An intuitive analysis software solution for protein complex native massspectrometry data

ABSTRACT Native top down mass spectrometrynTDMSis a multi tiered tandem mass spectrometry technique able to characterize proteoforms and intact protein complexes in their native state and represents a potentially revolutionary technology still in theearly adoptersstage of the technology life cycleBy utilizing gentle sample preparation and analysis methodsnTDMS can provide a direct measure of the endogenous noncovalent protein protein and protein ligand interactions critical for biological regulationIn additionwith the new wave of therapeutic protein moleculesnTDMS is being relied upon more and more to provide answers to different biotechnology questionsRecent instrument advances have widely increased the accessibility to nTDMS by enabling more mass spectrometers to be capable of nTDMS experimentsOverallthese applications and technology improvements have led to a rapid rise in the number of researchers using nTDMSHoweverthe advances propelling nTDMS have not been matched with software advances to handle these new datasetswhich contain many non covalent ligand and cofactor binding events as well as information on the subunit stoichiometry of protein complexesAs suchusers have had to manually process much of the dataultimately holding back nTDMS from reaching its true potentialProteinaceous has previously developed data analysis solutions to uncover important biological information from denaturing mass spectrometry analyses of intact proteins and now proposes a software named ProSight Native to address the pressing bioinformatics needs of nTDMS scientistsProSight Native will get in at the ground floor of nTDMS as the first software directly developed to serve as a complete nTDMS analysis packagefrom determination of protein complex subunit and cofactor stoichiometry down to full proteoform characterization at the subunit levelIn this SBIRProteinaceous will implement two critical features for bioinformatics analysis of data produced by nTDMShandling ofnativemodifications and noncovalent ligands and the computational characterization and scoring of protein complex stoichiometryThese new features will be thoroughly validated using data from the largest repository of nTDMS protein complexes published to dateproviding a robust software platform that can process the complexity of data generated from both academia and industryThe work proposed in Phase I provides a strong initial foundation for further advancements during Phase IIincluding more advanced scoring methodologies accompanied with high throughput searchingIn summaryProSight Native will serve as an analysis tool focused on characterizing intact protein complexes from data produced by nTDMS and will enable new and valuable insights in biological and biotechnology research PROJECT NARRATIVE Native top down mass spectrometry is a powerful technique able to identify and characterize intact protein complexes and native proteoformsProteinaceous is developing innovativevendor neutral analysis software to enable precision data analysis solutions for the examination of protein complexes to better clarify the role protein complexes play in disease and as therapeutics