Spinal cord injury (SCI) has shown to induce changes in healthy gut microbiome and cause gut dysbiosis, leading to a reduction of bacteria responsible for the synthesis of short-chain fatty acids (SCFA). SCFAs have a variety of anti-inflammatory and immune properties, and it has been hypothesised that SCI leads to changes in concentration of circulating SCFAs, leading to a variety of health issues, including neural damage. Due to this, SCFAs pose as clinical markers, and the effect of SCI on SCFA concentration can be studied in rat models. SCFAs are usually quantified using gas chromatography coupled with mass spectrometry (GC-MS) because of their volatility. However, there is a growing number of quantification studies done using liquid chromatography coupled with mass spectrometry (LC-MS). To examine SCFAs as clinical markers, the derivatization and extraction methods were optimised as were parameters used for multiple reaction monitoring (MRM) using tandem mass spectrometry. The protocol included derivatisation using 3- nitrophenylhydrazine hydrochloride (3-NPH). Following derivatisation, eleven SCFA standards were injected onto a liquid chromatography tandem mass spectrometry (LC-MS/MS) system for MRM parameters optimization. Deuterated internal standards (ISTD) were used to identify and account for the matrix effect (ME) and method recovery. SCFAs from plasma samples of SCI rats and sham-control rats (n=5 per group) were extracted and analysed using the LC-MS/MS method to test whether there is a difference in SCFA concentration between sham and SCI samples. Results showed a successful chromatographic separation of all SCFA standards, however only three out of eleven SCFAs showed a statistically significant difference in concentrations between SCI and sham groups. To draw firm conclusions, the experiment should be performed on a larger sample size.