The metabolome is characterized by a large number of molecules exhibiting a high diversity of chemical structures and abundances, requiring complementary analytical platforms for extensive coverage. Of these analytical platforms, atmospheric pressure ionization Fourier transform mass spectrometry (FT/MS) instruments are popular because they provide accurate mass measurements with ppm and even sub-ppm errors, and also high and ultra-high resolving power. In this article, we evaluate the improvements provided for metabolomics by different types of FT/MS instruments, together with the ability of these platforms to cover the various analytical requirements: global metabolite profiling, absolute quantification and also structural characterization, of metabolomics. The specificities of FT/MS in terms of data pre-processing and the input of accurate mass measurements for biological interpretation and for highlighting metabolic networks are also addressed.
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