Targeted profiling of organic acids offers a comprehensive view of cellular energy metabolism, covering glycolysis, the TCA cycle, and fatty acid oxidation. These metabolites act as critical indicators of mitochondrial efficiency, redox status, and metabolic flux. Quantitative organic acid profiling supports studies on energy homeostasis, oxidative stress, and nutritional metabolism, providing mechanistic insights into how cells regulate energy production and metabolic balance under different physiological or environmental conditions.

Quantitative analysis of organic acids enables precise characterization of metabolic dysregulation associated with inborn errors of metabolism, organic acidemias, and chronic metabolic diseases. Distinct organic acid signatures can reveal pathway disruptions, enzyme deficiencies, or accumulated intermediates, offering diagnostic value and clinical insight. These measurable biomarkers facilitate disease diagnosis, progression monitoring, and therapeutic response evaluation, advancing precision medicine and translational metabolomics research.

Many organic acids, including hippuric, phenolic, and indolic acids, arise from gut microbial metabolism and host–microbe interactions. Targeted LC–MS/MS quantification of these co-metabolites provides valuable insights into gut microbial activity, detoxification processes, and diet-induced metabolic modulation. This approach supports studies on nutrition, metabolic health, and microbiome function, enabling discovery of microbial biomarkers and evaluation of dietary or probiotic interventions.

In plants, organic acids are central intermediates in photosynthesis, respiration, and secondary metabolite biosynthesis. Their levels dynamically respond to abiotic and biotic stresses such as drought, salinity, and temperature fluctuations. Targeted profiling of TCA intermediates, phenolic acids, and shikimic acid derivatives reveals key pathways involved in carbon flow regulation, stress tolerance, and metabolic reprogramming. These insights support crop improvement, metabolic engineering, and quality evaluation in plant science research.