Inositol phosphates (InsPs) are ubiquitous in all eukaryotes. However, since there are 63 possible different phosphate ester isomers, the analysis of InsPs is challenging. In particular, InsP ₁ , InsP _2, and InsP ₃ already amass 41 different isomers, of which some occur as enantiomers. Profiling of these "lower" inositol phosphates in mammalian tissues requires powerful analytical methods and reference compounds. Here, we report an analysis of InsP ₂ and InsP ₃ with capillary electrophoresis coupled to electrospray ionization mass spectrometry (CE-ESI-MS). Using this method, the bacterial effector RipBL1 was analyzed and found to degrade InsP ₆ to Ins(1,2,3)P ₃ , an understudied InsP ₃ isomer. This new reference molecule then aided us in the assignment of the isomeric identity of an InsP ₃ while profiling human samples: in urine and kidney stones, we describe for the first time the presence of defined and abundant InsP ₃ isomers, namely Ins(1,2,3)P ₃ , Ins(1,2,6)P ₃ and/or Ins(2,3,4)P ₃ .