Cooperation of GlycoPOST and UniCarb-DR towards a comprehensive glycomics data repository workflow

Xu C, Ng DTW. Glycosylation-directed quality control of protein folding. Nat Rev Mol Cell Biol. 2015;16:742–52. https://doi.org/10.1038/nrm4073.

Article  CAS  PubMed  Google Scholar 

Day CJ, Tran EN, Semchenko EA, Tram G, Hartley-Tassell LE, Ng PSK, King RM, Ulanovsky R, McAtamney S, Apicella MA, Tiralongo J, Morona R, Korolik V, Jennings MP. Glycan:glycan interactions: high affinity biomolecular interactions that can mediate binding of pathogenic bacteria to host cells. Proc Natl Acad Sci. 2015;112:E7266–75. https://doi.org/10.1073/pnas.1421082112.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Skehel JJ, Wiley DC. Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin. Annu Rev Biochem. 2000;69:531–69.

Article  CAS  PubMed  Google Scholar 

Varki A, Cummings RD, Esko JD, Stanley P, Hart GW, Aebi M, Mohnen D, Kinoshita T, Packer NH, Prestegard JH, Schnaar RL, Seeberger PH. Essentials of glycobiology, 4th ed. Cold Spring Harbor (NY); 2022.

Michele DE, Barresi R, Kanagawa M, Saito F, Cohn RD, Satz JS, Dollar J, Nishino I, Kelley RI, Somer H, Straub V, Mathews KD, Moore SA, Campbell KP. Post-translational disruption of dystroglycan-ligand interactions in congenital muscular dystrophies. Nature. 2002;418:417–22. https://doi.org/10.1038/nature00837.

Article  CAS  PubMed  Google Scholar 

Bao X, Kobayashi M, Hatakeyama S, Angata K, Gullberg D, Nakayama J, Fukuda MN, Fukuda M. Tumor suppressor function of laminin-binding α-dystroglycan requires a distinct β3-N-acetylglucosaminyltransferase. Proc Natl Acad Sci. 2009;106:12109–14. https://doi.org/10.1073/pnas.0904515106.

Article  PubMed  PubMed Central  Google Scholar 

Gorelik E, Galili U, Raz A. On the role of cell surface carbohydrates and their binding proteins (lectins) in tumor metastasis. Cancer Metastasis Rev. 2001;20:245–77. https://doi.org/10.1023/A:1015535427597.

Article  CAS  PubMed  Google Scholar 

Chen Z, Yu Q, Yu Q, Johnson J, Shipman R, Zhong X, Huang J, Asthana S, Carlsson C, Okonkwo O, Li L. In-depth site-specific analysis of N-glycoproteome in human cerebrospinal fluid and glycosylation landscape changes in Alzheimer’s disease. Mol Cell Proteomics. 2021;20. https://doi.org/10.1016/j.mcpro.2021.100081.

Sinha A, Hussain A, Ignatchenko V, Ignatchenko A, Tang KH, Ho VWH, Neel BG, Clarke B, Bernardini MQ, Ailles L, Kislinger T. N-Glycoproteomics of patient-derived xenografts: a strategy to discover tumor-associated proteins in high-grade serous ovarian cancer. Cell Syst. 2019;8:345-351.e4. https://doi.org/10.1016/j.cels.2019.03.011.

Article  CAS  PubMed  Google Scholar 

Zhang Q, Ma C, Chin L-S, Li L. Integrative glycoproteomics reveals protein N-glycosylation aberrations and glycoproteomic network alterations in Alzheimer’s disease. Sci Adv. 6:eabc5802. https://doi.org/10.1126/sciadv.abc5802.

Wilkinson MD, Dumontier M, IjJ A, Appleton G, Axton M, Baak A, Blomberg N, Boiten J-W, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, ’t Hoen PAC, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone S-A, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B,. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016;3: 160018. https://doi.org/10.1038/sdata.2016.18.

Article  PubMed  PubMed Central  Google Scholar 

Sayers EW, Cavanaugh M, Clark K, Ostell J, Pruitt KD, Karsch-Mizrachi I. GenBank. Nucleic Acids Res. 2020;48:D84–6. https://doi.org/10.1093/nar/gkz956.

Article  CAS  PubMed  Google Scholar 

Perez-Riverol Y, Bai J, Bandla C, García-Seisdedos D, Hewapathirana S, Kamatchinathan S, Kundu DJ, Prakash A, Frericks-Zipper A, Eisenacher M, Walzer M, Wang S, Brazma A, Vizcaíno JA. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 2022;50:D543–52. https://doi.org/10.1093/nar/gkab1038.

Article  CAS  PubMed  Google Scholar 

Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R. The PeptideAtlas project. Nucleic Acids Res. 2006;34:D655–8. https://doi.org/10.1093/nar/gkj040.

Article  CAS  PubMed  Google Scholar 

Okuda S, Watanabe Y, Moriya Y, Kawano S, Yamamoto T, Matsumoto M, Takami T, Kobayashi D, Araki N, Yoshizawa AC, Tabata T, Sugiyama N, Goto S, Ishihama Y. jPOSTrepo: an international standard data repository for proteomes. Nucleic Acids Res. 2017;45:D1107–11. https://doi.org/10.1093/nar/gkw1080.

