Abstract
Untargeted metabolomics is a technique used to detect the presence of all metabolites, or small-molecular-weight molecules, within a given sample. This technique is often accomplished through the use of liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). LC-MS/MS provides raw data that require the use of bioinformatics software to extract significant features. Many bioinformatics software options are available, such as Compound Discoverer and MS-DIAL. This protocol details the processing of raw data through both software for functional comparison and optimization.