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Yiying Zhu, Ph.D. received her doctoral degree from Brown University and completed her post-doctoral training at the Forsyth Institute (Harvard School of Dental Medicine). She worked at Cell Signaling Technology Inc. (MA, USA) as a senior scientist until joining Tsinghua University (Beijing, China) as a core facility director. Her primary research input is on developing methods for the characterization of protein post-translational modifications (PTMs) using LC-MS/MS. As part of her doctoral projects, she participated in a worldwide interlaboratory study on the characterization of PSA glycosylation. While working at Cell Signaling Technology, she developed immunoaffinity enrichment tools and LC-MS/MS methods for mapping various PTMs. Skyline has been an amazing tool for analyzing protein PTMs, and she has been using it for nearly a decade.
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Analysis of glycopeptides using LC-MS/MS is a challenging task mainly due to the complexity of glycans. Recent developments in searching algorithms have made it possible to identify glycopeptides on a large scale. The pGlyco software can determine the glycan structure isomers by their differential fragmentation in MS/MS spectra.
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However, MS1 quantitation of glycopeptides is still challenging due to missing values and difficulty integrating small peaks. Skyline is an excellent software for MS1 peptide quantitation, and our goal is to integrate the identification of glycopeptides via searching software like pGlyco with subsequent quantitation by Skyline. However, Skyline has difficulty differentiating glycan structure isomers because the modification identifiers are based on masses, and different glycan isomers attached glycopeptides are treated as the same peptides. In this study, we successfully discriminated glycan isomers by in-silico shifting their masses through isotope replacement. We further applied this method to the discovery of diagnostic biomarkers in the sera of breast cancer patients.
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