The dataset presented in here is generated in a project named "Effects of sanitary and health status on amino acid and energy metabolism of growing-finishing pigs." The metabolomics data from two samples types in pigs were generated in collaboration with Metabolomics Facility Leiden, The Netherlands and Wageningen Livestock Research, The Netherlands. This collaboration was realized and funded by Enabling Technology Hotels programme, ZonMW, NWO, The Netherlands (project number: 435005015). Targeted quantification of metabolites in two metabolomic platforms covering amines and oxidative stress metabolites in the blood and saliva samples in pigs. The samples were collected from a feeding trial. Briefly, After weaning, i.e., at week 4, pigs were fed a starter (4-9 weeks), grower (9-14 weeks), and finisher (14-22 weeks) diet containing either starch or fat as an energy source. At week 9, before the pigs were fed the grower diet, blood plasma and saliva samples were collected from the pigs (n=6) and the animals were stratified according to different hygiene conditions. At week 14, i.e., before the pigs received the finisher diet, and at week 22, i.e., at the end of this experiment, blood plasma and saliva samples were collected from the pigs (n=6) in the cohort receiving a diet with a different energy source under contrasting sanitary status. Targeted quantification of metabolites in two metabolomic platforms covering amines and oxidative stress metabolites in the blood and saliva samples in pigs. The number of identified metabolites are shown in Table 1. Table 1: Number of identified amines and lipids metabolites in blood plasma and saliva samples in pigs. Data reported as Peak areas1 Relative response ratios4 Confidence2 Caution3 Confidence Caution Amines Blood plasma not required not required 58 2 Saliva not required not required 52 5 Lipids (low pH) Blood plasma 47 17 47 17 Saliva 18 34 52 11 Lipids (High pH) Blood plasma 24 25 24 25 Saliva 28 17 28 17 1 For the lipid platform, large variations in internal standard were observed between study samples. This could be due to the difference in matrix effect between the study samples, i.e., blood plasma and saliva. It is known that the matrix effect varies significantly depending on the origin of the samples and is influenced by phenotypic characteristics such as species, age, and gender. Therefore, peak areas were provided as an additional data set that can be used as input data for downstream metabolomics analysis. 2 Metabolite signaling complied with the acceptance criteria of RSDqc <15%. 3 Metabolite signaling did not comply with the acceptance criteria of our quality control i.e. of RSDqc <15%, but they present RSDs up to 30%. 4 target area/ISTD area; unit free. Available data-set: -Four different signaling lipids data-set: 1) peak areas for plasma samples, 2) peak area ratios (metabolite to ISTD) for plasma samples, 3) peak areas for saliva samples, and 4) peak area ratios (metabolite to ISTD) for saliva samples. - Two signalling amine data-set: 1) peak area ratios (metabolite to ISTD) for plasma samples, and 2) peak area ratios (metabolite to ISTD) for saliva samples.