Nicholas McIlvain Riley

This paper improves ETD-based fragmentation for glycopeptide analysis by optimizing ion handling and scan parameters, making it faster and more efficient for both N- and O-glycopeptides.

This paper introduces a high-resolving power DIA-PTCR method for glycoproteoform analysis, enabling isotopically resolved mass measurements and integration with other glycoproteomics approaches.

GlycoDiveR provides a modular R framework for analyzing and visualizing high-dimensional glycoproteomics data, improving accessibility and flexibility in glycosylation analysis.

This study shows that sialoglycans on human T cells reduce Fas receptor-mediated apoptosis but not other TNF receptor pathways.

This study identifies four antibody mechanisms that disrupt FimH-mediated bacterial adhesion by altering its conformation and glycan binding.

GlyCounter is a tool to extract glycan-specific ions from glycopeptide MS/MS spectra, enabling analysis of glycan features without database searches.

The paper introduces irCLIP-RNP and Re-CLIP methods to identify dynamic RNA-protein assemblies, revealing new patterns of RBP-RNA associations and EGF-induced remodeling.

This paper compares five glycoproteomic software tools using a tailored glycan database, finding that Protein Prospector has the highest agreement with known glycosites.

This study maps the organism-wide secretome response to exercise in mice, identifying 200+ exercise-regulated protein pairs and uncovering anti-obesity and anti-diabetic roles of a liver-secreted proteoform.

O-Pair Search identifies O-glycopeptides and localizes O-glycosites using collision- and electron-based dissociation spectra, improving speed and identification rates.

This study investigates the roles of PKA and HOG signaling in anaerobic xylose fermentation and stress tolerance in yeast engineered for biofuel production, finding that HOG1 mutations specifically enhance xylose usage while PKA activity affects growth but not xylose fermentation.

This study captures site-specific N-glycoproteome heterogeneity using AI-ETD, identifying 1,545 N-glycosites from mouse brain tissue and developing new visualizations for glycopeptide analysis.