Rationale Rapid structural elucidation of unknown pharmaceutical impurities is critical throughout the whole life cycle of drug development. It can be achieved by using multi-stage mass spectrometric analysis, in conjunction with the understanding of fragmentation mechanisms of the ions generated by electrospray ionization. Methods Liquid chromatography-UV/photo diode array detection - high resolution multi-stage mass spectrometric analysis (HiRes MS n) was used to elucidate the structure of an impurity of silodosin. The structure was confirmed by 1D and 2D NMR spectroscopy. Results The impurity is identified as N-cyanomethylsilodosin, a solution degradant of silodosin. A novel 1,3-sigmatropic rearrangement was observed during one of its MS 3 fragmentation pathways. A mechanism is proposed for the 1,3-sigmatropic rearrangement, which is supported by the MS n behavior of a 13C-isotope labelled derivative of N-cyanomethylsilodosin. Conclusion Elucidation of such an intra-molecular rearrangement mechanism not only enriches our understanding of the gas phase fragmentation chemistry, but also should facilitate future rapid structural characterization of unknown pharmaceutical impurities and metabolites using multi-stage mass spectrometric analysis.