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Review

Technical advancement and practical considerations of LC-MS/MS-based methods for host cell protein identification and quantitation to support process development

, , , , &
Article: 2213365 | Received 25 Jan 2023, Accepted 09 May 2023, Published online: 22 May 2023

References

  • Jones M, Palackal N, Wang F, Gaza-Bulseco G, Hurkmans K, Zhao Y, Chitikila C, Clavier S, Liu S, Menesale E, et al. “High-risk” host cell proteins (HCPs): a multi-company collaborative view. Biotechnol Bioeng. 2021;118(8):2870–15. doi:10.1002/bit.27808.
  • FDA. Points to consider in the manufacture and testing of monoclonal antibody products for human use. FDA-1994-D-0318 1994.
  • EMA. DNA and host cell protein impurities, routine testing versus validation studies. 1997; CPMP/BWP/382/97.
  • Pharmacopeia US. 2016. Residual host cell protein measurement in biopharmaceuticals. USP. Published General Chapter 1132. 39:1416–36.
  • Pharmacopeia EU. Host-cell protein assays. European pharmacopoeia monograph 2.6.34. 2017;4:20634.
  • Zhu-Shimoni J, Yu C, Nishihara J, Wong RM, Gunawan F, Lin M, Krawitz D, Liu P, Sandoval W, Vanderlaan M. Host cell protein testing by ELISAs and the use of orthogonal methods. Biotechnol Bioeng. 2014;111(12):2367–79. doi:10.1002/bit.25327.
  • Yang F, Li D, Kufer R, Cadang L, Zhang J, Dai L, Guo J, Wohlrab S, Greenwood-Goodwin M, Shen A, et al. Versatile LC–MS-Based workflow with robust 0.1 ppm sensitivity for identifying residual HCPs in biotherapeutic products. Anal Chem. 2022;94(2):723–31. doi:10.1021/acs.analchem.1c03095.
  • Urabe M, Ding C, Kotin RM. Insect cells as a factory to produce adeno-associated virus type 2 vectors. Hum Gene Ther. 2002;13(16):1935–43. doi:10.1089/10430340260355347.
  • Kulagina N, Besseau S, Godon C, Goldman GH, Papon N, Courdavault V. Yeasts as biopharmaceutical production platforms. Front Fungal Biol. 2021;2. doi:10.3389/ffunb.2021.733492.
  • Reisinger V, Toll H, Mayer RE, Visser J, Wolschin F. A mass spectrometry-based approach to host cell protein identification and its application in a comparability exercise. Anal Biochem. 2014;463:1–6. doi:10.1016/j.ab.2014.06.005.
  • Molden R, Hu M, Yen ES, Saggese D, Reilly J, Mattila J, Qiu H, Chen G, Bak H, Li N. Host cell protein profiling of commercial therapeutic protein drugs as a benchmark for monoclonal antibody-based therapeutic protein development. MAbs. 2021;13(1):1955811. doi:10.1080/19420862.2021.1955811.
  • Graf T, Tomlinson A, Yuk IH, Kufer R, Spensberger B, Falkenstein R, Shen A, Li H, Duan D, Liu W, et al. Identification and characterization of polysorbate-degrading enzymes in a monoclonal antibody formulation. J Pharm Sci. 2021;110(11):3558–67. doi:10.1016/j.xphs.2021.06.033.
  • Walker DE, Yang F, Carver J, Joe K, Michels DA, Yu XC. A modular and adaptive mass spectrometry-based platform for support of bioprocess development toward optimal host cell protein clearance. MAbs. 2017;9(4):654–63. doi:10.1080/19420862.2017.1303023.
  • Jin M, Szapiel N, Zhang J, Hickey J, Ghose S. Profiling of host cell proteins by two-dimensional difference gel electrophoresis (2D-DIGE): implications for downstream process development. Biotechnol Bioeng. 2010;105(2):306–16. doi:10.1002/bit.22532.
  • Hogwood CEM, Bracewell DG, Smales CM. Measurement and control of host cell proteins (HCPs) in CHO cell bioprocesses. Curr Opin Biotechnol. 2014;30:153–60. doi:10.1016/j.copbio.2014.06.017.
  • The antibody society, Inc. Antibody therapeutics approved or in regulatory review in the EU or US. [assessed Mar 8, 2023]. www.antibodysociety.org/antibody-therapeutics-product-data.
