From Mass Spectrometry to Glycan Microarrays: An Overview of Analytical Techniques in Glycomics

Year 2024, Volume: 11 Issue: 1, 218 - 235, 31.05.2024

Burcu Tekin , Rafig Gurbanov

https://doi.org/10.35193/bseufbd.1322614

Abstract

Glycans, complex carbohydrate molecules, play crucial roles in various biological processes, significantly affecting health and disease. The comprehensive analysis of glycans requires a combination of advanced analytical techniques. This review provides a detailed workflow of the various methods employed in glycan analysis, including sample preparation, glycan enrichment, glycan release, labeling, separation, and detection. Each step's principles, applications, and advantages are described, highlighting their contributions to glycan research. Additionally, the review emphasizes the importance of selecting appropriate techniques for specific glycan analysis goals. The workflow provides a comprehensive understanding of glycans, unraveling their roles in biological systems and facilitating the development of novel therapeutic interventions.

Keywords

Glycomics, Analytical techniques, Mass spectrometry, Liquid chromatography, Glycan microarrays

Kütle Spektrometresinden Glikan Mikrodizilerine: Glikomikte Analitik Tekniklere Genel Bir Bakış

Abstract

Glikanlar, çeşitli biyolojik süreçlerde önemli rol oynayan ve sağlık ile hastalık üzerinde önemli etkileri olan karmaşık karbonhidrat molekülleri olarak bilinmektedir. Glikanların kapsamlı bir şekilde analiz edilmesi, gelişmiş analitik tekniklerin bir kombinasyonunu gerektirmektedir. Bu derleme, glikan analizinde kullanılan çeşitli tekniklerin, örnekleme hazırlığı, glikan zenginleştirme, glikan salımı, etiketleme, ayrıştırma ve tespit gibi adımlarının ayrıntılı bir iş akışını sunmaktadır. Her adımın prensipleri, uygulamaları ve avantajları açıklanarak, glikan araştırmalarına katkıları vurgulanmaktadır. Ayrıca, spesifik glikan analiz hedefleri için uygun tekniklerin seçiminin önemi üzerinde durulmaktadır. Bu iş akışı, glikanların kapsamlı bir anlayışını sağlayarak, biyolojik sistemlerdeki rollerini açığa çıkarmaya ve yeni terapötik müdahalelerin geliştirilmesine yardımcı olmaktadır.

Keywords

Glikomik, Analitik teknikler, Kütle spektrometrisi, Sıvı kromatografi, Glikan mikroarrayleri

References

• Hart, G. W., & Copeland, R. J. (2010). Glycomics hits the big time. Cell, 143(5), 672-676.
• Kleene, R., & Schachner, M. (2004). Glycans and neural cell interactions. Nature Reviews Neuroscience, 5(3), 195-208.
• Molinari, M. (2007). N-glycan structure dictates extension of protein folding or onset of disposal. Nature Chemical Biology, 3(6), 313-320.
• Garner, O. B., & Baum, L. G. (2008). Galectin–glycan lattices regulate cell-surface glycoprotein organization and signalling. Biochemical Society Transactions, 36(6), 1472-1477.
• Varki, A. (2017). Biological roles of glycans. Glycobiology, 27(1), 3-49.
• Brockhausen, I. (2006). Mucin‐type O‐glycans in human colon and breast cancer: glycodynamics and functions. EMBO reports, 7(6), 599-604.
• Lattová, E., Skřičková, J., Hausnerová, J., Frola, L., Křen, L., Ihnatová, I., Zdráhal, Z., Bryant, J., & Popovič, M. (2020). N-Glycan profiling of lung adenocarcinoma in patients at different stages of disease. Modern Pathology, 33(6), 1146-1156.
• Shimodaira, K., Nakayama, J., Nakamura, N., Hasebe, O., Katsuyama, T., & Fukuda, M. (1997). Carcinoma-associated expression of core 2 β-1, 6-N-acetylglucosaminyltransferase gene in human colorectal cancer: role of O-glycans in tumor progression. Cancer Research, 57(23), 5201-5206.
• Irvine, E. B., & Alter, G. (2020). Understanding the role of antibody glycosylation through the lens of severe viral and bacterial diseases. Glycobiology, 30(4), 241-253.
• Mettu, R., Chen, C.-Y., & Wu, C.-Y. (2020). Synthetic carbohydrate-based vaccines: challenges and opportunities. Journal of Biomedical Science, 27, 1-22.
• Kumbhar, P. S., Pandya, A. K., Manjappa, A. S., Disouza, J. I., & Patravale, V. B. (2021). Carbohydrates-based diagnosis, prophylaxis and treatment of infectious diseases: Special emphasis on COVID-19. Carbohydrate Polymer Technologies and Applications, 2, 100052.
• Eichler, J. (2019). Protein glycosylation. Current Biology, 29(7), R229-R231.
• Bucala, R., Makita, Z., Koschinsky, T., Cerami, A., & Vlassara, H. (1993). Lipid advanced glycosylation: pathway for lipid oxidation in vivo. Proceedings of the National Academy of Sciences, 90(14), 6434-6438.
• Flynn, R. A., Pedram, K., Malaker, S. A., Batista, P. J., Smith, B. A., Johnson, A. G., George, B. M., Majzoub, K., Villalta, P. W., & Carette, J. E. (2021). Small RNAs are modified with N-glycans and displayed on the surface of living cells. Cell, 184(12), 3109-3124. e3122.
