Uncovering protein glycosylation dynamics and heterogeneity using deep quantitative glycoprofiling (DQGlyco)

Nature Structural & Molecular Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 10, 2025

Abstract Protein glycosylation regulates essential cellular processes such as signaling, adhesion and cell–cell interactions; however, dysregulated is associated with diseases cancer. Here we introduce deep quantitative glycoprofiling (DQGlyco), a robust method that integrates high-throughput sample preparation, highly sensitive detection precise multiplexed quantification to investigate protein dynamics at an unprecedented depth. Using DQGlyco, profiled the mouse brain glycoproteome, identifying 177,198 unique N -glycopeptides—25 times more than previous studies. We quantified glycopeptide changes in human cells treated fucosylation inhibitor characterized surface-exposed glycoforms. Furthermore, analyzed tissue-specific patterns mice demonstrated defined gut microbiota substantially remodels shedding light on link between microbiome functions. Additionally, developed novel strategy evaluate glycoform solubility, offering new insights into their biophysical properties. Overall, in-depth profiling offered by DQGlyco uncovered extensive complexity regulation.

Language: Английский

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Experimental and data analysis advances in thermal proteome profiling

Cell Reports Methods, Journal Year: 2024, Volume and Issue: 4(2), P. 100717 - 100717

Published: Feb. 1, 2024

Method development for mass spectrometry (MS)-based thermal shift proteomic assays have advanced to probe small molecules with known and unknown protein-ligand interaction mechanisms specificity, which is predominantly used in characterization of drug-protein interactions. In the discovery target off-target interactions, a thorough investigation method their impact on sensitivity accuracy protein-small molecule protein-protein interactions warranted. this review, we discuss areas improvement at each stage proteome profiling data analysis that includes processing MS-based data, development, effect overall quality profiles. We also overview optimization experimental strategies prioritization an increased number independent biological replicates over evaluated temperatures.

Language: Английский

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Characterizing protein-protein interactions with thermal proteome profiling

Current Opinion in Structural Biology, Journal Year: 2024, Volume and Issue: 89, P. 102946 - 102946

Published: Oct. 31, 2024

Language: Английский

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