Liquid chromatography-mass spectrometry (LC-MS) based nontargeted metabolomics has been applied to a wide range of biological samples and can provide information on thousands of compounds. However, reliable identification of the compounds remains a challenge affecting result interpretation. In this protocol, we describe comparable yeast cell and whole blood metabolome sample preparation for extracting similar compound groups, and we present a LC-MS method using the all ion fragmentation (AIF) approach for the purposes of increasing accuracy in metabolite annotation. Our method enables database-dependent targeted as well as nontargeted metabolomics analysis from the same data acquisition, while simultaneously improving the accuracy in metabolite identification to increase the quality of the resulting biological information.
Keywords: All ion fragmentation (AIF); Liquid chromatography–mass spectrometry (LC-MS); Metabolite annotation; Metabolomics.