• Arnold, J. N., Wormald, M. R., Sim, R. B., Rudd, P. M., & Dwek, R. A. (2007). The impact of glycosylation on the biological function and structure of human immunoglobulins. Annual Review of Immunology., 25, 21-50.
• Wang, Z., Zhu, J., & Lu, H. (2020). Antibody glycosylation: impact on antibody drug characteristics and quality control. Applied Microbiology and Biotechnology, 104, 1905-1914.
• Indellicato, R., & Trinchera, M. (2021). Epigenetic Regulation of Glycosylation. The Role of Glycosylation in Health and Disease, 173-186.
• Reily, C., Stewart, T. J., Renfrow, M. B., & Novak, J. (2019). Glycosylation in health and disease. Nature Reviews Nephrology, 15(6), 346-366.
• Marshall, R. (1972). Glycoproteins. Annual Review of Biochemistry, 41(1), 673-702.
• Mitra, N., Sinha, S., Ramya, T. N., & Surolia, A. (2006). N-linked oligosaccharides as outfitters for glycoprotein folding, form and function. Trends in Biochemical Sciences, 31(3), 156-163.
• Watanabe, Y., Bowden, T. A., Wilson, I. A., & Crispin, M. (2019). Exploitation of glycosylation in enveloped virus pathobiology. Biochimica et Biophysica Acta (BBA)-General Subjects, 1863(10), 1480-1497.
• Pabst, M., & Altmann, F. (2011). Glycan analysis by modern instrumental methods. Proteomics, 11(4), 631-643.
• Sperandio, M., Gleissner, C. A., & Ley, K. (2009). Glycosylation in immune cell trafficking. Immunological Reviews, 230(1), 97-113.
• Jensen, P. H., Kolarich, D., & Packer, N. H. (2010). Mucin‐type O‐glycosylation–putting the pieces together. The FEBS Journal, 277(1), 81-94.
• Mulloy, B., Hart, G. W., & Stanley, P. (2009). Structural analysis of glycans. Essentials of Glycobiology 2th ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor (NY), Chapter 47.
• Ongay, S., Boichenko, A., Govorukhina, N., & Bischoff, R. (2012). Glycopeptide enrichment and separation for protein glycosylation analysis. Journal of Separation Science, 35(18), 2341-2372.
• Kosanović, M., Milutinović, B., Goč, S., Mitić, N., & Janković, M. (2017). Ion-exchange chromatography purification of extracellular vesicles. Biotechniques, 63(2), 65-71.
• Alvarez-Manilla, G., Atwood III, J., Guo, Y., Warren, N. L., Orlando, R., & Pierce, M. (2006). Tools for glycoproteomic analysis: size exclusion chromatography facilitates identification of tryptic glycopeptides with N-linked glycosylation sites. Journal of Proteome Research, 5(3), 701-708.
• Dwek, R. A., Edge, C. J., Harvey, D. J., Wormald, M. R., & Parekh, R. B. (1993). Analysis of glycoprotein-associated oligosaccharides. Annual Review of Biochemistry, 62(1), 65-100.
• Ruhaak, L., Zauner, G., Huhn, C., Bruggink, C., Deelder, A., & Wuhrer, M. (2010). Glycan labeling strategies and their use in identification and quantification. Analytical and Bioanalytical Chemistry, 397, 3457-3481.
• Marino, K., Bones, J., Kattla, J. J., & Rudd, P. M. (2010). A systematic approach to protein glycosylation analysis: a path through the maze. Nature Chemical Biology, 6(10), 713-723.
• Qing, G., Yan, J., He, X., Li, X., & Liang, X. (2020). Recent advances in hydrophilic interaction liquid interaction chromatography materials for glycopeptide enrichment and glycan separation. TrAC Trends in Analytical Chemistry, 124, 115570.
• Kozlik, P., Vaclova, J., & Kalikova, K. (2021). Mixed-mode hydrophilic interaction/ion-exchange liquid chromatography–Separation potential in peptide analysis. Microchemical Journal, 165, 106158.
• Cummins, P. M., Rochfort, K. D., & O’Connor, B. F. (2017). Ion-exchange chromatography: basic principles and application. Protein Chromatography: Methods and Protocols, 209-223.
• Szabo, Z., Thayer, J. R., Agroskin, Y., Lin, S., Liu, Y., Srinivasan, K., ... & Pohl, C. (2017). In-depth analyses of native N-linked glycans facilitated by high-performance anion exchange chromatography-pulsed amperometric detection coupled to mass spectrometry. Analytical and Bioanalytical Chemistry, 409(12), 3089-3101.
• Zhou, J. X., Dermawan, S., Solamo, F., Flynn, G., Stenson, R., Tressel, T., & Guhan, S. (2007). pH–conductivity hybrid gradient cation-exchange chromatography for process-scale monoclonal antibody purification. Journal of Chromatography A, 1175(1), 69-80.
• Akash, M. S. H., Rehman, K., Akash, M. S. H., & Rehman, K. (2020). High performance liquid chromatography. Essentials of Pharmaceutical Analysis, 175-184.
