Radio isotopes are commonly used as tracers to study the fate of acetate in anaerobic digester [7,11]. Radio isotope tracer is not a method of choice due to the strict safety requirement in handling radioisotopes [3]. An alternative method is the use of stable isotope pairing and the measurement of isotopically enriched products with hyphenated mass spectrometry techniques (GC/MSand HPLC/MS). GC/MS and HPLC/MS have been successfully employed for determining isotope enrichment of SCFA from plasma and urine samples in the field of clinical chemistry [12]. The separation of individual SCFA from a complex biological sample is provided by either HPLC or GC, whereas the tracer/trace ratio (TTR) which is proportional to the ion-current ratio of the labeled/unlabeled species is determined by the mass spectrometer.