Comparison of analytical methods for profiling N- and O-linked glycans from cultured cell lines: HUPO Human Disease Glycomics/Proteome Initiative multi-institutional study

Glycoconjugate Journal

Volumn 33, Issue 3, 2016, Pages 405-415

  Ito, Hiromi ^a,n   Kaji, Hiroyuki ^a   Togayachi, Akira ^a   Azadi, Parastoo ^b   Ishihara, Mayumi ^b   Geyer, Rudolf ^c   Galuska, Christina ^c   Geyer, Hildegard ^c   Kakehi, Kazuaki ^d   Kinoshita, Mitsuhiro ^d   Karlsson, Niclas G ^e   Jin, Chunsheng ^e   Kato, Koichi ^f   Yagi, Hirokazu ^f   Kondo, Sachiko ^f   Kawasaki, Nana ^g,o   Hashii, Noritaka ^g   Kolarich, Daniel ^h   Stavenhagen, Kathrin ^h,p   Packer, Nicolle H ⁱ   Thaysen Andersen, Morten ⁱ   Nakano, Miyako ^i,q   Taniguchi, Naoyuki ^j   Kurimoto, Ayako ^j   Wada, Yoshinao ^k   Tajiri, Michiko ^k   Yang, Pengyuan ^l   Cao, Weiqian ^l   Li, Hong ^l   Rudd, Pauline M ^m   Narimatsu, Hisashi ^a   more..

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b UNIVERSITY OF GEORGIA   (United States)

^c JUSTUS LIEBIG UNIVERSITY   (Germany)

^d KINKI UNIVERSITY   (Japan)

^e UNIVERSITY OF GOTHENBURG   (Sweden)

^f NAGOYA CITY UNIVERSITY   (Japan)

^g NATIONAL INSTITUTE OF HEALTH SCIENCES   (Japan)

^h MAX PLANCK INSTITUTE OF COLLOIDS AND INTERFACES   (Germany)

ⁱ MACQUARIE UNIVERSITY   (Australia)

^j RIKEN   (Japan)

^k RESEARCH INSTITUTE FOR MATERNAL AND CHILD HEALTH   (Japan)

^l FUDAN UNIVERSITY   (China)

^m NATIONAL INSTITUTE FOR BIOPROCESSING RESEARCH AND TRAINING   (Ireland)

ⁿ FUKUSHIMA MEDICAL UNIVERSITY   (Japan)

^o YOKOHAMA CITY UNIVERSITY   (Japan)

^p HIROSHIMA UNIVERSITY   (Japan)

^q VU UNIVERSITY AMSTERDAM   (Netherlands)

more..

Author keywords

Glycoproteomics; Human disease glycomics proteome initiative (HGPI); Human proteome organization (HUPO)

Indexed keywords

ALDITOL; FUCOSE; GLYCOPEPTIDE; GLYCOPROTEIN; IMMUNOGLOBULIN G; N LINKED GLYCAN; O LINKED GLYCAN; SIALIC ACID; SIALYL LEWIS X ANTIGEN; TRANSFERRIN; UNCLASSIFIED DRUG; BIOLOGICAL MARKER; POLYSACCHARIDE;

ANALYTIC METHOD; ARTICLE; CANCER CELL LINE; CARBOHYDRATE ANALYSIS; CELL CULTURE; CELL LYSATE; CELL MEMBRANE; CONTROLLED STUDY; CYTOSOLIC FRACTION; ELECTROSPRAY MASS SPECTROMETRY; EXTRACTION; FOLLOW UP; GLYCOBIOLOGY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; INTERMETHOD COMPARISON; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PILOT STUDY; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN GLYCOSYLATION; QUANTITATIVE ANALYSIS; REPRODUCIBILITY; CHEMISTRY; CLINICAL TRIAL; COMPARATIVE STUDY; HUMAN; MASS SPECTROMETRY; MOLECULAR DIAGNOSIS; MULTICENTER STUDY; PROCEDURES; PROTEOMICS; STANDARDS; TUMOR CELL LINE;

BIOMARKERS; CELL LINE, TUMOR; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; GLYCOMICS; GLYCOPROTEINS; HUMANS; MASS SPECTROMETRY; MOLECULAR DIAGNOSTIC TECHNIQUES; POLYSACCHARIDES; PROTEOMICS; REPRODUCIBILITY OF RESULTS;

EID: 84975780471     PISSN: 02820080     EISSN: 15734986     Source Type: Journal    
DOI: 10.1007/s10719-015-9625-3     Document Type: Article

References (26)