• Campbell, M. P., Royle, L., Radcliffe, C. M., Dwek, R. A., & Rudd, P. M. (2008). GlycoBase and autoGU: tools for HPLC-based glycan analysis. Bioinformatics, 24(9), 1214-1216.
• Coskun, O. (2016). Separation techniques: chromatography. Northern Clinics of Istanbul, 3(2), 156.
• Andrade-Eiroa, A., Le-Cong, T., Nguyen, M.-L., & Dagaut, P. (2011). Reverse-high performance liquid chromatography mechanism explained by polarization of stationary phase. CheM, 1, 62-79.
• Ni, W. (2013). Advances in protein post-translational modifications (PTMS) using liquid chromatography-mass spectrometry. Doctoral dissertation, Northeastern University, Department of Chemistry and Chemical Biology, College of Science.
• Selman, M. H., Derks, R. J., Bondt, A., Palmblad, M., Schoenmaker, B., Koeleman, C. A., van de Geijn, F. E., Dolhain, R. J., Deelder, A. M., & Wuhrer, M. (2012). Fc specific IgG glycosylation profiling by robust nano-reverse phase HPLC-MS using a sheath-flow ESI sprayer interface. Journal of Proteomics, 75(4), 1318-1329.
• Prater, B. D., Connelly, H. M., Qin, Q., & Cockrill, S. L. (2009). High-throughput immunoglobulin G N-glycan characterization using rapid resolution reverse-phase chromatography tandem mass spectrometry. Analytical Biochemistry, 385(1), 69-79.
• Wuhrer, M., de Boer, A. R., & Deelder, A. M. (2009). Structural glycomics using hydrophilic interaction chromatography (HILIC) with mass spectrometry. Mass Spectrometry Reviews, 28(2), 192-206.
• Gutierrez Reyes, C. D., Jiang, P., Donohoo, K., Atashi, M., & Mechref, Y. S. (2021). Glycomics and glycoproteomics: Approaches to address isomeric separation of glycans and glycopeptides. Journal of Separation Science, 44(1), 403-425.
• McCalley, D. V. (2017). Understanding and manipulating the separation in hydrophilic interaction liquid chromatography. Journal of Chromatography A, 1523, 49-71.
• Mariño, K., Lane, J. A., Abrahams, J. L., Struwe, W. B., Harvey, D. J., Marotta, M., Hickey, R. M., & Rudd, P. M. (2011). Method for milk oligosaccharide profiling by 2-aminobenzamide labeling and hydrophilic interaction chromatography. Glycobiology, 21(10), 1317-1330.
• Zauner, G., Koeleman, C. A., Deelder, A. M., & Wuhrer, M. (2010). Protein glycosylation analysis by HILIC‐LC‐MS of Proteinase K‐generated N‐and O‐glycopeptides. Journal of Separation Science, 33(6‐7), 903-910.
• Iwaki, J., & Hirabayashi, J. (2018). Carbohydrate-binding specificity of human galectins: an overview by frontal affinity chromatography. Trends in Glycoscience and Glycotechnology, 30(172), SE137-SE153.
• Monzo, A., Bonn, G. K., & Guttman, A. (2007). Lectin-immobilization strategies for affinity purification and separation of glycoconjugates. TrAC Trends in Analytical Chemistry, 26(5), 423-432.
• Tateno, H., Nakamura-Tsuruta, S., & Hirabayashi, J. (2007). Frontal affinity chromatography: sugar–protein interactions. Nature Protocols, 2(10), 2529-2537.
• Cummings, R. D., Etzler, M., Hahn, M. G., Darvill, A., Godula, K., Woods, R. J., & Mahal, L. K. (2022). Glycan-recognizing probes as tools. Essentials of Glycobiology 4th ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor (NY), Chapter 48.
• Suzuki, S. (2013). Recent developments in liquid chromatography and capillary electrophoresis for the analysis of glycoprotein glycans. Analytical Sciences, 29(12), 1117-1128.
• Haslam, S. M., Freedberg, D. I., Mulloy, B., Dell, A., Stanley, P., & Prestegard, J. H. (2022). Structural Analysis of Glycans. Essentials of Glycobiology 4th ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor (NY), Chapter 50.
• Lu, G., Crihfield, C. L., Gattu, S., Veltri, L. M., & Holland, L. A. (2018). Capillary electrophoresis separations of glycans. Chemical Reviews, 118(17), 7867-7885.
• Geyer, H., & Geyer, R. (2006). Strategies for analysis of glycoprotein glycosylation. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1764(12), 1853-1869.
• Dave, M. B., Dherai, A. J., Udani, V. P., Hegde, A. U., Desai, N. A., & Ashavaid, T. F. (2018). Comparison of transferrin isoform analysis by capillary electrophoresis and HPLC for screening congenital disorders of glycosylation. Journal of Clinical Laboratory Analysis, 32(1), e22167.
• Morelle, W., & Michalski, J.-C. (2007). Analysis of protein glycosylation by mass spectrometry. Nature Protocols, 2(7), 1585-1602.
• North, S. J., Hitchen, P. G., Haslam, S. M., & Dell, A. (2009). Mass spectrometry in the analysis of N-linked and O-linked glycans. Current Opinion in Structural Biology, 19(5), 498-506.
• Zauner, G., Koeleman, C. A., Deelder, A. M., & Wuhrer, M. (2012). Mass spectrometric O-glycan analysis after combined O-glycan release by beta-elimination and 1-phenyl-3-methyl-5-pyrazolone labeling. Biochimica et Biophysica Acta (BBA)-General Subjects, 1820(9), 1420-1428.
