AppNote 216: In-time TMS Derivatization and GC-MS Determination of Sugars, Organic Acids and Amino Acids for High Throughput Metabolomics Studies


Metabolomics aims to identify the changes in endogenous metabolites of biological systems in response to intrinsic and extrinsic factors in clinical, food and nutrition, and environmental-based research. Gas chromatography-mass spectrometry (GC-MS) instruments are among the most commonly used in metabolomics studies, due to their high separation efficiency and good reproducibility compared to other platforms. This is primarily due to the robust, reproducible, and selective nature of the technique,
as well as the large number of well-established commercial libraries and authentic metabolite standards available to researchers. However, metabolomics-based samples require chemical modifications/ derivatization before GC-MS analysis. When processing large batches (> 20-40 samples), several potential issues can arise in the derivatization process. Sample-to-sample reproducibility for polar metabolites can vary significantly throughout sequences of large batches when all samples are derivatized simultaneously. This challenge lies predominantly in the time differences between when the samples are derivatized, and when the first and all subsequent samples are injected into the GC-MS. This issue is further exacerbated as the sample batch size becomes larger. Here we show how a GERSTEL MultiPurpose Sampler (MPS) with automatic tool exchange coupled to an Agilent 5977 GC-MSD can be used to overcome such challenges and improve the quality and reliability of the generated metabolomics data.