1. Development, O. for E.C. and, Co-operation, O.E., Oecd, D.: Policy issues for the development and use of biomarkers in health. (2011)
2. Kim, Y.J., Varki, A.: Perspectives on the significance of altered glycosylation of glycoproteins in cancer. Glycoconj. J. 14, 569–576 (1997)
3. Freire-de-Lima, L.: Sweet and sour: the impact of differential glycosylation in cancer cells undergoing epithelial-mesenchymal transition. Front. Oncol. 4, 59 (2014)
4. Rivinoja, A., Pujol, F.M., Hassinen, A., Kellokumpu, S.: Golgi pH, its regulation and roles in human disease. Ann. Med. 44, 542–554 (2012)
5. Lauc, G., Essafi, A., Huffman, J.E., Hayward, C., Knezevic, A., Kattla, J.J., Polasek, O., Gornik, O., Vitart, V., Abrahams, J.L., Pucic, M., Novokmet, M., Redzic, I., Campbell, S., Wild, S.H., Borovecki, F., Wang, W., Kolcic, I., Zgaga, L., Gyllensten, U., Wilson, J.F., Wright, A.F., Hastie, N.D., Campbell, H., Rudd, P.M., Rudan, I.: Genomics meets glycomics-the first GWAS study of human N-Glycome identifies HNF1alpha as a master regulator of plasma protein fucosylation. PLoS Genet. 6, e1001256 (2010)
6. Saldova, R., Dempsey, E., Perez-Garay, M., Marino, K., Watson, J.A., Blanco-Fernandez, A., Struwe, W.B., Harvey, D.J., Madden, S.F., Peracaula, R., McCann, A., Rudd, P.M.: 5-AZA-2′-deoxycytidine induced demethylation influences N-glycosylation of secreted glycoproteins in ovarian cancer. Epigenetics 6, 1362–1372 (2011)
7. Abbott, K.L., Nairn, A.V., Hall, E.M., Horton, M.B., McDonald, J.F., Moremen, K.W., Dinulescu, D.M., Pierce, M.: Focused glycomic analysis of the N-linked glycan biosynthetic pathway in ovarian cancer. Proteomics 8, 3210–3220 (2008)
8. Guo, H., Nairn, A., dela Rosa, M., Nagy, T., Zhao, S., Moremen, K., Pierce, M.: Transcriptional regulation of the protocadherin beta cluster during Her-2 protein-induced mammary tumorigenesis results from altered N-glycan branching. J. Biol. Chem 287, 24941–24954 (2012)
9. Zhao, P., Nairn, A.V., Hester, S., Moremen, K.W., O’Regan, R.M., Oprea, G., Wells, L., Pierce, M., Abbott, K.L.: Proteomic identification of glycosylphosphatidylinositol anchor-dependent membrane proteins elevated in breast carcinoma. J. Biol. Chem. 287, 25230–25240 (2012)
10. Wada, Y., Azadi, P., Costello, C.E., Dell, A., Dwek, R.A., Geyer, H., Geyer, R., Kakehi, K., Karlsson, N.G., Kato, K., Kawasaki, N., Khoo, K.-H., Kim, S., Kondo, A., Lattova, E., Mechref, Y., Miyoshi, E., Nakamura, K., Narimatsu, H., Novotny, M.V., Packer, N.H., Perreault, H., Peter-Katalinić, J., Pohlentz, G., Reinhold, V.N., Rudd, P.M., Suzuki, A., Taniguchi, N.: Comparison of the methods for profiling glycoprotein glycans—HUPO Human Disease Glycomics/Proteome Initiative multi-institutional study. Glycobiol. 17, 411–422 (2007)
11. Wada, Y., Dell, A., Haslam, S.M., Tissot, B., Canis, K., Azadi, P., Bäckström, M., Costello, C.E., Hansson, G.C., Hiki, Y., Ishihara, M., Ito, H., Kakehi, K., Karlsson, N., Hayes, C.E., Kato, K., Kawasaki, N., Khoo, K.H., Kobayashi, K., Kolarich, D., Kondo, A., Lebrilla, C., Nakano, M., Narimatsu, H., Novak, J., Novotny, M.V., Ohno, E., Packer, N.H., Palaima, E., Renfrow, M.B., Tajiri, M., Thomsson, K.A., Yagi, H., Yu, S.Y., Taniguchi, N.: Comparison of methods for profiling O-glycosylation: Human Proteome Organisation Human Disease Glycomics/Proteome Initiative multi-institutional study of IgA1. Mol. Cell. Proteomics 9, 719–727 (2010)
12. Yagi, H., Ohno, E., Kondo, S., Yoshida, A., Kato, K.: Development and application of multidimensional HPLC mapping method for O-linked oligosaccharides. Biomolecules. 1, 48–62 (2011)
13. Takahashi, N., Kato, K.: GALAXY (Glycoanalysis by the Three Axes of MS and Chromatography): a web application that assists structural analyses of N-Glycans. Trends. Glycosci. Glycotechnol. 15, 235–251 (2003)
14. Pabst, M., Bondili, J.S., Stadlmann, J., Mach, L., Altmann, F.: Mass + retention time = structure: a strategy for the analysis of N-glycans by carbon LC-ESI-MS and its application to fibrin N-glycans. Anal. Chem. 79, 5051–5057 (2007)