Article  CAS  PubMed  Google Scholar 

Deutsch EW, Bandeira N, Perez-Riverol Y, Sharma V, Carver JJ, Mendoza L, Kundu DJ, Wang S, Bandla C, Kamatchinathan S, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA. The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Res. 2023;51:D1539–48. https://doi.org/10.1093/nar/gkac1040.

Article  PubMed  Google Scholar 

Watanabe Y, Aoki-Kinoshita KF, Ishihama Y, Okuda S. GlycoPOST realizes FAIR principles for glycomics mass spectrometry data. Nucleic Acids Res. 2021;49:D1523–8. https://doi.org/10.1093/nar/gkaa1012.

Article  PubMed  Google Scholar 

Rojas-Macias MA, Mariethoz J, Andersson P, Jin C, Venkatakrishnan V, Aoki NP, Shinmachi D, Ashwood C, Madunic K, Zhang T, Miller RL, Horlacher O, Struwe WB, Watanabe Y, Okuda S, Levander F, Kolarich D, Rudd PM, Wuhrer M, Kettner C, Packer NH, Aoki-Kinoshita KF, Lisacek F, Karlsson NG. Towards a standardized bioinformatics infrastructure for N- and O-glycomics. Nat Commun. 2019;10:3275. https://doi.org/10.1038/s41467-019-11131-x.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yamada I, Shiota M, Shinmachi D, Ono T, Tsuchiya S, Hosoda M, Fujita A, Aoki NP, Watanabe Y, Fujita N, Angata K, Kaji H, Narimatsu H, Okuda S, Aoki-Kinoshita KF. The GlyCosmos Portal: a unified and comprehensive web resource for the glycosciences. Nat Methods. 2020;17:649–50. https://doi.org/10.1038/s41592-020-0879-8.

Article  CAS  PubMed  Google Scholar 

Ceroni A, Maass K, Geyer H, Geyer R, Dell A, Haslam SM. GlycoWorkbench: a tool for the computer-assisted annotation of mass spectra of glycans. J Proteome Res. 2008;7:1650–9. https://doi.org/10.1021/pr7008252.

Article  CAS  PubMed  Google Scholar 

York WS, Agravat S, Aoki-Kinoshita KF, McBride R, Campbell MP, Costello CE, Dell A, Feizi T, Haslam SM, Karlsson N, Khoo K-H, Kolarich D, Liu Y, Novotny M, Packer NH, Paulson JC, Rapp E, Ranzinger R, Rudd PM, Smith DF, Struwe WB, Tiemeyer M, Wells L, Zaia J, Kettner C. MIRAGE: the minimum information required for A glycomics experiment. Glycobiology. 2014;24:402–6. https://doi.org/10.1093/glycob/cwu018.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Struwe WB, Agravat S, Aoki-Kinoshita KF, Campbell MP, Costello CE, Dell A, Feizi T, Haslam SM, Karlsson NG, Khoo K-H, Kolarich D, Liu Y, McBride R, Novotny MV, Packer NH, Paulson JC, Rapp E, Ranzinger R, Rudd PM, Smith DF, Tiemeyer M, Wells L, York WS, Zaia J, Kettner C. The Minimum Information Required for A Glycomics Experiment (MIRAGE) project: sample preparation guidelines for reliable reporting of glycomics datasets. Glycobiology. 2016;26:907–10. https://doi.org/10.1093/glycob/cww082.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Campbell MP, Abrahams JL, Rapp E, Struwe WB, Costello CE, Novotny M, Ranzinger R, York WS, Kolarich D, Rudd PM, Kettner C. The Minimum Information Required for A Glycomics Experiment (MIRAGE) project: LC guidelines. Glycobiology. 2019;29:349–54. https://doi.org/10.1093/glycob/cwz009.

Article  CAS  PubMed  Google Scholar 

Kolarich D, Rapp E, Struwe WB, Haslam SM, Zaia J, McBride R, Agravat S, Campbell MP, Kato M, Ranzinger R, Kettner C, York WS. The Minimum Information Required for A Glycomics Experiment (MIRAGE) Project: improving the standards for reporting mass-spectrometry-based glycoanalytic data. Mol Cell Proteomics. 2013;12:991–5. https://doi.org/10.1074/mcp.O112.026492.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fujita A, Aoki NP, Shinmachi D, Matsubara M, Tsuchiya S, Shiota M, Ono T, Yamada I, Aoki-Kinoshita KF. The international glycan repository GlyTouCan version 3.0. Nucleic Acids Res. 2021;49:D1529–33. https://doi.org/10.1093/nar/gkaa947.

Article  CAS  PubMed  Google Scholar 

Varki A, Cummings RD, Aebi M, Packer NH, Seeberger PH, Esko JD, Stanley P, Hart G, Darvill A, Kinoshita T, Prestegard JJ, Schnaar RL, Freeze HH, Marth JD, Bertozzi CR, Etzler ME, Frank M, Vliegenthart JF, Lütteke T, Perez S, Bolton E, Rudd P, Paulson J, Kanehisa M, Toukach P, Aoki-Kinoshita KF, Dell A, Narimatsu H, York W, Taniguchi N, Kornfeld S. Symbol nomenclature for graphical representations of glycans. Glycobiology. 2015;25:1323–4. https://doi.org/10.1093/glycob/cwv091.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky LI, Perez-Riverol Y. A proteomics sample metadata representation for multiomics integration and big data analysis. Nat Commun. 2021;12:5854. https://doi.org/

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