• Tie, C., & Zhang, X.-X. (2012). A new labelling reagent for glycans analysis by capillary electrophoresis-mass spectrometry. Analytical Methods, 4(2), 357-359.
• Suttapitugsakul, S., Sun, F., & Wu, R. (2019). Recent advances in glycoproteomic analysis by mass spectrometry. Analytical Chemistry, 92(1), 267-291.
• Zhou, S., Wooding, K. M., & Mechref, Y. (2017). Analysis of permethylated glycan by liquid chromatography (LC) and mass spectrometry (MS). High-Throughput Glycomics and Glycoproteomics: Methods and Protocols, 83-96.
• Hu, Y., & Mechref, Y. (2012). Comparing MALDI‐MS, RP‐LC‐MALDI‐MS and RP‐LC‐ESI‐MS glycomic profiles of permethylated N‐glycans derived from model glycoproteins and human blood serum. Electrophoresis, 33(12), 1768-1777.
• Stadlmann, J., Pabst, M., Kolarich, D., Kunert, R., & Altmann, F. (2008). Analysis of immunoglobulin glycosylation by LC‐ESI‐MS of glycopeptides and oligosaccharides. Proteomics, 8(14), 2858-2871.
• Sparbier, K., Asperger, A., Resemann, A., Kessler, I., Koch, S., Wenzel, T., Stein, G., Vorwerg, L., Suckau, D., & Kostrzewa, M. (2007). Analysis of glycoproteins in human serum by means of glycospecific magnetic bead separation and LC-MALDI-TOF/TOF analysis with automated glycopeptide detection. Journal of Biomolecular Techniques: JBT, 18(4), 252.
• Otto, V. I., Damoc, E., Cueni, L. N., Schürpf, T., Frei, R., Ali, S., Callewaert, N., Moise, A., Leary, J. A., & Folkers, G. (2006). N-glycan structures and N-glycosylation sites of mouse soluble intercellular adhesion molecule-1 revealed by MALDI-TOF and FTICR mass spectrometry. Glycobiology, 16(11), 1033-1044.
• Wuhrer, M., Koeleman, C. A., Hokke, C. H., & Deelder, A. M. (2004). Nano-scale liquid chromatography-mass spectrometry of 2-aminobenzamide-labeled oligosaccharides at low femtomole sensitivity. International Journal of Mass Spectrometry, 232(1), 51-57.
• Ceroni, A., Maass, K., Geyer, H., Geyer, R., Dell, A., & Haslam, S. M. (2008). GlycoWorkbench: a tool for the computer-assisted annotation of mass spectra of glycans. Journal of Proteome Research, 7(4), 1650-1659.
• Apte, A., & Meitei, N. S. (2010). Bioinformatics in glycomics: Glycan characterization with mass spectrometric data using SimGlycan™. Functional Glycomics: Methods and Protocols, 269-281.
• Liu, M.-Q., Zeng, W.-F., Fang, P., Cao, W.-Q., Liu, C., Yan, G.-Q., Zhang, Y., Peng, C., Wu, J.-Q., & Zhang, X.-J. (2017). pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification. Nature communications, 8(1), 438.
• Dotz, V., Haselberg, R., Shubhakar, A., Kozak, R. P., Falck, D., Rombouts, Y., Reusch, D., Somsen, G. W., Fernandes, D. L., & Wuhrer, M. (2015). Mass spectrometry for glycosylation analysis of biopharmaceuticals. TrAC Trends in Analytical Chemistry, 73, 1-9.
• Battistel, M. D., Azurmendi, H. F., Yu, B., & Freedberg, D. I. (2014). NMR of glycans: shedding new light on old problems. Progress in Nuclear Magnetic Resonance Spectroscopy, 79, 48-68.
• Lundborg, M., & Widmalm, G. (2011). Structural analysis of glycans by NMR chemical shift prediction. Analytical Chemistry, 83(5), 1514-1517.
• Fellenberg, M., Çoksezen, A., & Meyer, B. (2010). Characterization of picomole amounts of oligosaccharides from glycoproteins by 1 H NMR spectroscopy. Angewandte Chemie International Edition, 14(49), 2630-2633.
• Broberg, A., Thomsen, K. K., & Duus, J. Ø. (2000). Application of nano-probe NMR for structure determination of low nanomole amounts of arabinoxylan oligosaccharides fractionated by analytical HPAEC-PAD. Carbohydrate Research, 328(3), 375-382.
• Łowicki, D., Czarny, A., & Mlynarski, J. (2013). NMR of carbohydrates. Nuclear Magnetic Resonance, 383-419.
• Malkina, O., Hricovini, M., Bizik, F., & Malkin, V. (2001). Chemical Shifts and Spin− Spin Coupling Constants in Me α-d-Xylopyranoside: A DFT Approach. The Journal of Physical Chemistry A, 105(40), 9188-9195.
• Wormald, M. R., Petrescu, A. J., Pao, Y.-L., Glithero, A., Elliott, T., & Dwek, R. A. (2002). Conformational studies of oligosaccharides and glycopeptides: complementarity of NMR, X-ray crystallography, and molecular modelling. Chemical Reviews, 102(2), 371-386.