15. Jensen, P.H., Karlsson, N.G., Kolarich, D., Packer, N.H.: Structural analysis of N- and O-glycans released from glycoproteins. Nat. Protoc. 7, 1299–1310 (2012)
16. Campbell, M.P., Nguyen-Khuong, T., Hayes, C.A., Flowers, S.A., Alagesan, K., Kolarich, D., Packer, N.H., Karlsson, N.G.: Validation of the curation pipeline of UniCarb-DB: building a global glycan reference MS/MS repository. Biochim. Biophys. Acta 1844, 108–116 (2014)
17. Pabst, M., Altmann, F.: Influence of electrosorption, solvent, temperature, and ion polarity on the performance of LC-ESI-MS using graphitic carbon for acidic oligosaccharides. Anal. Chem. 80, 7534–7542 (2008)
18. Kellokumpu, S., Sormunen, R., Kellokumpu, I.: Abnormal glycosylation and altered Golgi structure in colorectal cancer: dependence on intra-Golgi pH. FEBS Lett. 516, 217–224 (2002)
19. Saldova, R., Asadi Shehni, A., Haakensen, V.D., Steinfeld, I., Hilliard, M., Kifer, I., Helland, A., Yakhini, Z., Børresen-Dale, A.L., Rudd, P.M.: Association of N-glycosylation with breast carcinoma and systemic features using high-resolution quantitative UPLC. J. Proteome Res. 13, 2314–2327 (2014)
20. Kolarich, D., Rapp, E., Struwe, W.B., Haslam, S.M., Zaia, J., McBride, R., Agravat, S., Campbell, M.P., Kato, M., Ranzinger, R., Kettner, C., York, W.S.: The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting mass-spectrometry-based glycoanalytic data. Mol. Cell. Proteomics 12, 991–995 (2013)
21. York, W.S., Agravat, S., Aoki-Kinoshita, K.F., McBride, R., Campbell, M.P., Costello, C.E., Dell, A., Feizi, T., Haslam, S.M., Karlsson, N., Khoo, K.H., Kolarich, D., Liu, Y., Novotny, M., Packer, N.H., Paulson, J.C., Rapp, E., Ranzinger, R., Rudd, P.M., Smith, D.F., Struwe, W.B., Tiemeyer, M., Wells, L., Zaia, J., Kettner, C.: MIRAGE: the minimum information required for a glycomics experiment. Glycobiology 24, 402–406 (2014)
22. Huffman, J.E., Pucic-Bakovic, M., Klaric, L., Hennig, R., Selman, M.H.J., Vuckovic, F., Novokmet, M., Kristic, J., Borowiak, M., Muth, T., Polasek, O., Razdorov, G., Gornik, O., Plomp, R., Theodoratou, E., Wright, A.F., Rudan, I., Hayward, C., Campbell, H., Deelder, A.M., Reichl, U., Aulchenko, Y.S., Rapp, E., Wuhrer, M., Lauc, G.: Comparative performance of four methods for high-throughput glycosylation analysis of immunoglobulin G in genetic and epidemiological research. Mol. Cell. Proteomics 13, 1598–1610 (2014)
23. Reusch, D., Haberger, M., Falck, D., Peter, B., Maier, B., Gassner, J., Hook, M., Wagner, K., Bonnington, L., Bulau, P., Wuhrer, M.: Comparison of methods for the analysis of therapeutic immunoglobulin G Fc-glycosylation profiles-Part 2: mass spectrometric methods. MAbs 7, 732–742 (2015)
24. Sinha, S., Pipes, G., Topp, E.M., Bondarenko, P.V., Treuheit, M.J., Gadgil, H.S.: Comparison of LC and LC/MS methods for quantifying N-glycosylation in recombinant IgGs. J. Am. Soc. Mass Spectrom. 19, 1643–1654 (2008)
25. Mariño, K., Bones, J., Kattla, J.J., Rudd, P.M.: A systematic approach to protein glycosylation analysis: a path through the maze. Nat. Chem. Biol. 6, 713–723 (2010)
26. Leymarie, N., Griffin, P.J., Jonscher, K., Kolarich, D., Orlando, R., McComb, M., Zaia, J., Aguilan, J., Alley, W.R., Altmann, F., Ball, L.E., Basumallick, L., Bazemore-Walker, C.R., Behnken, H., Blank, M.A., Brown, K.J., Bunz, S.-C., Cairo, C.W., Cipollo, J.F., Daneshfar, R., Desaire, H., Drake, R.R., Go, E.P., Goldman, R., Gruber, C., Halim, A., Hathout, Y., Hensbergen, P.J., Horn, D.M., Hurum, D., Jabs, W., Larson, G., Ly, M., Mann, B.F., Marx, K., Mechref, Y., Meyer, B., Moginger, U., Neusubeta, C., Nilsson, J., Novotny, M.V., Nyalwidhe, J.O., Packer, N.H., Pompach, P., Reiz, B., Resemann, A., Rohrer, J.S., Ruthenbeck, A., Sanda, M., Schulz, J.M., Schweiger-Hufnagel, U., Sihlbom, C., Song, E., Staples, G.O., Suckau, D., Tang, H., Thaysen-Andersen, M., Viner, R.I., An, Y., Valmu, L., Wada, Y., Watson, M., Windwarder, M., Whittal, R., Wuhrer, M., Zhu, Y., Zou, C.: Interlaboratory study on differential analysis of protein glycosylation by mass spectrometry: the ABRF glycoprotein research multi-institutional study 2012. Mol. Cell. Proteomics 12, 2935–2951 (2013)