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For: Pioch M, Hoffmann M, Pralow A, Reichl U, Rapp E. glyXtoolMS: An Open-Source Pipeline for Semiautomated Analysis of Glycopeptide Mass Spectrometry Data. Anal Chem 2018;90:11908-11916. [DOI: 10.1021/acs.analchem.8b02087] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Number Cited by Other Article(s)
1
Nagai-Okatani C, Tominaga D, Tomioka A, Sakaue H, Goda N, Ko S, Kuno A, Kaji H. GRable Version 1.0: A Software Tool for Site-Specific Glycoform Analysis With Improved MS1-Based Glycopeptide Detection With Parallel Clustering and Confidence Evaluation With MS2 Information. Mol Cell Proteomics 2024;23:100833. [PMID: 39181535 PMCID: PMC11421343 DOI: 10.1016/j.mcpro.2024.100833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 08/16/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024]  Open
2
Reinig S, Kuo C, Wu CC, Huang SY, Yu JS, Shih SR. Specific long-term changes in anti-SARS-CoV-2 IgG modifications and antibody functions in mRNA, adenovector, and protein subunit vaccines. J Med Virol 2024;96:e29793. [PMID: 39023111 DOI: 10.1002/jmv.29793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 06/17/2024] [Accepted: 07/02/2024] [Indexed: 07/20/2024]
3
Kuhnen G, Class LC, Badekow S, Hanisch KL, Rohn S, Kuballa J. Python workflow for the selection and identification of marker peptides-proof-of-principle study with heated milk. Anal Bioanal Chem 2024;416:3349-3360. [PMID: 38607384 PMCID: PMC11106092 DOI: 10.1007/s00216-024-05286-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 04/13/2024]
4
Reinig S, Kuo C, Wu CC, Huang SY, Yu JS, Shih SR. Specific long-term changes in anti-SARS-CoV-2 IgG modifications and antibody functions in mRNA, adenovector, and protein subunit vaccines. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.06.16.23291455. [PMID: 38559243 PMCID: PMC10980124 DOI: 10.1101/2023.06.16.23291455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
5
Sun W, Zhang Q, Zhang X, Tran NH, Ziaur Rahman M, Chen Z, Peng C, Ma J, Li M, Xin L, Shan B. Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics. Nat Commun 2023;14:4046. [PMID: 37422459 PMCID: PMC10329677 DOI: 10.1038/s41467-023-39699-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 06/19/2023] [Indexed: 07/10/2023]  Open
6
Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023;42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
7
Pujić I, Perreault H. Recent advancements in glycoproteomic studies: Glycopeptide enrichment and derivatization, characterization of glycosylation in SARS CoV2, and interacting glycoproteins. MASS SPECTROMETRY REVIEWS 2022;41:488-507. [PMID: 33393161 DOI: 10.1002/mas.21679] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
8
Kawahara R, Chernykh A, Alagesan K, Bern M, Cao W, Chalkley RJ, Cheng K, Choo MS, Edwards N, Goldman R, Hoffmann M, Hu Y, Huang Y, Kim JY, Kletter D, Liquet B, Liu M, Mechref Y, Meng B, Neelamegham S, Nguyen-Khuong T, Nilsson J, Pap A, Park GW, Parker BL, Pegg CL, Penninger JM, Phung TK, Pioch M, Rapp E, Sakalli E, Sanda M, Schulz BL, Scott NE, Sofronov G, Stadlmann J, Vakhrushev SY, Woo CM, Wu HY, Yang P, Ying W, Zhang H, Zhang Y, Zhao J, Zaia J, Haslam SM, Palmisano G, Yoo JS, Larson G, Khoo KH, Medzihradszky KF, Kolarich D, Packer NH, Thaysen-Andersen M. Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis. Nat Methods 2021;18:1304-1316. [PMID: 34725484 DOI: 10.1101/2021.03.14.435332] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/22/2021] [Indexed: 05/18/2023]
9
Oliveira T, Thaysen-Andersen M, Packer NH, Kolarich D. The Hitchhiker's guide to glycoproteomics. Biochem Soc Trans 2021;49:1643-1662. [PMID: 34282822 PMCID: PMC8421054 DOI: 10.1042/bst20200879] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/03/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023]
10
Pralow A, Nikolay A, Leon A, Genzel Y, Rapp E, Reichl U. Site-specific N-glycosylation analysis of animal cell culture-derived Zika virus proteins. Sci Rep 2021;11:5147. [PMID: 33664361 PMCID: PMC7933209 DOI: 10.1038/s41598-021-84682-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/18/2021] [Indexed: 01/09/2023]  Open
11
Pralow A, Hoffmann M, Nguyen-Khuong T, Pioch M, Hennig R, Genzel Y, Rapp E, Reichl U. Comprehensive N-glycosylation analysis of the influenza A virus proteins HA and NA from adherent and suspension MDCK cells. FEBS J 2021;288:4869-4891. [PMID: 33629527 DOI: 10.1111/febs.15787] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/04/2021] [Accepted: 02/22/2021] [Indexed: 12/25/2022]
12
Cao W, Liu M, Kong S, Wu M, Zhang Y, Yang P. Recent Advances in Software Tools for More Generic and Precise Intact Glycopeptide Analysis. Mol Cell Proteomics 2021;20:100060. [PMID: 33556625 PMCID: PMC8724820 DOI: 10.1074/mcp.r120.002090] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
13