• Pollex-Krüger, A., Meyer, B., Stuike-Prill, R., Sinnwell, V., Matta, K. L., & Brockhausen, I. (1993). Preferred conformations and dynamics of five core structures of mucin type O-glycans determined by NMR spectroscopy and force field calculations. Glycoconjugate Journal, 10, 365-380.
• Kumar, A., Narayanan, V., & Sekhar, A. (2019). Characterizing post-translational modifications and their effects on protein conformation using NMR spectroscopy. Biochemistry, 59(1), 57-73.
• Liang, P.-H., Wu, C.-Y., Greenberg, W. A., & Wong, C.-H. (2008). Glycan arrays: biological and medical applications. Current Opinion in Chemical Biology, 12(1), 86-92.
• Gao, J., Ma, L., Liu, D., & Wang, Z. (2012). Microarray-based technology for glycomics analysis. Combinatorial Chemistry & High Throughput Screening, 15(1), 90-99.
• Fittolani, G., Shanina, E., Guberman, M., Seeberger, P. H., Rademacher, C., & Delbianco, M. (2021). Automated Glycan Assembly of 19F‐labeled Glycan Probes Enables High‐Throughput NMR Studies of Protein–Glycan Interactions. Angewandte Chemie International Edition, 60(24), 13302-13309.
• Song, X., Xia, B., Lasanajak, Y., Smith, D. F., & Cummings, R. D. (2008). Quantifiable fluorescent glycan microarrays. Glycoconjugate Journal, 25, 15-25.
• Shinohara, Y., & Furukawa, J.-i. (2014). Surface Plasmon Resonance as a Tool to Characterize Lectin–Carbohydrate Interactions. Lectins: Methods and Protocols, 185-205.
• Day, C. J., Poole, J., Pluschke, G., & Jennings, M. P. (2022). Investigation of Mycobacterium ulcerans Glycan Interactions Using Glycan Array and Surface Plasmon Resonance. Mycobacterium ulcerans: Methods and Protocols, 29-40.
• Kim, Y., Hyun, J. Y., & Shin, I. (2022). Glycan microarrays from construction to applications. Chemical Society Reviews.
• Belický, Š., Katrlík, J., & Tkáč, J. (2016). Glycan and lectin biosensors. Essays in Biochemistry, 60(1), 37-47.
• Domann, P. J., Pardos‐Pardos, A. C., Fernandes, D. L., Spencer, D. I. R., Radcliffe, C. M., Royle, L., Dwek, R. A., & Rudd, P. M. (2007). Separation‐based glycoprofiling approaches using fluorescent labels. Proteomics, 7(S1), 70-76.
• Bigge, J., Patel, T., Bruce, J., Goulding, P., Charles, S., & Parekh, R. (1995). Nonselective and efficient fluorescent labeling of glycans using 2-amino benzamide and anthranilic acid. Analytical Biochemistry, 230(2), 229-238.
• Kamoda, S., Nakano, M., Ishikawa, R., Suzuki, S., & Kakehi, K. (2005). Rapid and sensitive screening of N-glycans as 9-fluorenylmethyl derivatives by high-performance liquid chromatography: a method which can recover free oligosaccharides after analysis. Journal of Proteome Research, 4(1), 146-152.
• Wu, X., & Bruchez, M. P. (2004). Labeling cellular targets with semiconductor quantum dot conjugates. In Methods in Cell Biology (Vol. 75, pp. 171-183). Elsevier.
• Johansson, M. K., & Cook, R. M. (2003). Intramolecular dimers: a new design strategy for fluorescence‐quenched probes. Chemistry–A European Journal, 9(15), 3466-3471.
• Sapsford, K. E., Berti, L., & Medintz, I. L. (2006). Materials for fluorescence resonance energy transfer analysis: beyond traditional donor–acceptor combinations. Angewandte Chemie International Edition, 45(28), 4562-4589.
• Vogelsang, J., Kasper, R., Steinhauer, C., Person, B., Heilemann, M., Sauer, M., & Tinnefeld, P. (2008). A reducing and oxidizing system minimizes photobleaching and blinking of fluorescent dyes. Angewandte Chemie International Edition, 47(29), 5465-5469.
• Hahne, H., Neubert, P., Kuhn, K., Etienne, C., Bomgarden, R., Rogers, J. C., & Kuster, B. (2012). Carbonyl-reactive tandem mass tags for the proteome-wide quantification of N-linked glycans. Analytical chemistry, 84(8), 3716-3724.
• Zhong, X., Chen, Z., Snovida, S., Liu, Y., Rogers, J. C., & Li, L. (2015). Capillary electrophoresis-electrospray ionization-mass spectrometry for quantitative analysis of glycans labeled with multiplex carbonyl-reactive tandem mass tags. Analytical Chemistry, 87(13), 6527-6534.
• Iliuk, A., Galan, J., & Tao, W. A. (2009). Playing tag with quantitative proteomics. Analytical and Bioanalytical Chemistry, 393, 503-513.
• Zhu, W., Smith, J. W., & Huang, C.-M. (2009). Mass spectrometry-based label-free quantitative proteomics. Journal of Biomedicine and Biotechnology, 2010.
• Walker, S. H., Taylor, A. D., & Muddiman, D. C. (2013). Individuality normalization when labeling with isotopic glycan hydrazide tags (INLIGHT): a novel glycan-relative quantification strategy. Journal of the American Society for Mass Spectrometry, 24(9), 1376-1384.
