Examples

This section provides examples of publications that report glycomics data in compliance with the MIRAGE Guidelines. In addition, we also plan to make completed tables available which represent the guideline specific parameters along with the metadata (data describing data) on the materials and methods as well as experimental results.

 

Guidelines

Examples

Support

Mass Spectrometry

Publications

 

Glycan Microarrays

Publications

Template, data example

Liquid Chromatography

Publications

 

Publications in compliance with the MIRAGE MS guidelines

 

R. Raghunathan, N.K. Polinski, J.A. Klein, J.D. Hogan, C. Shao, K. Khatri, D.R. Leon, M.E. McComb, F.P. Manfredsson, C.E. Sortwell, and J. Zaia (2018) Glycomic and Proteomic changes in aging brain nigrostriatal pathway; Mol Cell Proteomics; doi:10.1074/mcp.RA118.000680. [Epub ahead of print].

J.D. Hogan, J.A. Klein, J. Wu, P. Chopra, G.J. Boons, L. Carvalho, C. Lin, and J. Zaia (2018) Software for peak finding and elemental composition assignment for glycosaminoglycan tandem mass spectra; Mol Cell Proteomics; 17; 1448-1456.

J. Wu, J. Wei, J.D. Hogan, P. Chopra, A. Joshi, W. Lu, J. Klein, G.J. Boons, C. Lin, and J. Zaia (2018) Negative Electron Transfer Dissociation Sequencing of 3-O-Sulfation-Containing Heparan Sulfate Oligosaccharides; J Am Soc Mass Spectrom; 29; 1262-1272.

J. Zaia, K. Khatri, J.A. Klein, C. Shao, Y. Sheng, and R. Viner (2016) Complete Molecular Weight Profiling of Low Molecular Weight Heparins Using Size Exclusion Chromatography-Ion Suppressor-High Resolution Mass Spectrometry; Anal Chem; 88; 10654-10660.

Y. Huang, X. Yu, Y. Mao, C.E. Costello, J. Zaia, and C. Lin (2013) De Novo Sequencing of Heparan Sulfate Oligosaccharides by Electron-Activated Dissociation; Anal Chem; 85; 11979-11986.

C. Jin, D.T. Kenny, E.C. Skoog, M. Padra, B. Adamczyk, V. Vitizeva, A. Thorell, V. Venkatakrishnan, S.K. Lindén, N.G. Karlsson (2017) Structural Diversity of Human Gastric Mucin Glycans. Mol Cell Proteomics. 16(5):743-758. doi:10.1074/mcp.M116.067983. PMID:28461410.

Publications in compliance with the MIRAGE Glycan Microarray Guidelines

 

Lenmana A., Liacib A.M., Liu Y., Frängsmyra L., Frank M., Blaumb B.S., Chaic W.,
Podgorskie I.I., Harrache B., Benk M., Feiz T., Stehle T., and Arnberga N. (2018) Polysialic acid is a cellular receptor for human adenovirus 52. Proc. Natl. Acad. Sci. USA, 115(18):4264-4273.
doi:10.1073/pnas.1716900115
Suppl. Information: doi:10.1073/pnas.1716900115

Li Z., Gao C., Zhang Y., Palma A.S., Childs R.A. , Silva L.M., Liu Y., Jiang X., Liu Y., Chai W. and Feizi T. (2018) O-Glycome beam search arrays for carbohydrate ligand discovery. Molecular & Cellular Proteomics, 17:121-133
doi:10.1074/mcp.RA117.000285

Stappers M.H.T., Clark A.E., Aimanianda V., Bidula S., Reid D.M., Asamaphan P., Hardison S.E., Dambuza I.M., Valsecchi I., Kerscher B., Plato A., Wallace C.A., Yuecel R., Hebecker B., da Glória Teixeira Sousa M., Cunha C., Liu Y., Feizi T., Brakhage A.A., Kwon-Chung K.J., Gow N.A.R., Zanda M., Piras M., Zanato C., Jaeger M., Netea M.G., van de Veerdonk F.L., Lacerda J.F., Campos A., Carvalho A., Willment J.A., Latgé J.P., Brown G.D. (2018) Recognition of DHN-melanin by a C-type lectin receptor is required for immunity to Aspergillus. Nature, 555: 382-386.
doi:10.1038/nature25974 Supplementary Table 3