  • Falkenberg H, Waldera-Lupa DM, Vanderlaan M, Schwab T, Krapfenbauer K, Studts JM, Flad T, Waerner T. Mass spectrometric evaluation of upstream and downstream process influences on host cell protein patterns in biopharmaceutical products. Biotechnol Prog. 2019;35(3):e2788. doi:10.1002/btpr.2788.
  • Bracewell DG, Francis R, Smales CM. The future of host cell protein (HCP) identification during process development and manufacturing linked to a risk-based management for their control. Biotechnol Bioeng. 2015;112(9):1727–37. doi:10.1002/bit.25628.
  • Vanderlaan M, Zhu-Shimoni J, Lin S, Gunawan F, Waerner T, Van Cott KE. Experience with host cell protein impurities in biopharmaceuticals. Biotechnol Prog. 2018;34(4):828–37. doi:10.1002/btpr.2640.
  • Bracewell DG, Smith V, Delahaye M, Smales CM. Analytics of host cell proteins (HCPs): lessons from biopharmaceutical mAb analysis for gene therapy products. Curr Opin Biotechnol. 2021;71:98–104. doi:10.1016/j.copbio.2021.06.026.
  • Krutzke L, Rosler R, Allmendinger E, Engler T, Wiese S, Kochanek S. Process- and product-related impurities in the ChAdOx1 nCov-19 vaccine. Elife. 2022;11:11. doi:10.7554/eLife.78513.
  • Yuk IH, Nishihara J, Walker D Jr., Huang E, Gunawan F, Subramanian J, Pynn AFJ, Yu XC, Zhu-Shimoni J, Vanderlaan M, et al. More similar than different: host cell protein production using three null CHO cell lines. Biotechnol Bioeng. 2015;112(10):2068–83. doi:10.1002/bit.25615.
  • Hamaker NK, Min L, Lee KH. Comprehensive assessment of host cell protein expression after extended culture and bioreactor production of CHO cell lines. Biotechnol Bioeng. 2022;119(8):2221–38. doi:10.1002/bit.28128.
  • Chiu J, Valente KN, Levy NE, Min L, Lenhoff AM, Lee KH. Knockout of a difficult-to-remove CHO host cell protein, lipoprotein lipase, for improved polysorbate stability in monoclonal antibody formulations. Biotechnol Bioeng. 2017;114(5):1006–15. doi:10.1002/bit.26237.
  • Carver J, Kern M, Ko P, Greenwood-Goodwin M, Yu XC, Duan D, Tang D, Misaghi S, Auslaender S, Haley B, et al. A ribonucleoprotein-based decaplex CRISPR/Cas9 knockout strategy for CHO host engineering. Biotechnol Prog. 2022;38(1):e3212. doi:10.1002/btpr.3212.
  • Vanderlaan M, Sandoval W, Liu P, Nishihara J, Tsui G, Lin M, Gunawan F, Parker S, Wong RM, Low J , et al. Hamster phospholipase B-like 2 (PLBL2): A host-cell protein impurity in therapeutic monoclonal antibodies derived from Chinese hamster ovary cells. BioProcess International. 2015;13(4):18–29.
  • Zhang Q, Goetze AM, Cui H, Wylie J, Trimble S, Hewig A, Flynn GC. Comprehensive tracking of host cell proteins during monoclonal antibody purifications using mass spectrometry. MAbs. 2014;6(3):659–70. doi:10.4161/mabs.28120.
  • Gilgunn S, El-Sabbahy H, Albrecht S, Gaikwad M, Corrigan K, Deakin L, Jellum G, Bones J. Identification and tracking of problematic host cell proteins removed by a synthetic, highly functionalized nonwoven media in downstream bioprocessing of monoclonal antibodies. J Chromatogr A. 2019;1595:28–38. doi:10.1016/j.chroma.2019.02.056.
  • Chen Y, Xu CF, Stanley B, Evangelist G, Brinkmann A, Liu S, McCarthy S, Xiong L, Jones E, Sosic Z, et al. A highly sensitive LC-MS/MS method for targeted quantitation of lipase host cell proteins in biotherapeutics. J Pharm Sci. 2021;110(12):3811–18. doi:10.1016/j.xphs.2021.08.024.
