Coupling matrix-assisted ionization with high resolution mass spectrometry and electron transfer dissociation to characterize intact proteins and post-translational modifications.

Matrix-assisted ionization (MAI) is a recently developed ionization technique that produces multiply charged ions on either electrospray ionization (ESI) or matrix-assisted laser desorption/ionization (MALDI) platform without the need of high voltage or laser ablation. In this study, MAI has been coupled to a high resolution accurate mass (HRAM) hybrid instrument, the Orbitrap Elite mass spectrometer, with electron transfer dissociation (ETD) module for fast peptide and intact protein characterization. The softness of MAI process preserves labile post-translational modifications (PTM) and allows fragmentation and localization by ETD. Moreover, MAI on ESI platform allows rapid sample preparation and analysis (~ 1 min/sample) due to the easiness of sample introduction. It significantly improves the throughput compared to ESI direct infusion and MAI on MALDI platform, which usually takes more than 10 min/sample. Intact protein standards, protein mixtures, and neural tissue extracts have been characterized using this instrument platform with both full MS and MS/MS (CID, HCD, and ETD) analyses. Furthermore, the performances of ESI, MALDI, and MAI on both platforms have been tested to provide a systematic comparison among these techniques. With improved ETD performance and PTM analysis capabilities, we anticipate that the HRAM MAI-MS with ETD module will offer greater utilities in large molecule characterization with enhanced speed and coverage. These advancements will enable promising applications in bottom-up and top-down protein analyses. Graphical abstract Matrix-assisted ionization (MAI) for characterizing intact proteins and post-translational modifications with representative mass spectra from intact proteins.