• Sun, Z., Qin, H., Wang, F., Cheng, K., Dong, M., Ye, M., & Zou, H. (2012). Capture and dimethyl labeling of glycopeptides on hydrazide beads for quantitative glycoproteomics analysis. Analytical Chemistry, 84(20), 8452-8456.
• Huang, J., Qin, H., Sun, Z., Huang, G., Mao, J., Cheng, K., Zhang, Z., Wan, H., Yao, Y., & Dong, J. (2015). A peptide N-terminal protection strategy for comprehensive glycoproteome analysis using hydrazide chemistry based method. Scientific Reports, 5(1), 1-15.
• Zeng, X., Hood, B. L., Sun, M., Conrads, T. P., Day, R. S., Weissfeld, J. L., Siegfried, J. M., & Bigbee, W. L. (2010). Lung cancer serum biomarker discovery using glycoprotein capture and liquid chromatography mass spectrometry. Journal of Proteome Research, 9(12), 6440-6449.
• Zhang, Y., Hu, Z., Zhang, C., Liu, B.-F., & Liu, X. (2020). A robust glycan labeling strategy using a new cationic hydrazide tag for MALDI-MS-based rapid and sensitive glycomics analysis. Talanta, 219, 121356.
• Best, M. D. (2009). Click chemistry and bioorthogonal reactions: unprecedented selectivity in the labeling of biological molecules. Biochemistry, 48(28), 6571-6584.
• Gil, M. V., Arévalo, M. J., & Lopez, O. (2007). Click chemistry-what’s in a name? Triazole synthesis and beyond. Synthesis, 2007(11), 1589-1620.
• Zhang, X., & Zhang, Y. (2013). Applications of azide-based bioorthogonal click chemistry in glycobiology. Molecules, 18(6), 7145-7159.
• Liu, B. (2019). Bio-orthogonal click chemistry for in vivo bioimaging. Trends in Chemistry, 1(8), 763-778.
• Smeekens, J. M., Chen, W., & Wu, R. (2014). Mass spectrometric analysis of the cell surface N-glycoproteome by combining metabolic labeling and click chemistry. Journal of the American Society for Mass Spectrometry, 26(4), 604-614.
• Kim, E., & Koo, H. (2019). Biomedical applications of copper-free click chemistry: in vitro, in vivo, and ex vivo. Chemical Science, 10(34), 7835-7851.
• McKay, C. S., & Finn, M. (2014). Click chemistry in complex mixtures: bioorthogonal bioconjugation. Chemistry & Biology, 21(9), 1075-1101.
• Park, S., Lee, M.-R., & Shin, I. (2008). Chemical tools for functional studies of glycans. Chemical Society Reviews, 37(8), 1579-1591.
• Lopez Aguilar, A., Briard, J. G., Yang, L., Ovryn, B., Macauley, M. S., & Wu, P. (2017). Tools for studying glycans: recent advances in chemoenzymatic glycan labeling. ACS Chemical Biology, 12(3), 611-621.
• Lindhout, T., Iqbal, U., Willis, L. M., Reid, A. N., Li, J., Liu, X., Moreno, M., & Wakarchuk, W. W. (2011). Site-specific enzymatic polysialylation of therapeutic proteins using bacterial enzymes. Proceedings of the National Academy of Sciences, 108(18), 7397-7402.
• Rashidian, M., Dozier, J. K., & Distefano, M. D. (2013). Enzymatic labeling of proteins: techniques and approaches. Bioconjugate Chemistry, 24(8), 1277-1294.
• Moremen, K. W., & Haltiwanger, R. S. (2019). Emerging structural insights into glycosyltransferase-mediated synthesis of glycans. Nature Chemical Biology, 15(9), 853-864.
• Wu, Z. L., & Ertelt, J. M. (2022). Endoglycosidase assay using enzymatically synthesized fluorophore-labeled glycans as substrates to uncover enzyme substrate specificities. Communications Biology, 5(1), 501.
• Bynum, M. A., Yin, H., Felts, K., Lee, Y. M., Monell, C. R., & Killeen, K. (2009). Characterization of IgG N-glycans employing a microfluidic chip that integrates glycan cleavage, sample purification, LC separation, and MS detection. Analytical Chemistry, 81(21), 8818-8825.
• Zhang, S., Li, W., Lu, H., & Liu, Y. (2017). Quantification of N-glycosylation site occupancy status based on labeling/label-free strategies with LC-MS/MS. Talanta, 170, 509-513.
• Temme, J. S., & Gildersleeve, J. C. (2022). General strategies for glycan microarray data processing and analysis. Glycan Microarrays: Methods and Protocols, 67-87.
• Shah, B., Jiang, X. G., Chen, L., & Zhang, Z. (2014). LC-MS/MS peptide mapping with automated data processing for routine profiling of N-glycans in immunoglobulins. Journal of the American Society for Mass Spectrometry, 25(6), 999-1011.
• Jansen, B. C., Reiding, K. R., Bondt, A., Hipgrave Ederveen, A. L., Palmblad, M., Falck, D., & Wuhrer, M. (2015). MassyTools: a high-throughput targeted data processing tool for relative quantitation and quality control developed for glycomic and glycoproteomic MALDI-MS. Journal of Proteome Research, 14(12), 5088-5098.
