Installation protocol for charge transfer dissociation mass spectrometry on ion trapping mass spectrometers.

Rationale: Charge transfer dissociation (CTD) is a novel fragmentation technique that demonstrates enhanced structural characterization for a wide variety of molecules compared to standard fragmentation techniques like collision‐induced dissociation (CID). Alternative fragmentation techniques, such as electron transfer dissociation, electron capture dissociation, and ultraviolet photodissociation, also overcome many of the shortfalls of CID, but none of them are a silver bullet that can adequately characterize a wide variety of structures and charge states of target compounds. Given the diversity of structural classes and their occasional obstinance towards certain activation techniques, alternative fragmentation techniques are required that rely on novel or alternative modes of activation. Methods: Herein, we present a step‐by‐step protocol for the installation of CTD on a quadrupole ion trap mass spectrometer and best practices for optimizing the signal‐to‐noise ratio and acquisition times for CTD mass spectra. Results: In addition to two CTD installations in the Jackson laboratory, CTD has also been installed, and is currently in operation, on two 3D ion trap mass spectrometers in France: one in the laboratory of Dr. David Ropartz and Dr. Hélène Rogneaux at INRAE in Nantes, and the other in the laboratory of Dr. Jean‐Yves Salpin at Université d'Évry Val‐d'Essonne, part of the Paris‐Saclay University system. Conclusions: Here, we provide a visual protocol to help others accomplish the instrument modification. [ABSTRACT FROM AUTHOR]