GC-MS for untargeted metabolomics is a well-established technique. Small molecules and molecules made volatile by derivatization can be measured and those compounds are key players in main biological pathways. This tutorial provides ready-to-use protocols for GC-MS-based metabolomics, using either the well-known low resolution approach (GC-Q-MS) with nominal mass or the more recent high resolution approach (GC-QTOF-MS) with accurate mass, discussing their corresponding strengths and limitations. Analytical procedures are covered for different types of biofluids (plasma/serum, bronchoalveolar lavage, urine, amniotic fluid) tissue samples (brain/hippocampus, optic nerve, lung, kidney, liver, pancreas) and samples obtained from cell cultures (adipocytes, macrophages, Leishmania promastigotes, mitochondria and culture media). Together with the sample preparation and data acquisition, data processing strategies are described specially focused on Agilent equipment’s, including deconvolution software and database annotation using spectral libraries. Manual curation strategies and quality control are also deemed. Finally, considerations to obtain a semiquantitative value for the metabolites are also described. As a case study, an illustrative example from one of our experiments at CEMBIO Research Center, is described and findings discussed.

用于非靶向代谢组学的 GC-MS 是一项成熟的技术。可以测量通过衍生化而产生挥发性的小分子和分子，这些化合物是主要生物途径中的关键参与者。本教程为基于 GC-MS 的代谢组学提供即用型方案，使用具有标称质量的众所周知的低分辨率方法 (GC-Q-MS) 或更新的高分辨率方法 (GC-QTOF-MS)精确质量，讨论它们的相应优势和局限性。涵盖不同类型的生物流体（血浆/血清、支气管肺泡灌洗液、尿液、羊水）组织样本（脑/海马、视神经、肺、肾、肝、胰腺）和从细胞培养物中获得的样本（脂肪细胞、巨噬细胞）的分析程序,利什曼原虫前鞭毛体、线粒体和培养基）。除了样品制备和数据采集之外，还特别针对安捷伦设备描述了数据处理策略，包括反卷积软件和使用光谱库的数据库注释。还考虑了手动管理策略和质量控制。最后，还描述了获得代谢物半定量值的考虑。作为案例研究，我们描述了我们在 CEMBIO 研究中心进行的一项实验的说明性示例，并讨论了结果。