigating the effects of n-3 PUFAs or fatty fish on HDL particle subspecies have reported increases in large HDL particles and/or decreases of small HDL particles. In our pilot study, fatty fish intake at least 4 times per week increased HDL particle size. Considering whole dietary patterns, positive Benzethonium Chloride associations have been reported between a high-fat, high-sucrose and low fiber dietary pattern and concentrations of serum triglycerides and small dense HDL particles, larger Tg-enriched VLDL particles and small dense LDL particles. We have previously shown that a diet rich in whole grain and low insulin response grain products, fatty fish and berries alter plasma lipidomic profile and improves glucose metabolism and markers of endothelial function and inflammation. In the present secondary analyses of the same trial, we take the advantage of the comprehensive information provided by the new serum NMR-based metabolomics platform and examine the combined effects of these food items on the systemic metabolic profiles and lipid transfer protein activities in subjects with the metabolic syndrome. Furthermore, we study the associations between the changes in fish intake and changes in variables related to large HDL particles, and cross-sectional correlations between the lipid transfer protein activities and variables related to large HDL particles, and between average diameter of HDL and LDL particles and serum Tg. Based on primary aim of seeing changes in glucose metabolism, the power calculations were calculated based on fasting glucose. By using test significance a-level 0.05, 80% power, SD 0.4665 for variability, aim to see 5% difference between the groups in fasting glucose and power analysis method for two-sample t-test, the appropriate sample size was 37 per group. Statistical analyses were performed using the IBM SPSS statistical software, R Project for Statistical Computing version 2.7.2 and nlme R-package version 3.1�C96.