Quorum: glycopeptide discovery via mass spectrometry and spectral networking

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Glycosylation is a pervasive modification estimated to modify more than 50% of human proteins and is a key component of host-pathogen interactions, adaptive and innate immunity, and therapeutic development. Computational tools for glycoprotein analysis make simplifying assumptions about possible glycan structures, limiting their utility in many scenarios. This proposal aims to comprehensively characterize glycoproteins, including novel and unexpected glycans, with Digital Proteomics’ Quorum mass spectrometry data analysis software, and enable further glycoprotein characterization through the development of antibodies targeting discovered glycopeptides. The Quorum software builds on the spectral networking paradigm that posits that structurally similar molecules produce similar mass spectra. In Quorum for glycopeptide analysis, networked spectra represent different glycan structures on the same glycosite of a protein. Similar to traditional approaches to glycopeptide identification, Quorum matches glycopeptide spectra to a protein sequence database and glycan structure database. Unlike traditional approaches, Quorum employs a rigorous false-discovery rate calculation based on variant glycan structures in target-decoy analysis. In addition, Quorum increases the identification rate of glycopeptides by propagating identifications along edges in the network, enabling the discovery of glycan structures that are not in the structure database and may be completely novel. Quorum will be benchmarked on glycoprotein standards, well-characterized NIST monoclonal antibody reference material, and total IgG which will establish a baseline for spectral network variant glycopeptide discovery. The Quorum software is deployed to the cloud, as part of our extensible platform Quorum Cloud, where the glycoprotein analysis is a plugin to generic spectral networking analysis. Enlisted testers of the cloud platform have applications in glycoengineering, glycoenrichment assays, and therapeutic development.