• Artemenko, N. V., Campbell, M. P., & Rudd, P. M. (2010). GlycoExtractor: a web-based interface for high throughput processing of HPLC-glycan data. Journal of Proteome Research, 9(4), 2037-2041.
• Bao, B., Kellman, B. P., Chiang, A. W., Zhang, Y., Sorrentino, J. T., York, A. K., Mohammad, M. A., Haymond, M. W., Bode, L., & Lewis, N. E. (2021). Correcting for sparsity and interdependence in glycomics by accounting for glycan biosynthesis. Nature Communications, 12(1), 4988.
• Lacher, N. A., Roberts, R. K., He, Y., Cargill, H., Kearns, K. M., Holovics, H., & Ruesch, M. N. (2010). Development, validation, and implementation of capillary gel electrophoresis as a replacement for SDS‐PAGE for purity analysis of IgG2 mAbs. Journal of Separation Science, 33(2), 218-227.
• Uh, H.-W., Klarić, L., Ugrina, I., Lauc, G., Smilde, A. K., & Houwing-Duistermaat, J. J. (2020). Choosing proper normalization is essential for discovery of sparse glycan biomarkers. Molecular Omics, 16(3), 231-242.
• Misra, B. B., & van der Hooft, J. J. (2016). Updates in metabolomics tools and resources: 2014–2015. Electrophoresis, 37(1), 86-110.
• Chang, D., & Zaia, J. (2022). Methods to improve quantitative glycoprotein coverage from bottom‐up LC‐MS data. Mass Spectrometry Reviews, 41(6), 922-937.
• Gillet, L. C., Navarro, P., Tate, S., Röst, H., Selevsek, N., Reiter, L., Bonner, R., & Aebersold, R. (2012). Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Molecular & Cellular Proteomics, 11(6).
• Rambla-Alegre, M., Esteve-Romero, J., & Carda-Broch, S. (2012). Is it really necessary to validate an analytical method or not? That is the question. Journal of Chromatography A, 1232, 101-109.
• Araujo, P. (2009). Key aspects of analytical method validation and linearity evaluation. Journal of Chromatography B, 877(23), 2224-2234.
• Trbojević-Akmačić, I., Ugrina, I., & Lauc, G. (2017). Comparative analysis and validation of different steps in glycomics studies. In Methods in Enzymology (Vol. 586, pp. 37-55). Elsevier.
• Campbell, M. P., Nguyen-Khuong, T., Hayes, C. A., Flowers, S. A., Alagesan, K., Kolarich, D., Packer, N. H., & Karlsson, N. G. (2014). Validation of the curation pipeline of UniCarb-DB: building a global glycan reference MS/MS repository. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1844(1), 108-116.
• Yuwono, M., & Indrayanto, G. (2005). Validation of chromatographic methods of analysis. Profiles of Drug Substances, Excipients and Related Methodology, 32, 243-259.
• Arbogast, L. W., Delaglio, F., Schiel, J. E., & Marino, J. P. (2017). Multivariate analysis of two-dimensional 1H, 13C methyl NMR spectra of monoclonal antibody therapeutics to facilitate assessment of higher order structure. Analytical Chemistry, 89(21), 11839-11845.
• Taichrib, A., Pioch, M., & Neusüß, C. (2012). Multivariate statistics for the differentiation of erythropoietin preparations based on intact glycoforms determined by CE-MS. Analytical and Bioanalytical Chemistry, 403, 797-805.
• Planinc, A., Dejaegher, B., Heyden, Y. V., Viaene, J., Van Praet, S., Rappez, F., Van Antwerpen, P., & Delporte, C. (2017). LC-MS analysis combined with principal component analysis and soft independent modelling by class analogy for a better detection of changes in N-glycosylation profiles of therapeutic glycoproteins. Analytical and Bioanalytical Chemistry, 409, 477-485.
• Bojar, D., Powers, R. K., Camacho, D. M., & Collins, J. J. (2021). Deep-learning resources for studying glycan-mediated host-microbe interactions. Cell Host & Microbe, 29(1), 132-144. e133.
• Li, H., Chiang, A. W., & Lewis, N. E. (2022). Artificial intelligence in the analysis of glycosylation data. Biotechnology Advances, 108008.
• Xiao, H., Suttapitugsakul, S., Sun, F., & Wu, R. (2018). Mass spectrometry-based chemical and enzymatic methods for global analysis of protein glycosylation. Accounts of Chemical Research, 51(8), 1796-1806.
• Gupta, G., Surolia, A., & Sampathkumar, S.-G. (2010). Lectin microarrays for glycomic analysis. Omics: A Journal of Integrative Biology, 14(4), 419-436.
• Das, A. K., Ghosh, N., Mandal, A., & Sil, P. C. (2022). Glycobiology of cellular expiry: decrypting the role of glycan-lectin regulatory complex and therapeutic strategies focusing on cancer. Biochemical Pharmacology, 115367.
• Trbojević-Akmačić, I., Lageveen-Kammeijer, G. S., Heijs, B., Petrović, T., Deris, H., Wuhrer, M., & Lauc, G. (2022). High-throughput glycomic methods. Chemical Reviews, 122(20), 15865-15913.
