Full validation of therapeutic antibody sequences by middle-up mass measurements and middle-down protein sequencing

mAbs

Volumn 8, Issue 2, 2016, Pages 318-330

  Resemann, Anja ^a   Jabs, Wolfgang ^a   Wiechmann, Anja ^a   Wagner, Elsa ^b   Colas, Olivier ^b   Evers, Waltraud ^a   Belau, Eckhard ^a   Vorwerg, Lars ^a   Evans, Catherine ^a   Beck, Alain ^b   Suckau, Detlev ^a  

^a BRUKER DALTONIK GMBH   (Germany)

^b Centre d Immunologie Pierre   (France)

Author keywords

Biotherapeutics; Cetuximab; IgG; Middle down; Middle up; Natalizumab; Panitumumab; Sequence validation; Top down protein sequencing

Indexed keywords

ANTIBODY; CETUXIMAB; DISULFIDE; IMMUNOGLOBULIN FC FRAGMENT; NATALIZUMAB; PANITUMUMAB; MONOCLONAL ANTIBODY;

AMINO ACID SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; QUADRUPOLE MASS SPECTROMETRY; SEQUENCE ANALYSIS; TIME OF FLIGHT MASS SPECTROMETRY; VALIDATION PROCESS; CHEMISTRY; GENETICS; HUMAN; PROCEDURES;

ANTIBODIES, MONOCLONAL; CETUXIMAB; HUMANS; NATALIZUMAB; SEQUENCE ANALYSIS, PROTEIN;

EID: 84964412990     PISSN: 19420862     EISSN: 19420870     Source Type: Journal    
DOI: 10.1080/19420862.2015.1128607     Document Type: Article

References (43)

