EU UGM 2023: Annotation of topdown mass spectra of proteins and oligonucleotides

This talk covers advancements in oligonucleotide and protein mass spectrometry, focusing on recent improvements and workflows in mass spectrometry analysis. Marshall Bern speaks to intact mass analysis, top-down MS/MS analysis, and developments in digested oligonucleotide analysis, particularly for mRNA. The presentation highlights the differences in workflows between oligonucleotide and protein analysis, such as the assumption of negative mode and the use of isotope resolution for determining charge states. Advanced algorithms and integrated tools for accurate mass peak matching and molecule specification are discussed, showcasing the robustness and iterative nature of the deconvolution processes.

Additionally, the webinar introduces a new MS/MS annotation tool, currently tailored for oligonucleotides but adaptable for proteins, demonstrating its capabilities with data from Genentech. Challenges and advancements in annotating complex spectra, handling various fragmentation types, and ensuring accurate sequence coverage are addressed. Dr Bern also touches on experimental methods for digested mRNA analysis, incorporating features from peptide mapping software to accommodate nucleotide sequences.