  • Pilely K, Johansen MR, Lund RR, Kofoed T, Jorgensen TK, Skriver L, Mørtz E. Monitoring process-related impurities in biologics–host cell protein analysis. Anal Bioanal Chem. 2022;414(2):747–58. doi:10.1007/s00216-021-03648-2.
  • Wohlrab S, Wiedmann M, Aschner M, Reusch D, Bulau P, Haindl M. Tracking host cell proteins while biopharmaceutical manufacturing: advanced methodologies to improve product quality. Am Pharm Rev. 2018;21:36–39.
  • Gunawan F, Nishihara J, Liu P, Sandoval W, Vanderlaan M, Zhang H, Krawitz D. Comparison of platform host cell protein ELISA to process-specific host cell protein ELISA. Biotechnol Bioeng. 2018;115(2):382–89. doi:10.1002/bit.26466.
  • Hu M, Molden R, Hu Y, Huang Y, Qiu H, Li N. Host cell protein identification in monoclonal antibody high molecular weight species. J Chromatogr B Analyt Technol Biomed Life Sci. 2022;1210:123448. doi:10.1016/j.jchromb.2022.123448.
  • Hecht ES, Mehta S, Wecksler AT, Aguilar B, Swanson N, Phung W, Dubey Kelsoe A, Benner WH, Tesar D, Kelley RF, et al. Insights into ultra-low affinity lipase-antibody noncovalent complex binding mechanisms. MAbs. 2022;14(1):2135183. doi:10.1080/19420862.2022.2135183.
  • Seisenberger C, Graf T, Haindl M, Wegele H, Wiedmann M, Wohlrab S. Questioning coverage values determined by 2D western blots: a critical study on the characterization of anti-HCP ELISA reagents. Biotechnol Bioeng. 2021;118(3):1116–26. doi:10.1002/bit.27635.
  • Waldera-Lupa DM, Jasper Y, Kohne P, Schwichtenhovel R, Falkenberg H, Flad T, Happersberger P, Reisinger B, Dehghani A, Moussa R, et al. Host cell protein detection gap risk mitigation: quantitative IAC-MS for ELISA antibody reagent coverage determination. MAbs. 2021;13(1):1955432. doi:10.1080/19420862.2021.1955432.
  • Henry SM, Sutlief E, Salas-Solano O, Valliere-Douglass J. ELISA reagent coverage evaluation by affinity purification tandem mass spectrometry. MAbs. 2017;9(7):1065–75. doi:10.1080/19420862.2017.1349586.
  • Seisenberger C, Graf T, Haindl M, Wegele H, Wiedmann M, Wohlrab S. Toward optimal clearance: a universal affinity-based mass spectrometry approach for comprehensive ELISA reagent coverage evaluation and HCP hitchhiker analysis. Biotechnol Prog. 2022;38(3):e3244. doi:10.1002/btpr.3244.
  • Rumachik NG, Malaker SA, Poweleit N, Maynard LH, Adams CM, Leib RD, Cirolia G, Thomas D, Stamnes S, Holt K, et al. Methods matter: standard production platforms for recombinant AAV produce chemically and functionally distinct vectors. Mol Ther Methods Clin Dev. 2020;18:98–118. doi:10.1016/j.omtm.2020.05.018.
  • Aloor A, Zhang J, Gashash EA, Parameswaran A, Chrzanowski M, Ma C, Diao Y, Wang P, Xiao W. Site-specific N-glycosylation on the AAV8 capsid protein. Viruses. 2018;10(11):644. doi:10.3390/v10110644.
  • Johnson S, Wheeler JX, Thorpe R, Collins M, Takeuchi Y, Zhao Y. Mass spectrometry analysis reveals differences in the host cell protein species found in pseudotyped lentiviral vector. Biologicals. 2018;52:7. doi:10.1016/j.biologicals.2017.12.005.
  • Trauchessec M, Hesse AM, Kraut A, Berard Y, Herment L, Fortin T, Bruley C, Ferro M, Manin C. An innovative standard for LC-MS-based HCP profiling and accurate quantity assessment: application to batch consistency in viral vaccine samples. Proteomics. 2021;21(5):e2000152. doi:10.1002/pmic.202000152.
  • Doneanu CE, Chen W. Analysis of host-cell proteins in biotherapeutic proteins by LC/MS approaches. Methods Mol Biol. 2014;1129:341–50. doi:10.1007/978-1-62703-977-2_25.