1. BeckA, WurchT, BaillyC, CorvaiaN.Strategies and challenges for the next generation of therapeutic antibodies. Nat Rev Immunol2010; 10(5):345–52; PMID:20414207; http://dx.doi.org/10.1038/nri2747
2. ReichertJM.Antibodies to watch in 2016. MAbs2016; 8(2):in press
3. WurchT, LoweP, CaussanelV, BesC, BeckA, CorvaiaN.Development of novel protein scaffolds as alternatives to whole antibodies for imaging and therapy: status on discovery research and clinical validation. Curr Pharm Biotechnol2008; 9(6):502–9; PMID:19075688; http://dx.doi.org/10.2174/138920108786786385
4. DuY, WangF, MayK, XuW, LiuH.Determination of deamidation artifacts introduced by sample preparation using 18O-labeling and tandem mass spectrometry analysis. Anal Chem2012; 84(15):6355–60; PMID:22881398; http://dx.doi.org/10.1021/ac3013362
5. FornelliL, DamocE, ThomasPM, KelleherNL, AizikovK, DenisovE, MakarovA, TsybinYO.Analysis of intact monoclonal antibody IgG1 by electron transfer dissociation Orbitrap FTMS. Mol Cell Proteomics2012; 11(12):1758–67; PMID:22964222; http://dx.doi.org/10.1074/mcp.M112.019620
6. TsybinYO, FornelliL, StoermerC, LuebeckM, ParraJ, NalletS, WurmFM, HartmerR.Structural analysis of intact monoclonal antibodies by electron transfer dissociation mass spectrometry. Anal Chem2011; 83(23):8919–27; PMID:22017162; http://dx.doi.org/10.1021/ac201293m
7. MaoY, ValejaSG, RouseJC, HendricksonCL, MarshallAG.Topdown structural analysis of an intact monoclonal antibody by electron capture dissociation-Fourier transform ion cyclotron resonance-mass spectrometry. Anal Chem2013; 85(9):4239–46; PMID:23551206; http://dx.doi.org/10.1021/ac303525n
8. FornelliL, AyoubD, AizikovK, BeckA, TsybinYO.Middle-down analysis of monoclonal antibodies with electron transfer dissociation orbitrap fourier transform mass spectrometry. Anal Chem2014Mar 18; 86(6):3005–12; PMID:24588056; http://dx.doi.org/10.1021/ac4036857
9. LennonJJ, WalshKA.Direct sequence analysis of proteins by insource fragmentation during delayed ion extraction. Protein Sci. 1997; 6(11):2446–53; PMID:9385647; http://dx.doi.org/10.1002/pro.5560061118
10. SuckauD, ResemannA.T3-sequencing: targeted characterization of the N-and C-termini of undigested proteins by mass spectrometry. Anal Chem. 2003; 75(21):5817–24; PMID:14588022; http://dx.doi.org/10.1021/ac034362b
11. SuckauD, ResemannA, SchuerenbergM, HufnagelP, FranzenJ, HolleA.A novel MALDI LIFT-TOF/TOF mass spectrometer for proteomics. Anal Bioanal Chem. 2003; 376(7):952–65; PMID:12830354; http://dx.doi.org/10.1007/s00216-003-2057-0
12. HardouinJ.Protein sequence information by matrix-assisted laser desorption/ionization in-source decay mass spectrometry. Mass Spectrom Rev. 2007; 26(5):672–82; PMID:17492750; http://dx.doi.org/10.1002/mas.20142
13. TakayamaM.N-Ca Bond Cleavage of the Peptide Backbone via Hydrogen Abstraction. J Am Soc Mass Spectrom. 2001; 12:1044–49; http://dx.doi.org/10.1016/S1044-0305(01)00289-6
14. DemeureK, GabelicaV, De PauwEA.New advances in the understanding of the in-source decay fragmentation of peptides in MALDI-TOF-MS. J Am Soc Mass Spectrom2010; 21(11):1906–17; PMID:20832332; http://dx.doi.org/10.1016/j.jasms.2010.07.009
15. HanischFG.Top-down sequencing of O-glycoproteins by in-source decay matrix-assisted laser desorption ionization mass spectrometry for glycosylation site analysis. Anal Chem2011; 83(12):4829–37; PMID:21526855; http://dx.doi.org/10.1021/ac200493c
16. YooC, SuckauD, SauerlandV, RonkM, MaM.Toward topdown determination of PEGylation site using MALDI in-source decay MS analysis. J Am Soc Mass Spectrom2009; 20(2):326–33; PMID:19019698; http://dx.doi.org/10.1016/j.jasms.2008.10.013
17. ResemannA, WunderlichD, RothbauerU, WarscheidB, LeonhardtH, FuchserJ, KuhlmannK, SuckauD.Top-down de Novo Protein Sequencing of a 13.6 kDa Camelid Single Heavy Chain Antibody by Matrix-Assisted Laser Desorption Ionization-Time-of-Flight/Timeof-Flight Mass Spectrometry. Anal Chem2010; 82(8):3283–92; PMID:20329751; http://dx.doi.org/10.1021/ac1000515
18. AyoubD, JabsW, ResemannA, EversW, EvansC, MainL, BaessmannC, Wagner-RoussetE, SuckauD, BeckA.Correct primary structure assessment and extensive glyco-profiling of cetuximab by a combination of intact, middle-up, middle-down and bottom-up ESI and MALDI mass spectrometry techniques. MAbs2013; 5(5):699–710; PMID:23924801; http://dx.doi.org/10.4161/mabs.25423
19. von Pawel-RammingenU, JohanssonBP, BjÖrckL.IdeS, a novel streptococcal cysteine proteinase with unique specificity for immunoglobulin G. EMBO J. 2002; 21(7):1607–15; PMID:11927545; http://dx.doi.org/10.1093/emboj/21.7.1607
20. AnY, ZhangY, MuellerHM, ShameemM, ChenX.A new tool for monoclonal antibody analysis: Application of IdeS proteolysis in IgG domain-specific characterization. MAbs.2014; 6(4):879–93; PMID:24927271; http://dx.doi.org/10.4161/mabs.28762
21. LiS, SchmitzKR, JeffreyPD, WiltziusJJ, KussieP, FergusonKM.Structural basis for inhibition of the epidermal growth factor receptor by cetuximab. Cancer Cell2005; 7(4):301–11; PMID:15837620; http://dx.doi.org/10.1016/j.ccr.2005.03.003
