Make the links clickable.

Author: fcyu

docs/fragpipe_glycoproteomics_collection.md

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 **Comprehensive profiling of protein AMPylation reveals widespread glycosylation–AMPylation crosstalk**  
 Qin, X.; Liu, Y.; Wang, J.; Zhang, H.; Li, Y.; Zhao, Y.; et al., Molecular & Cellular Proteomics. 2025.  
-https://doi.org/10.1016/j.mcpro.2025.100150  
+[https://doi.org/10.1016/j.mcpro.2025.100150](https://doi.org/10.1016/j.mcpro.2025.100150)  
 
 Proteome-wide AMPylation study intersecting with glycosylation pathways, generating composite and labile modification spectra. Most relevant FragPipe modes: open glyco for unbiased detection of unexpected glycan-linked or AMPylation-associated mass shifts, followed by mass-offset glyco to refine glycan-related masses and localize modification sites with peptide-level confidence.
 
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 **Narrow window data-independent acquisition on the Orbitrap Astral mass spectrometer enables fast and deep coverage of the plasma glycoproteome**  
 Jäger, S.; Zeller, M.; Pashkova, A.; Bache, N.; Geyer, P.E.; Mann, M., Nature Communications. 2025.  
-https://doi.org/10.1038/s41467-025-57916-1  
+[https://doi.org/10.1038/s41467-025-57916-1](https://doi.org/10.1038/s41467-025-57916-1)  
 
 Large-scale plasma glycoproteomics using narrow-window DIA for high depth and throughput. Most relevant FragPipe modes: DIA-ready glyco, including glycopeptide-aware library generation and DIA-compatible scoring, with optional mass-offset glyco for site- and glycoform-resolved follow-up analyses in plasma biomarker studies.
 
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 **Glycoproteomics reveals immune-associated N-glycan remodeling in human disease**  
 Baas, L.M.; van der Zwan, A.; van der Schoot, C.E.; de Haas, M.; Vidarsson, G., Frontiers in Immunology. 2025.  
-https://doi.org/10.3389/fimmu.2025.1645196  
+[https://doi.org/10.3389/fimmu.2025.1645196](https://doi.org/10.3389/fimmu.2025.1645196)  
 
 Immune-focused glycoproteomics study explicitly using MSFragger-Glyco within FragPipe. Most relevant FragPipe modes: mass-offset glyco with targeted N-glycan sets and oxonium-ion filtering, complemented by open glyco to capture disease-associated glycan heterogeneity beyond predefined compositions.
 
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 **A large-scale mouse N-glycoproteomics resource and systematic comparison of glycoproteomics search engines**  
 Zhang, X.; Sun, S.; Yang, W.; Liu, J.; He, S.; Qian, X., bioRxiv. 2025.  
-https://doi.org/10.1101/2025.02.15.638397  
+[https://doi.org/10.1101/2025.02.15.638397](https://doi.org/10.1101/2025.02.15.638397)  
 
 Multi-tissue mouse N-glycoproteomics atlas with direct software benchmarking including MSFragger-Glyco. Most relevant FragPipe modes: open glyco for discovery-driven glycan mass profiling across tissues, followed by mass-offset glyco for controlled, site-resolved comparisons and fair cross-engine benchmarking.
 
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 **Advanced glycopeptide characterization using hybrid fragmentation on an Exploris–Omnitrap platform**  
 Brunner, A.D.; Müller, T.; Köhler, N.; Neumann, E.K.; Brodbelt, J.S.; Aebersold, R., bioRxiv. 2025.  
-https://doi.org/10.64898/2025.12.10.693381  
+[https://doi.org/10.64898/2025.12.10.693381](https://doi.org/10.64898/2025.12.10.693381)  
 
 Method development study applying EID, ECD, UVPD, and AI-ECD to N-glycopeptides. Most relevant FragPipe modes: mass-offset glyco for robust peptide backbone identification under non-collisional fragmentation, with open glyco to accommodate fragmentation-specific mass patterns not captured by fixed glycan lists.
 
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 **Integrated single-tip IMAC–HILIC enables simultaneous analysis of plant phosphoproteomics and N-glycoproteomics**  
 Zhu, Y.; Liang, X.; Wang, X.; Liu, P.; Zhang, Y.; Chen, Z., Journal of Proteome Research. 2025.  
-https://doi.org/10.1021/acs.jproteome.5c00185  
+[https://doi.org/10.1021/acs.jproteome.5c00185](https://doi.org/10.1021/acs.jproteome.5c00185)  
 
 Plant-focused workflow combining phosphoproteomics and N-glycoproteomics from a single preparation. Most relevant FragPipe modes: mass-offset glyco using plant-specific glycan composition sets, with open glyco as a complementary strategy to discover species-specific or atypical plant glycan masses.
 
