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Myo-Inositol phosphates (InsPs) are second messengers involved in signaling processes in eukaryotes. In principle, 63 phosphorylated InsPs can be generated by sequential phosphorylation of the OH groups of inositol, resulting in significant analytical ramifications. Moreover, the fully phosphorylated inositol hexakisphosphate InsP6, the usually most abundant species, can be further phosphorylated to diphospho-inositol polyphosphates (PP-InsPs), called inositol pyrophosphates. The analysis of myo-inositol phosphates (InsPs) and myo-inositol pyrophosphates (PP-InsPs) is a daunting challenge due to the large number of possible isomers, the absence of a chromophore, the high charge density, the low abundance, and the instability of the esters and anhydrides. In this service, capillary electrophoresis (CE) coupled to electrospray ionization mass spectrometry (ESI-MS) is implemented to analyze complex mixtures of InsPs and PP-InsPs with high sensitivity.