Fragmentation patterns of boron‐dipyrromethene (BODIPY) dyes by electrospray ionization high‐resolution tandem mass spectrometry

Rationale 4,4‐Difluoro‐4‐bora‐3 a ,4 a ‐diaza‐ s ‐indacene derivatives (BODIPYs) are fluorescent organic dyes that are widely used as non‐radioactive labels in biological analyses. The fragmentation behaviour of ten structurally related BODIPYs was studied using tandem mass spectrometry (MS/MS), to support the structural elucidation process during synthesis. Methods The BODIPYs were investigated by electrospray ionization (ESI)‐MS/MS, utilizing collision‐induced dissociation (CID) data from triple quadrupole MS and high‐resolution, accurate mass CID data from Fourier transform ion cyclotron resonance (FTICR) experiments. Results Unusual radical molecular cations ([M] +• ) were formed directly during the ESI process. These radical species dissociated into a large range of product ions during the subsequent CID experiments. Superimposed dissociations originating from parallel [M] +• and [M+H] + decompositions significantly complicated the interpretation of the MS/MS spectra. Conclusions Detailed dissociation mechanisms were proposed in this study for BODIPY dyes. The elemental formulae of CID product ions were unambiguously assigned using FTICR‐MS and unique fragment ions were discovered for the rapid identification of methyl, ethyl, butyl, tert ‐butyl, and phenyl substituents of individual dyes in BODIPY synthesis mixtures by low‐resolution MS. Copyright © 2015 John Wiley & Sons, Ltd.