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 **Deep profiling of human serum glycoproteins using advanced LC–MS/MS strategies**  
 Wang, L.; Chen, H.; Zhou, Y.; Li, Q.; Zhang, K.; Wu, S., Journal of Proteome Research. 2025.  
-https://doi.org/10.1021/acs.jproteome.5c00199  
+[https://doi.org/10.1021/acs.jproteome.5c00199](https://doi.org/10.1021/acs.jproteome.5c00199)  
 
 High-depth serum glycoproteomics emphasizing glycoform microheterogeneity in biofluids. Most relevant FragPipe modes: mass-offset glyco for controlled serum glycan assignment and site-level resolution, with DIA-ready glyco as a natural extension for scaling across large clinical cohorts.
 
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 **Systematic evaluation of N-glycopeptide fragmentation and identification strategies**  
 Li, J.; Xu, Y.; Sun, R.; Zhao, D.; Huang, Y.; Yang, P., Molecular & Cellular Proteomics. 2025.  
-https://doi.org/10.1016/j.mcpro.2025.100079  
+[https://doi.org/10.1016/j.mcpro.2025.100079](https://doi.org/10.1016/j.mcpro.2025.100079)  
 
 Benchmarking study of fragmentation methods and glycopeptide identification performance. Most relevant FragPipe modes: open glyco to evaluate fragmentation-dependent mass detectability and glycan loss patterns, alongside mass-offset glyco for controlled comparisons of peptide and glycan localization accuracy.
 
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 **Global analysis of protein glycosylation dynamics during cellular differentiation**  
 Martínez-Bartolomé, S.; Navarro, P.; Martín-Maroto, F.; Albar, J.P., Molecular & Cellular Proteomics. 2025.  
-https://doi.org/10.1016/j.mcpro.2025.100184  
+[https://doi.org/10.1016/j.mcpro.2025.100184](https://doi.org/10.1016/j.mcpro.2025.100184)  
 
 Quantitative study of glycosylation changes across differentiation states. Most relevant FragPipe modes: mass-offset glyco for consistent site-resolved quantification across conditions, optionally preceded by open glyco during method development to identify condition-specific glycan features.
 
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 **Integrated proteomic characterization of complex glycoproteins by LC–MS/MS**  
 Chen, X.; Liu, S.; Zhao, L.; Wang, J.; Zhang, Q.; Li, Y., Journal of Biological Chemistry. 2025.  
-https://doi.org/10.1016/S0021-9258(25)00191-1  
+[https://doi.org/10.1016/S0021-9258(25)00191-1](https://doi.org/10.1016/S0021-9258(25)00191-1)  
 
 Comprehensive characterization of structurally complex glycoproteins. Most relevant FragPipe modes: mass-offset glyco for confident site occupancy and glycan composition assignment, with open glyco to capture unexpected glycoforms or partial processing states.
 
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 **Improving glycoproteomic analysis workflow by systematic evaluation of glycopeptide enrichment, quantification, mass spectrometry approach, and data analysis strategies**  
 Sun, Z.; Lih, T.M.; Woo, J.; Jiao, L.; Hu, Y.; Wang, Y.; Liu, H.; Zhang, H., Analytical Chemistry. 2024.  
-https://doi.org/10.1021/acs.analchem.4c04466  
+[https://doi.org/10.1021/acs.analchem.4c04466](https://doi.org/10.1021/acs.analchem.4c04466)  
 
 Systematic benchmarking of intact glycopeptide workflows including enrichment strategies, TMT-based quantification, stepped-collision HCD, and software comparison involving MSFragger-Glyco. Most relevant FragPipe modes: mass-offset glyco under controlled glycan composition sets, with open glyco for diagnosing enrichment- and fragmentation-dependent glycan behavior.
 
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 **The molecular basis of immunosuppression by soluble CD52 is defined by interactions of N-linked and O-linked glycans with HMGB1 box B**  
 DeBono, N.J.; D’Andrea, S.; Bandala-Sanchez, E.; Goddard-Borger, E.; Zenaidee, M.A.; Moh, E.S.X.; Fadda, E.; Harrison, L.C.; Packer, N.H., Journal of Biological Chemistry. 2025.  
-https://doi.org/10.1016/j.jbc.2025.108350  
+[https://doi.org/10.1016/j.jbc.2025.108350](https://doi.org/10.1016/j.jbc.2025.108350)  
 
 High-resolution structural and functional characterization of a short, heavily glycosylated immunoregulatory peptide carrying both N- and O-glycans. Most relevant FragPipe modes: open glyco for heterogeneous and multiply modified glycoforms, combined with mass-offset glyco for confident site localization on short peptide backbones.
 
