In this work, the separation and characterization of ionizable organic polymers nonsoluble in water is carried out using nonaqueous capillary electrophoresis-ion trap mass spectrometry (NACE-MS). The polymers studied are poly(N(epsilon)-trifluoroacetyl-l-lysine) (poly(TFA-Lys)) obtained by ring-opening polymerization of the corresponding N-carboxyanhydride. Different parameters (i.e., liquid sheath nature and flow rate, electrospray temperature, and separation buffer composition) are optimized in order to obtain both an adequate CE separation and a high MS signal of the samples under study. The optimum NACE-MS separation conditions allow the molecular mass characterization of poly(TFA-Lys) up to a degree of polymerization of 38. NACE-MS provides interesting information on the chemical structure of (i). the polymer end groups and (ii). other final byproducts. The MS spectra obtained by using this CE-MS protocol confirm that the polymerization was initiated by the reaction of n-hexylamine (initiator) on the monomer. CE-MS-MS and CE-MS-MS-MS results demonstrate that two different termination reactions occurred during the polymerization process leading to the transformation of the reactive amine end group into a carboxylic or a formyl groups. Byproducts such as 3-hydantoinacetic acid or diketopiperazine were also detected. To our knowledge, this is the first work in which the great possibilities of NACE-MS and NACE-MS(n) for characterizing synthetic polymers are demonstrated.