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Data-independent oxonium ion profiling of multi-glycosylated biotherapeutics

, , , ORCID Icon & ORCID Icon
Pages 968-978 | Received 22 Mar 2018, Accepted 24 Jun 2018, Published online: 01 Aug 2018

References

  • Moremen KW, Tiemeyer M, Nairn AV. Vertebrate protein glycosylation: diversity, synthesis and function. Nat Rev Mol Cell Biol. 2012;13:448–462. doi:10.1038/nrm3383.
  • Spiro RG. Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds. Glycobiology. 2002;12:43R–56R.
  • Jefferis R. Glycosylation as a strategy to improve antibody-based therapeutics. Nat Rev Drug Discov. 2009;8:226–234. doi:10.1038/nrd2804.
  • Natsume A, Niwa R, Satoh M. Improving effector functions of antibodies for cancer treatment: enhancing ADCC and CDC. Drug Des Devel Ther. 2009;3:7–16.
  • Kellner C, Derer S, Valerius T, Peipp M. Boosting ADCC and CDC activity by Fc engineering and evaluation of antibody effector functions. Methods. 2014;65:105–113. doi:10.1016/j.ymeth.2013.06.036.
  • Zhu L, Guo Q, Guo H, Liu T, Zheng Y, Gu P, Chen X, Wang H, Hou S, Guo Y. Versatile characterization of glycosylation modification in CTLA4-Ig fusion proteins by liquid chromatography-mass spectrometry. MAbs. 2014;6:1474–1485. doi:10.4161/mabs.36313.
  • Houel S, Hilliard M, Yu YQ, McLoughlin N, Martin SM, Rudd PM, Williams JP, Chen W. N-and O-glycosylation analysis of etanercept using liquid chromatography and quadrupole time-of-flight mass spectrometry equipped with electron-transfer dissociation functionality. Anal Chem. 2013;86:576–584. doi:10.1021/ac402726h.
  • Larsen CP, Pearson TC, Adams AB, Tso P, Shirasugi N, Strobert E, Anderson D, Cowan S, Price K, Naemura J, et al. Rational development of LEA29Y (belatacept), a high‐affinity variant of CTLA4‐Ig with potent immunosuppressive properties. Am J Transplant. 2005;5:443–453. doi:10.1111/j.1600-6143.2005.00749.x.
  • Balaratnasingam C, Dhrami-Gavazi E, McCann JT, Ghadiali Q, Freund KB. Aflibercept: a review of its use in the treatment of choroidal neovascularization due to age-related macular degeneration. Clin Ophthalmol. 2015;9:2355.
  • Berry JD. Introduction to Therapeutic Fc‐Fusion Proteins. Therapeutic Fc-Fusion Proteins. Wiley-VCH Verlag GmbH & Co. KGaA; 2013. p. 217–232.
  • Takahashi K, Wall SB, Suzuki H, Smith AD, Hall S, Poulsen K, Kilian M, Mobley JA, Julian BA, Mestecky J Clustered O-glycans of IgA1: defining macro- and microheterogeneity by use of electron capture/transfer dissociation. Mol Cell Proteomics. 2010;9:2545–2557. doi:10.1074/mcp.M110.001834.
  • Wada Y, Dell A, Haslam SM, Tissot B, Canis K, Azadi P, Bäckström M, Costello CE, Hansson GC, Hiki Y, et al. Comparison of methods for profiling o-glycosylation human proteome organisation human disease glycomics/proteome initiative multi-institutional study of iga1. Mol Cell Proteomics. 2010;9:719–727. doi:10.1074/mcp.M900450-MCP200.
  • Christiansen MN, Kolarich D, Nevalainen H, Packer NH, Jensen PH. Challenges of determining O-glycopeptide heterogeneity: a fungal glucanase model system. Anal Chem. 2010;82:3500–3509. doi:10.1021/ac901717n.
  • Desaire H. Glycopeptide analysis, recent developments and applications. Mol Cell Proteomics. 2013;12:893–901. doi:10.1074/mcp.R112.026567.