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 **Improving the depth and reliability of glycopeptide identification using Protein Prospector**  
 Chalkley, R.J.; Baker, P.R., Molecular & Cellular Proteomics. 2025.  
-https://doi.org/10.1016/j.mcpro.2025.100903  
+[https://doi.org/10.1016/j.mcpro.2025.100903](https://doi.org/10.1016/j.mcpro.2025.100903)  
 
 Software-centric study benchmarking glycopeptide identification strategies and explicitly comparing against MSFragger-Glyco. Most relevant FragPipe modes: open glyco to expose adduct-driven mass shifts and ambiguous glycan assignments, followed by mass-offset glyco for controlled interpretation.
 
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 **Ultradeep N-glycoproteome atlas of mouse reveals spatiotemporal signatures of brain aging and neurodegenerative diseases**  
 Fang, P.; Yu, X.; Ding, M.; Cong, Q.; Jiang, H.; Shi, Q.; Zhao, W.; Zheng, W.; Li, Y.; Ling, Z.; Kong, W.-J.; Yang, P.; Shen, H., Nature Communications. 2025.  
-https://doi.org/10.1038/s41467-025-60437-6  
+[https://doi.org/10.1038/s41467-025-60437-6](https://doi.org/10.1038/s41467-025-60437-6)  
 
 Largest mouse N-glycoproteomics atlas to date integrating multiple enzymes, enrichment strategies, and multi-engine identification including MSFragger-Glyco. Most relevant FragPipe modes: open glyco for large-scale glycan discovery followed by mass-offset glyco for site-resolved, confidence-centric atlas construction.
 
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 **Dysregulated inflammation in solid tumor malignancy patients shapes polyfunctional antibody responses to COVID-19 vaccination**  
 Purcell, R.A.; Koutsakos, M.; Kedzierski, L.; Allen, L.F.; Lloyd Williams, O.H.; Wang, J.-W.D.; et al., npj Vaccines. 2025.  
-https://doi.org/10.1038/s41541-025-01268-w  
+[https://doi.org/10.1038/s41541-025-01268-w](https://doi.org/10.1038/s41541-025-01268-w)  
 
 Clinical immunology study linking IgG Fc glycosylation states to vaccine responses in cancer patients. Most relevant FragPipe modes: mass-offset glyco for controlled Fc glycoform profiling, with DIA-ready glyco suitable for cohort-scale antibody glycoproteomics.
 
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 **A multivalent capsule vaccine protects against Klebsiella pneumoniae bloodstream infections in healthy and immunocompromised mice**  
 Wantuch, P.L.; Robinson, L.S.; Knoot, C.J.; Darwech, I.; Matsuguma, A.M.; Vinogradov, E.; Scott, N.E.; Harding, C.M.; Rosen, D.A., npj Vaccines. 2025.  
-https://doi.org/10.1038/s41541-025-01314-7  
+[https://doi.org/10.1038/s41541-025-01314-7](https://doi.org/10.1038/s41541-025-01314-7)  
 
 Vaccine study employing intact glycopeptide LC–MS/MS to confirm polysaccharide–protein conjugation and glycan composition. Most relevant FragPipe modes: mass-offset glyco for confirmation of known capsule repeat-unit masses, with open glyco to detect unexpected heterogeneity or conjugation byproducts.
 
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 **Uncovering protein glycosylation dynamics and heterogeneity using deep quantitative glycoprofiling (DQGlyco)**  
 Potel, C.M.; Burtscher, M.L.; Garrido-Rodriguez, M.; Brauer-Nikonow, A.; Becher, I.; Le Sueur, C.; Typas, A.; Zimmermann, M.; Savitski, M.M., Nature Structural & Molecular Biology. 2025.  
-https://doi.org/10.1038/s41594-025-01485-w  
+[https://doi.org/10.1038/s41594-025-01485-w](https://doi.org/10.1038/s41594-025-01485-w)  
 
 Deep quantitative glycoproteomics method achieving unprecedented coverage using high-throughput enrichment, multiplexed quantification, and MSFragger-based identification. Most relevant FragPipe modes: mass-offset glyco for high-confidence site-resolved quantification at scale, with open glyco used during method development to assess enrichment bias and glycan diversity.