Loureiro L.R., Sousa D.P., Ferreira D., Chai W., Lima L., Pereira C., Lopes C.B., Correia V.G., Silva L.M., Li C., Santos L.L., Ferreira J.A., Barbas A., Palma A.S., Novo C., Videira P.A. (2018) Novel monoclonal antibody L2A5 specifically targeting sialyl-Tn and short glycans terminated by alpha-2-6 sialic acids. Sci Rep., 8:1219.
doi:10.1038/s41598-018-30421-w Supplementary Data Table S2

Rudkin F.M., Raziunait I., Workman H., Essono S., Belmonte R., MacCallum D.M., Johnson E.M., Silva L.M., Palma A.S., Feizi T., Jensen A., Erwig L.P., Gow N.A.R. (2018) Single human B cell-derived monoclonal anti-Candida antibodies enhance phagocytosis and protect against disseminated candidiasis. Nat. Commun., 9:5288.
doi:10.1038/s41467-018-07738-1 Supplementary Note

 

Template and example for reporting glycan microarray data

  • DownloadDownload

    Supplementary Glycan Microarry Information Template

    This template (MS-Word, docx) supports authors of glycan microarray data to report this data completely and in compliance with the MIRAGE Glycan Microarray Guidelines.
    After completion, this file can be submitted as Supplementary Information (SI) together with the manuscript to a journal.

  • DownloadDownload

    MIRAGE Glycan Microarray data reporting example

    This example (PDF) aims at demonstrating which information is expected for each data type.

Publications in compliance with the MIRAGE Liquid Chromatography Guidelines

 

Alocci D., Mariethoz J., Gastaldello A., Gasteiger E., Karlsson N.G., Kolarich D., Packer N.H., Lisacek F. (2018) GlyConnect: glycoproteomics goes visual, interactive and analytical. J. Proteome Res.
doi:10.1021/acs.jproteome.8b00766. PMID:30574787

Möginger U., Grunewald S., Hennig R., Kuo C.W., Schirmeister F., Voth H., Rapp E., Khoo K.H., Seeberger P.H., Simon J.C., Kolarich D. (2018) Alterations of the Human Skin N- and O-Glycome in Basal Cell Carcinoma and Squamous Cell Carcinoma. Front Oncol. 8:70.
doi:10.3389/fonc.2018.00070. PMID:29619343

Rath C.B., Schirmeister F., Figl R., Seeberger P.H., Schäffer C., Kolarich D. (2018) Flagellin Glycoproteomics of the Periodontitis Associated Pathogen Selenomonas sputigena Reveals Previously Not Described O-glycans and Rhamnose Fragment Rearrangement Occurring on the Glycopeptides. Mol Cell Proteomics. 17(4):721-736.
doi:10.1074/mcp.RA117.000394. PMID:29339411

O'Neill E.C., Kuhaudomlarp S., Rejzek M., Fangel J.U., Alagesan K., Kolarich D., Willats W.G.T., Field R.A. (2017) Exploring the Glycans of Euglena gracilis. Biology (Basel). 6(4). pii: E45.
doi:10.3390/biology6040045. PMID:29244725

Hinneburg H., Korac P., Schirmeister F., Gasparov S., Seeberger P.H., Zoldoš V., Kolarich D. (2017) Unlocking Cancer Glycomes from Histopathological Formalin-fixed and Paraffin-embedded (FFPE) Tissue Microdissections.
Mol Cell Proteomics. 16(4):524-536.
doi:10.1074/mcp.M116.062414. PMID:28122943

Alagesan K., Khilji S.K., Kolarich D. (2017) It is all about the solvent: on the importance of the mobile phase for ZIC-HILIC glycopeptide enrichment. Anal Bioanal Chem. 409(2):529-538.
doi:10.1007/s00216-016-0051-6. PMID:27909778