Reconsidering mass spectrometric fragmentation in electron ionization mass spectrometry – new insights from recent instrumentation and isotopic labelling exemplified by ketoprofen and related compounds

Rationale In various fields of chemical analyses, structurally unknown analytes are considered. Proper structure confirmation may be challenged by the low amounts of analytes that are available, e.g. in early stage drug development, in metabolism studies, in toxicology or in environmental analyses. In these cases, mass spectrometric techniques are often used to build up structure proposals for these unknowns. Fragmentation reactions in mass spectrometry are known to follow definite pathways that may help to assign structural elements by fragment ion recognition. This work illustrates an investigation of fragmentation reactions for gas chromatography/electron ionization mass spectrometric characterization of benzophenone derivatives using the analgesic drug ketoprofen and seven of its related compounds as model compounds. Methods Deuteration and 18O‐labelling experiments along with high‐resolution accurate mass and tandem mass spectrometry (MS/MS) were used to further elucidate fragmentation pathways and to substantiate rationales for structure assignments. Low‐energy ionization was investigated to increase confidence in the identity of the molecular ion. Results The high‐resolution mass analyses yielded unexpected differences that led to reconsideration of the proposals. Site‐specific isotopic labelling helped to directly trace back fragment ions to their respective structural elements. The proposed fragmentation pathways were substantiated by MS/MS experiments. Conclusions The described method may offer a perspective to increase the level of confidence in unknown analyses, where reference material is not (yet) available.