Modern mass spectrometry faces increasing challenges in terms of sensitivity and selectivity, pushing the limits of current technology. These demands stem from the growing complexity of analysed samples, the need for high analytical throughput, and the inherent limitations of conventional fragmentation techniques. Ion fragmentation, a central element of tandem mass spectrometry, plays a crucial role in enhancing selectivity and sensitivity for the analysis of complex samples. However, collision-induced dissociation (CID), the dominant technique in most instruments, has significant limitations. These include difficulties in distinguishing isomers, sometimes insufficient selectivity, quantification issues due to non-specific fragmentations, and the loss of information on molecular modifications. To overcome these challenges, new fragmentation methods have emerged over the past few decades, notably electron-activated dissociation (EAD) and ultraviolet photodissociation (UVPD). While these techniques have proven useful in fields such as proteomics, glycomics, and lipidomics, their application to small molecule analysis remains limited.

As part of a collaboration with Sciex (Concord, ON, Canada), two mass spectrometers, a QTrap 6500+ and a ZenoTOF 7600, were modified both in hardware and software to integrate lasers (213, 266, and 355 nm) required for UVPD. These modifications addressed several technical challenges. On the hardware side, apertures were created to allow laser beam entry while maintaining vacuum integrity and supports allowing the positioning of lasers. For the ZenoTOF, a mirror was added to redirect the laser beam and precisely align its path with that of the ions, requiring for both instruments precise control of the potentials applied. In terms of acquisition software, numerous adaptations and tests were made to enable the sequential use of different fragmentation techniques, including UVPD, within a time frame compatible with chromatographic constraints.