Top-Down Mass Spectrometry of a Clinical Antibody Light Chain Using the Omnitrap-Orbitrap-Booster Platform

The Omnitrap-Orbitrap-Booster (OOB) mass spectrometry (MS) platform was developed to advance top-down (TD) MS analysis of proteins. It integrates a multimodal tandem mass spectrometry (MS/MS) ion trap system (OmnitrapTM), a high-resolution Orbitrap Fourier transform mass spectrometer (FTMS), and a high-performance data acquisition system (FTMS Booster) to improve fragmentation efficiency and spectral quality by increasing the signal-to-noise (S/N) ratio of product ions. In this study, we evaluate the OOB platform for electron capture dissociation (ECD)-based TD MS analysis of a clinical multiple myeloma antibody light chain (P15), benchmarking its performance against the “gold-standard” electron transfer dissociation (ETD)-based TD MS on an Orbitrap EclipseTM. Single precursor charge state analysis yielded comparable sequence coverage (68.2% vs. 74.3%) between ECD-based TD MS on OOB and ETD-based TD MS on EclipseTM. Notably, ECD exhibits lower spectral peak density (i.e., reduced spectral congestion) due to reduced redundancy of product ions. Furthermore, leveraging multiple precursor charge states (15+ to 19+) analysis consecutively across triplicate LC-MS/MS run on the OOB platform enhances sequence coverage to 93%, demonstrating its capacity for comprehensive protein characterization. These results establish the OOB platform as a powerful and efficient tool for TD MS of proteins.