Noor SI, Hoffmann M, Rinis N, Bartels MF, Winterhalter PR, Hoelscher C, Hennig R, Himmelreich N, Thiel C, Ruppert T, Rapp E, Strahl S. Glycosyltransferase POMGNT1 deficiency strengthens N-cadherin-mediated cell-cell adhesion. J Biol Chem 2021;296:100433. [PMID: 33610554 PMCID: PMC7994789 DOI: 10.1016/j.jbc.2021.100433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/08/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022]  Open
14
Glycan Compositions with GlyConnect Compozitor to Enhance Glycopeptide Identification. Methods Mol Biol 2021;2361:109-127. [PMID: 34236658 DOI: 10.1007/978-1-0716-1641-3_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
15
Cajic S, Hennig R, Burock R, Rapp E. Capillary (Gel) Electrophoresis-Based Methods for Immunoglobulin (G) Glycosylation Analysis. EXPERIENTIA SUPPLEMENTUM (2012) 2021;112:137-172. [PMID: 34687009 DOI: 10.1007/978-3-030-76912-3_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
16
Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis. Nat Methods 2021;18:1304-1316. [PMID: 34725484 PMCID: PMC8566223 DOI: 10.1038/s41592-021-01309-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022]
17
Schulze S, Oltmanns A, Fufezan C, Krägenbring J, Mormann M, Pohlschröder M, Hippler M. SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides. Bioinformatics 2020;36:5330-5336. [PMID: 33325487 DOI: 10.1093/bioinformatics/btaa1042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/26/2020] [Accepted: 12/07/2020] [Indexed: 02/07/2023]  Open
18
Lan R, Xin M, Hao Z, You S, Xu Y, Wu J, Dang L, Zhang X, Sun S. Biological Functions and Large-Scale Profiling of Protein Glycosylation in Human Semen. J Proteome Res 2020;19:3877-3889. [DOI: 10.1021/acs.jproteome.9b00795] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
19
Riley N, Malaker SA, Driessen MD, Bertozzi CR. Optimal Dissociation Methods Differ for N- and O-Glycopeptides. J Proteome Res 2020;19:3286-3301. [PMID: 32500713 PMCID: PMC7425838 DOI: 10.1021/acs.jproteome.0c00218] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Indexed: 01/29/2023]
20
Synthesis of lipid-linked oligosaccharides by a compartmentalized multi-enzyme cascade for the in vitro N-glycosylation of peptides. J Biotechnol 2020;322:54-65. [PMID: 32653637 DOI: 10.1016/j.jbiotec.2020.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 06/18/2020] [Accepted: 07/08/2020] [Indexed: 01/21/2023]
21
Zhu H, Wang S, Liu D, Ding L, Chen C, Liu Y, Wu Z, Bollag R, Liu K, Alexander WM, Yin J, Ma C, Li L, Wang PG. Identifying Sialylation Linkages at the Glycopeptide Level by Glycosyltransferase Labeling Assisted Mass Spectrometry (GLAMS). Anal Chem 2020;92:6297-6303. [PMID: 32271005 PMCID: PMC7750919 DOI: 10.1021/acs.analchem.9b05068] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
22
Cao WQ, Liu MQ, Kong SY, Wu MX, Huang ZZ, Yang PY. Novel methods in glycomics: a 2019 update. Expert Rev Proteomics 2020;17:11-25. [PMID: 31914820 DOI: 10.1080/14789450.2020.1708199] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
23
Zhu H, Aloor A, Ma C, Kondengaden SM, Wang PG. Mass Spectrometric Analysis of Protein Glycosylation. ACS SYMPOSIUM SERIES 2020. [DOI: 10.1021/bk-2020-1346.ch010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
24
Klein JA, Zaia J. A Perspective on the Confident Comparison of Glycoprotein Site-Specific Glycosylation in Sample Cohorts. Biochemistry 2019;59:3089-3097. [PMID: 31833756 DOI: 10.1021/acs.biochem.9b00730] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
25
Gray CJ, Migas LG, Barran PE, Pagel K, Seeberger PH, Eyers CE, Boons GJ, Pohl NLB, Compagnon I, Widmalm G, Flitsch SL. Advancing Solutions to the Carbohydrate Sequencing Challenge. J Am Chem Soc 2019;141:14463-14479. [PMID: 31403778 DOI: 10.1021/jacs.9b06406] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
26
Shipman JT, Su X, Hua D, Desaire H. DecoyDeveloper: An On-Demand, De Novo Decoy Glycopeptide Generator. J Proteome Res 2019;18:2896-2902. [PMID: 31129958 DOI: 10.1021/acs.jproteome.9b00203] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
27
Choo MS, Wan C, Rudd PM, Nguyen-Khuong T. GlycopeptideGraphMS: Improved Glycopeptide Detection and Identification by Exploiting Graph Theoretical Patterns in Mass and Retention Time. Anal Chem 2019;91:7236-7244. [PMID: 31079452 DOI: 10.1021/acs.analchem.9b00594] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
28
Gränicher G, Coronel J, Pralow A, Marichal-Gallardo P, Wolff M, Rapp E, Karlas A, Sandig V, Genzel Y, Reichl U. Efficient influenza A virus production in high cell density using the novel porcine suspension cell line PBG.PK2.1. Vaccine 2019;37:7019-7028. [PMID: 31005427 DOI: 10.1016/j.vaccine.2019.04.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/29/2019] [Accepted: 04/08/2019] [Indexed: 12/22/2022]
29
Hoffmann M, Pioch M, Pralow A, Hennig R, Kottler R, Reichl U, Rapp E. The Fine Art of Destruction: A Guide to In-Depth Glycoproteomic Analyses-Exploiting the Diagnostic Potential of Fragment Ions. Proteomics 2018;18:e1800282. [DOI: 10.1002/pmic.201800282] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/07/2018] [Indexed: 01/10/2023]
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