• Kailemia, M. J., Park, D., & Lebrilla, C. B. (2017). Glycans and glycoproteins as specific biomarkers for cancer. Analytical and Bioanalytical Chemistry, 409, 395-410.
• Pinho, S. S., & Reis, C. A. (2015). Glycosylation in cancer: mechanisms and clinical implications. Nature Reviews Cancer, 15(9), 540-555.
• Taniguchi, N., Hancock, W., Lubman, D. M., & Rudd, P. M. (2009). The second golden age of glycomics: from functional glycomics to clinical applications. Journal of Proteome Research, 8(2), 425-426.
• Rho, J.-h., Ladd, J. J., Li, C. I., Potter, J. D., Zhang, Y., Shelley, D., Shibata, D., Coppola, D., Yamada, H., & Toyoda, H. (2018). Protein and glycomic plasma markers for early detection of adenoma and colon cancer. Gut, 67(3), 473-484.
• Etxebarria, J., & Reichardt, N.-C. (2016). Methods for the absolute quantification of N-glycan biomarkers. Biochimica et Biophysica Acta (BBA)-General Subjects, 1860(8), 1676-1687.
• Li, J., Zhang, J., Xu, M., Yang, Z., Yue, S., Zhou, W., Gui, C., Zhang, H., Li, S., & Wang, P. G. (2022). Advances in glycopeptide enrichment methods for the analysis of protein glycosylation over the past decade. Journal of Separation Science, 45(16), 3169-3186.
• Planinc, A., Bones, J., Dejaegher, B., Van Antwerpen, P., & Delporte, C. (2016). Glycan characterization of biopharmaceuticals: updates and perspectives. Analytica Chimica Acta, 921, 13-27.
• Jenkins, N., Murphy, L., & Tyther, R. (2008). Post-translational modifications of recombinant proteins: significance for biopharmaceuticals. Molecular Biotechnology, 39, 113-118.
• Papathanasiou, M. M., & Kontoravdi, C. (2020). Engineering challenges in therapeutic protein product and process design. Current Opinion in Chemical Engineering, 27, 81-88.
• Dicker, M., & Strasser, R. (2015). Using glyco-engineering to produce therapeutic proteins. Expert Opinion on Biological Therapy, 15(10), 1501-1516.
• Agatemor, C., Buettner, M. J., Ariss, R., Muthiah, K., Saeui, C. T., & Yarema, K. J. (2019). Exploiting metabolic glycoengineering to advance healthcare. Nature Reviews Chemistry, 3(10), 605-620.
• Dong, X., Huang, Y., Cho, B. G., Zhong, J., Gautam, S., Peng, W., ... & Mechref, Y. (2018). Advances in mass spectrometry‐based glycomics. Electrophoresis, 39(24), 3063-3081.
• Ng, E. W., Wong, M. Y., & Poon, T. C. (2014). Advances in MALDI mass spectrometry in clinical diagnostic applications. Chemical Diagnostics: From Bench to Bedside, 139-175.
• Pabst, M., & Altmann, F. (2008). Influence of electrosorption, solvent, temperature, and ion polarity on the performance of LC-ESI-MS using graphitic carbon for acidic oligosaccharides. Analytical Chemistry, 80(19), 7534-7542.
• Yu, A., Zhao, J., Peng, W., Banazadeh, A., Williamson, S. D., Goli, M., ... & Mechref, Y. (2018). Advances in mass spectrometry‐based glycoproteomics. Electrophoresis, 39(24), 3104-3122.
• Wu, H., & Tang, K. (2020). Highly sensitive and robust capillary electrophoresis-electrospray ionization-mass spectrometry: Interfaces, preconcentration techniques and applications. Reviews in Analytical Chemistry, 39(1), 45-55.
• Helena, H., Ivona, V., Roman, Ř., & František, F. (2022). Current applications of capillary electrophoresis‐mass spectrometry for the analysis of biologically important analytes in urine (2017 to mid‐2021): A review. Journal of Separation Science, 45(1), 305-324.
• Gomes, F. P., & Yates III, J. R. (2019). Recent trends of capillary electrophoresis‐mass spectrometry in proteomics research. Mass Spectrometry Reviews, 38(6), 445-460.
• Giorgetti, J., D’atri, V., Canonge, J., Lechner, A., Guillarme, D., Colas, O., ... & François, Y. N. (2018). Monoclonal antibody N-glycosylation profiling using capillary electrophoresis–Mass spectrometry: Assessment and method validation. Talanta, 178, 530-537.
• Jin, W., Wang, C., Yang, M., Wei, M., Huang, L., & Wang, Z. (2019). Glycoqueuing: Isomer-specific quantification for sialylation-focused glycomics. Analytical Chemistry, 91(16), 10492-10500.
• Chen, X., & Flynn, G. C. (2007). Analysis of N-glycans from recombinant immunoglobulin G by on-line reversed-phase high-performance liquid chromatography/mass spectrometry. Analytical Biochemistry, 370(2), 147-161.
• Peng, W., Gutierrez Reyes, C. D., Gautam, S., Yu, A., Cho, B. G., Goli, M., ... & Mechref, Y. (2023). MS‐based glycomics and glycoproteomics methods enabling isomeric characterization. Mass Spectrometry Reviews, 42(2), 577-616.
• Yang, X., & Bartlett, M. G. (2019). Glycan analysis for protein therapeutics. Journal of Chromatography B, 1120, 29-40.