  • Mechref Y. Use of CID/ETD mass spectrometry to analyze glycopeptides. Curr Protoc Protein Sci. 2012;12(1):1–11.
  • Saba J, Dutta S, Hemenway E, Viner R. Increasing the productivity of glycopeptides analysis by using higher-energy collision dissociation-accurate mass-product-dependent electron transfer dissociation. Int J Proteomics. 2012;2012:1–7. doi:10.1155/2012/560391.
  • Singh C, Zampronio CG, Creese AJ, Cooper HJ. Higher energy collision dissociation (HCD) product ion-triggered Electron Transfer Dissociation (ETD) mass spectrometry for the analysis of N-linked glycoproteins. J Proteome Res. 2012;11:4517–4525. doi:10.1021/pr300257c.
  • Zhang L, Reilly JP. Extracting both peptide sequence and glycan structural information by 157 nm photodissociation of N-linked glycopeptides. J Proteome Res. 2008;8:734–742. doi:10.1021/pr800766f.
  • Madsen JA, Ko BJ, Xu H, Iwashkiw JA, Robotham SA, Shaw JB, Feldman MF, Brodbelt JS. Concurrent automated sequencing of the glycan and peptide portions of O-linked glycopeptide anions by ultraviolet photodissociation mass spectrometry. Anal Chem. 2013;85:9253–9261. doi:10.1021/ac4021177.
  • Sanda M, Goldman R. Data independent analysis of IgG glycoforms in samples of unfractionated human plasma. Anal Chem. 2016;88:10118–10125. doi:10.1021/acs.analchem.6b02554.
  • Sanda M, Zhang L, Edwards NJ, Goldman R. Site-specific analysis of changes in the glycosylation of proteins in liver cirrhosis using data-independent workflow with soft fragmentation. Anal Bioanal Chem. 2017;409:619–627. doi:10.1007/s00216-016-0041-8.
  • Pan K-T, Chen -C-C, Urlaub H, Khoo K-H. Adapting data-independent acquisition for mass spectrometry-based protein site-specific N-glycosylation analysis. Anal Chem. 2017;89:4532–4539. doi:10.1021/acs.analchem.6b04996.
  • Cao L, Tolić N, Qu Y, Meng D, Zhao R, Zhang Q, Moore RJ, Zink EM, Lipton MS, Paša-Tolić L, et al. Characterization of intact N-and O-linked glycopeptides using higher energy collisional dissociation. Anal Biochem. 2014;452:96–102. doi:10.1016/j.ab.2014.01.003.
  • Toyama A, Nakagawa H, Matsuda K, Sato T-A, Nakamura Y, Ueda K. Quantitative structural characterization of local N-glycan microheterogeneity in therapeutic antibodies by energy-resolved oxonium ion monitoring. Anal Chem. 2012;84:9655–9662. doi:10.1021/ac3023372.
  • Song E, Pyreddy S, Mechref Y. Quantification of glycopeptides by multiple reaction monitoring liquid chromatography/tandem mass spectrometry. Rapid Commun Mass Spectrom. 2012;26:1941–1954. doi:10.1002/rcm.6290.
  • Hart-Smith G, Raftery MJ. Detection and characterization of low abundance glycopeptides via higher-energy C-trap dissociation and orbitrap mass analysis. J Am Soc Mass Spectrom. 2012;23:124–140. doi:10.1007/s13361-011-0273-y.
  • Halim A, Westerlind U, Pett C, Schorlemer M, Rüetschi U, Brinkmalm G, Sihlbom C, Lengqvist J, Larson G, Nilsson J. Assignment of saccharide identities through analysis of oxonium ion fragmentation profiles in LC–MS/MS of glycopeptides. J Proteome Res. 2014;13:6024–6032. doi:10.1021/pr500898r.
  • Nasir W, Toledo AG, Noborn F, Nilsson J, Wang M, Bandeira N, Larson G. SweetNET: A bioinformatics workflow for glycopeptide MS/MS spectral analysis. J Proteome Res. 2016;15:2826–2840. doi:10.1021/acs.jproteome.6b00417.
