Mucinomics as the Next Frontier of Mass Spectrometry

There is a need to better understand and handle the “dark matter” of proteomics – the vast diversity of post-translational and chemical modifications that are unaccounted in a typical analysis and thus remain unidentified. We present a novel fragment-ion indexing method, and its implementation in peptide identification tool MSFragger, that enables an over 100-fold improvement in speed over most existing tools. Using some of the largest proteomic datasets to date, we demonstrate how MSFragger empowers the open database search concept for comprehensive identification of peptides and all their modified forms, uncovering dramatic differences in the modification rates across experimental samples and conditions. We further illustrate its utility using protein-RNA crosslinked peptide data, and using affinity purification experiments where we observe on average a 300% increase in the number of identified spectra for enriched proteins. We also discuss the benefits of open searching for improved false discovery rate estimation in proteomics.

Many cellular proteins are reversibly modified by O-linked N-acetylglucosamine (O-GlcNAc) moieties on Ser and Thr residues. Studies on the mechanisms and functions of O-GlcNAcylation and its links to metabolism reveal the importance of this modification in the maintenance of cellular and organismal homeostasis.