Multimodal Mass Spectrometry Analyses for Molecular Pathology

Mass spectrometry based proteomics, whether based on liquid chromatography or MALDI, has benefited from the introduction of high mass resolution instruments like FTICR and Orbitraps. The increased mass resolution and mass accuracy benefits bottom-up proteomics by increasing the number of confident identifications, and benefits top-down proteomics by clearly resolving the often complex fragmentation spectra. It has recently been demonstrated that the increased mass resolution is also beneficial for MALDI mass spectrometry imaging (MSI) of multiple molecular classes, including proteins, peptides, lipids and even metabolites directly on tissue sections. However, the very small number of cells sampled per each MALDI mass spectrum and the absence of an explicit analyte separation/purification steps means that a parallel LC-MS/MS analysis is necessary to increase the depth-of-coverage. In this work, a selection of different mass spectrometry techniques have been optimized and applied including a new method to improve MALDI and LC-MS/MS alignment. MALDI MS and MSI have been investigated for the analysis of intact proteins, demonstrating the full resolution and detection of disease specific proteoforms and the top-down characterization of proteins using in-source decay and pseudo-MS3. MALDI and LC-MS based top-down proteomics have been extensively optimized, including the implementation of UVPD fragmentation on a Q-Exactive Plus.