  • Czajkowsky DM, Hu J, Shao Z, Pleass RJ. Fc‐fusion proteins: new developments and future perspectives. EMBO Mol Med. 2012;4:1015–1028. doi:10.1002/emmm.201201379.
  • Washburn N, Schwab I, Ortiz D, Bhatnagar N, Lansing JC, Medeiros A, Tyler S, Mekala D, Cochran E, Sarvaiya H, et al. Controlled tetra-Fc sialylation of IVIg results in a drug candidate with consistent enhanced anti-inflammatory activity. Proc Natl Acad Sci. 2015;112:E1297–E306. doi:10.1073/pnas.1422481112.
  • Bern M, Cai Y, Goldberg D. Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry. Anal Chem. 2007;79:1393–1400. doi:10.1021/ac0617013.
  • Bern M, Kil YJ, Becker C. Byonic: advanced peptide and protein identification software. Curr Protoc Bioinformatics. 2012; 40:13.20.1&13.20.14..
  • Bondt A, Rombouts Y, Selman MH, Hensbergen PJ, Reiding KR, Hazes JM, Dolhain RJ, Wuhrer M. Immunoglobulin G (IgG) Fab glycosylation analysis using a new mass spectrometric high-throughput profiling method reveals pregnancy-associated changes. Mol Cell Proteomics. 2014;13:3029–3039. doi:10.1074/mcp.M114.039537.
  • van de Bovenkamp FS, Hafkenscheid L, Rispens T, Rombouts Y. The emerging importance of IgG Fab glycosylation in immunity. J Immunol. 2016;196:1435–1441. doi:10.4049/jimmunol.1502136.
  • Plomp R, Dekkers G, Rombouts Y, Visser R, Koeleman CA, Kammeijer GS, Jansen BC, Rispens T, Hensbergen PJ, Vidarsson G, et al. Hinge-region O-glycosylation of human immunoglobulin G3 (IgG3). Mol Cell Proteomics. 2015;14:1373–1384. doi:10.1074/mcp.M114.047381.
  • Gilar M, Yu Y-Q, Ahn J, Fournier J, Gebler JC. Mixed-mode chromatography for fractionation of peptides, phosphopeptides, and sialylated glycopeptides. J Chromatogr A. 2008;1191:162–170. doi:10.1016/j.chroma.2008.01.061.
  • Dong Q, Yan X, Liang Y, Stein SE. In-depth characterization and spectral library building of glycopeptides in the tryptic digest of a monoclonal antibody using 1D and 2D LC–MS/MS. J Proteome Res. 2016;15:1472–1486. doi:10.1021/acs.jproteome.5b01046.
  • Wang H, Wong CH, Chin A, Taguchi A, Taylor A, Hanash S, Sekiya S, Takahashi H, Murase M, Kajihara S, et al. Integrated mass spectrometry-based analysis of plasma glycoproteins and their glycan modifications. Nat Protoc. 2011;6:253–269. doi:10.1038/nprot.2010.176.
  • Madsen JA, Yin Y, Qiao J, Gill V, Renganathan K, Fu WY, Smith S, Anderson J. Covalent labeling denaturation mass spectrometry for sensitive localized higher order structure comparisons. Anal Chem. 2016;88:2478–2488. doi:10.1021/acs.analchem.5b04736.
  • R Core Team. R: A Language and Environment for Statistical Computing. 2014:http://www.R-project.org.
  • Gatto L, Lilley KS. MSnbase–an R/Bioconductor package for isobaric tagged mass spectrometry data visualisation, processing and quantitation. Bioinformatics. 2011;28:btr645.
  • Cleveland WS, Grosse E, Shyu WM. Local regression models. Stat Model S. 1992;2:309–376.
  • Eilers PH. Parametric time warping. Anal Chem. 2004;76:404–411. doi:10.1021/ac034800e.
  • Bloemberg TG, Gerretzen J, Wouters HJ, Gloerich J, van Dael M, Wessels HJ, van den Heuvel LP, Eilers PH, Buydens LM, Wehrens R. Improved parametric time warping for proteomics. Chemometr Intell Lab Syst. 2010;104:65–74. doi:10.1016/j.chemolab.2010.04.008.