Ultraviolet Photodissociation of ESI and MALDI generated protein ions on a Q-Exactive mass spectrometer

The identification of molecular ions produced by MALDI or ESI strongly relies on their fragmentation to structurally informative fragments. The widely diffused fragmentation techniques for ESI multiply charged ions, are either incompatible (ECD and ETD) or show lower efficiency (CID, HCD), with the predominantly singly charged peptide and protein ions formed by MALDI. In source decay (ISD) has been successfully adopted to sequence MALDI generated ions, but it further increases spectral complexity and it is not compatible with Mass Spectrometry Imaging. Excellent UVPD performances, in terms of number of fragment ions and sequence coverage has been demonstrated for electrospray ionization for multiple proteomics applications. UVPD showed a much lower charge state dependence and so protein ions produced by MALDI may exhibit equal propensity to fragment. Here we report UVPD implementation on an Orbitrap Q-Exactive plus equipped with a ESI/EP-MALDI. UVPD of MALDI generated ions was benchmarked against MALDI-IS...