Enhancing Proteoform Sequence Coverage Using Top-Down Mass Spectrometry with In-Source Fragmentation and Middle-Down Mass Spectrometry

The study of complex proteoforms with mutations and post-translational modifications has gained increasing attention with the advancement of mass spectrometry (MS)-based techniques. Achieving high proteoform sequence coverage by MS is essential for accurately characterizing these complex proteoforms. Extensive efforts have been made to increase the proteoform sequence coverage using deep bottom-up and top-down MS strategies. In this study, we evaluated top-down and middle-down MS approaches for enhancing proteoform sequence coverage using three proteins: ubiquitin, myoglobin, and carbonic anhydrase II. In the top-down MS approach, we applied in-source fragmentation (ISF) to generate pseudo-MS3 spectra, thereby improving sequence coverage. For the middle-down MS strategy, we performed short-duration enzymatic digestions to produce longer peptides that preserve more proteoform sequence information. Our experimental results demonstrated that ISF and partial digestion significantly increased the sequence coverage of the proteins, achieving coverage greater than 90%.