22. DuboisM, FenailleF, ClementG, LechmannM, TabetJC, EzanE, BecherF.Immunopurification and mass spectrometric quantification of the active form of a chimeric therapeutic antibody in human serum. Anal Chem2008; 80(5):1737–45; PMID:18225864; http://dx.doi.org/10.1021/ac7021234
23. AllhornM, CollinM.Sugar-free antibodies–the bacterial solution to autoimmunity?Ann N Y Acad Sci2009; 1173:664–9; PMID:19758213; http://dx.doi.org/10.1111/j.1749-6632.2009.04739.x
24. WangX, DasTK, SinghSK, KumarS.Potential aggregation prone regions in biotherapeutics: A survey of commercial monoclonal antibodies. MAbs2009; 1(3):254–67; PMID:20065649; http://dx.doi.org/10.4161/mabs.1.3.8035
25. GormanJJ, FergusonBL, NguyenTB.Use of 2,6-dihydroxyacetophenone for analysis of fragile peptides, disulphide bonding and small proteins by matrix-assisted laser desorption/ionization. Rapid Commun Mass Spectrom. 1996; 10(5):529–36; PMID:9053038; http://dx.doi.org/10.1002/(SICI)1097-0231(19960331)10:5<529::AIDRCM522>3.0.CO;2-9
26. BeckA, Biosimilar, biobetter and next generation therapeutic antibodies. MAbs2011; 3(2):107–10; PMID:21285536; http://dx.doi.org/10.4161/mabs.3.2.14785
27. SchoeningerMJ, DeNiroMJ.Nitrogen and carbon isotopic composition of bone collagen from marine and terrestrial animals. Geochim Cosmochim Acta1984; 48(12):625–39; http://dx.doi.org/10.1016/0016-7037(84)90091-7
28. BeavisRC.Chemical mass of carbon in proteins. Anal Chem1993; 65(4):496–7; http://dx.doi.org/10.1021/ac00052a030
29. SenkoMW, BeuSC, McLaffertyFW.Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J Am Soc Mass Spectrom1995; 6(4):229–33; PMID:24214167; http://dx.doi.org/10.1016/1044-0305(95)00017-8
30. KösterC, Mass spectrometry method for accurate mass determination of unknown ions. 2001, US 6,188,064 B1
31. MachtM, AspergerA, DeiningerSO.Comparison of laser-induced dissociation and high-energy collision-induced dissociation using matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI-TOF/TOF) for peptide and protein identification. Rapid Commun Mass Spectrom2004; 18(18):2093–2105; PMID:23857929; http://dx.doi.org/10.1002/rcm.1589
32. AsakawaD, SmargiassoN, De PauwE.New approach for pseudo-MS(3) analysis of peptides and proteins via MALDI in-source decay using radical recombination with 1,5-diaminonaphthalene. Anal Chem2014; 86(5):2451–7; PMID:24512348; http://dx.doi.org/10.1021/ac403285b
33. EdmanP.Sequence determination. Mol Biol Biochem Biophys1970; 8:211–55; PMID:4950190
34. KattaV, ChowDT, RohdeMF.Applications of in-source fragmentation of protein ions for direct sequence analysis by delayed extraction MALDI-TOF mass spectrometry. Anal Chem1998; 70(20):4410–6; PMID:9796424; http://dx.doi.org/10.1021/ac980034d
35. BungerMK, CargileBJ, NgunjiriA, BundyJL, StephensonJL, Jr.. Automated proteomics of E. coli via top-down electron-transfer dissociation mass spectrometry. Anal Chem2008; 80(5):1459–67; PMID:18229893; http://dx.doi.org/10.1021/ac7018409
36. DangX, ScotcherJ, WuS, ChuRK, TolićN, NtaiI, ThomasPM, FellersRT, EarlyBP, ZhengY, et al.The first pilot project of the consortium for top-down proteomics: a status report. Proteomics2014; 14(10):1130–40; PMID:24644084; http://dx.doi.org/10.1002/pmic.201300438
37. LemaireP, DeboisD, SmargiassoN, QuintonL, GabelicaV, De PauwEA.Use of 1,5-diaminonaphthalene to combine matrixassisted laser desorption/ionization in-source decay fragmentation with hydrogen/deuterium exchange. Rapid Commun Mass Spectrom2013; 27(16):1837–46; PMID:23857929; http://dx.doi.org/10.1002/rcm.6627
38. AyoubD, FornelliL, SrzenticK, LaskayU, BeckA, TsybinYO, Middle-Down and Extended Bottom-Up Mass Spectrometry for In-Depth and Rapid Characterization of Immunoglobulins and Their Mixtures. 2014, Proc. of the 62nd ASMS Conference on Mass Spectrometry and Allied Topics; June 15–19, 2014, Baltimore, Maryland: MOE-08:50
39. SrzentićK, FornelliL, LaskayLA, MonodM, BeckA, AyoubD, TsybinYO.Advantages of extended bottom-up proteomics using sap9 for analysis of monoclonal antibodies. Anal Chem2014; 86(19):9945–53; PMID:25207962; http://dx.doi.org/10.1021/ac502766n
40. FornelliL, ParraJ, HartmerR, StoermerC, LubeckM, TsybinYO.Top-down analysis of 30-80 kDa proteins by electron transfer dissociation time-of-flight mass spectrometry. Anal Bioanal Chem2013; 405(26):8505–14; PMID:23934349; http://dx.doi.org/10.1007/s00216-013-7267-5
41. MaM, ChenR, GeY, HeH, MarshallAG, LiL.Combining bottomup and top-down mass spectrometric strategies for de novo sequencing of the crustacean hyperglycemic hormone from Cancer borealis. Anal Chem2009; 81(1):240–7; PMID:19046072; http://dx.doi.org/10.1021/ac801910g
42. BeckS, MichalskiA, RaetherO, LubeckM, KasparS, GoedeckeN, BaessmannC, HornburgD, MeierF, ParonI, et al.The impact II, a very high resolution quadrupole time-of-flight instrument for deep shotgun proteomics. Mol Cell Proteomics2015; 14(7):2014–29; PMID:25991688; http://dx.doi.org/10.1074/mcp.M114.047407
43. CourseyJS, SchwabDJ, DragosetRA.Atomic Weights and Isotopic Compositions. http://physics.nist.gov/Comp2003, June 25, 2001, National Institute of Standards and Technology, Gaithersburg, MD, Vols. (version 2.3.1), [Online]