  • Levy NE, Valente KN, Choe LH, Lee KH, Lenhoff AM. Identification and characterization of host cell protein product-associated impurities in monoclonal antibody bioprocessing. Biotechnol Bioeng. 2014;111(5):904–12. doi:10.1002/bit.25158.
  • Doneanu CE, Anderson M, Williams BJ, Lauber MA, Chakraborty A, Chen W. Enhanced detection of low-abundance host cell protein impurities in high-purity monoclonal antibodies down to 1 ppm using ion mobility mass spectrometry coupled with multidimensional liquid chromatography. Anal Chem. 2015;87(20):10283–91. doi:10.1021/acs.analchem.5b02103.
  • Aebersold R, Mann M. Mass-spectrometric exploration of proteome structure and function. Nature. 2016;537(7620):347–55. doi:10.1038/nature19949.
  • Bomans K, Lang A, Roedl V, Adolf L, Kyriosoglou K, Diepold K, Eberl G, Mølhøj M, Strauss U, Schmalz C, et al. Identification and monitoring of host cell proteins by mass spectrometry combined with high performance immunochemistry testing. PLos One. 2013;8(11):e81639. doi:10.1371/journal.pone.0081639.
  • Thompson JH, Chung WK, Zhu M, Tie L, Lu Y, Aboulaich N, Strouse R, Mo WD. Improved detection of host cell proteins (HCPs) in a mammalian cell-derived antibody drug using liquid chromatography/mass spectrometry in conjunction with an HCP-enrichment strategy. Rapid Commun Mass Spectrom. 2014;28(8):855–60. doi:10.1002/rcm.6854.
  • Madsen JA, Farutin V, Carbeau T, Wudyka S, Yin Y, Smith S, Anderson J, Capila I. Toward the complete characterization of host cell proteins in biotherapeutics via affinity depletions, LC-MS/MS, and multivariate analysis. MAbs. 2015;7(6):1128–37. doi:10.1080/19420862.2015.1082017.
  • Soderquist RG, Trumbo M, Hart RA, Zhang Q, Flynn GC. Development of advanced host cell protein enrichment and detection strategies to enable process relevant spike challenge studies. Biotechnol Prog. 2015;31(4):983–89. doi:10.1002/btpr.2114.
  • Huang L, Wang N, Mitchell CE, Brownlee T, Maple SR, De Felippis MR. A novel sample preparation for shotgun proteomics characterization of HCPs in antibodies. Anal Chem. 2017;89(10):5436–44. doi:10.1021/acs.analchem.7b00304.
  • Kufer R, Haindl M, Wegele H, Wohlrab S. Evaluation of peptide fractionation and native digestion as two novel sample preparation workflows to improve HCP characterization by LC–MS/MS. Anal Chem. 2019;91(15):9716–23. doi:10.1021/acs.analchem.9b01259.
  • Chen IH, Xiao H, Daly T, Li N. Improved host cell protein analysis in monoclonal antibody products through molecular weight cutoff enrichment. Anal Chem. 2020;92(5):3751–57. doi:10.1021/acs.analchem.9b05081.
  • Zhang S, Xiao H, Li N. Ultrasensitive method for profiling host cell proteins by coupling limited digestion to ProteoMiner technology. Anal Biochem. 2022;657:114901. doi:10.1016/j.ab.2022.114901.
  • Deng Y, Gruppen H, Wierenga PA. Comparison of Protein Hydrolysis Catalyzed By Bovine, Porcine, And Human Trypsins. J Agric Food Chem. 2018;66(16):4219–32. doi:10.1021/acs.jafc.8b00679.
  • Nie S, Greer T, O’Brien Johnson R, Zheng X, Torri A, Li N. Simple and sensitive method for deep profiling of host cell proteins in therapeutic antibodies by combining ultra-low trypsin concentration digestion, long chromatographic gradients, and boxcar mass spectrometry acquisition. Anal Chem. 2021;93(10):4383–90. doi:10.1021/acs.analchem.0c03931.
  • Li D, Farchone A, Zhu Q, Macchi F, Walker DE, Michels DA, Yang F. Fast, robust, and sensitive identification of residual host cell proteins in recombinant monoclonal antibodies using sodium deoxycholate assisted digestion. Anal Chem. 2020;92(17):11888–94. doi:10.1021/acs.analchem.0c02258.
  • Wang Q, Slaney TR, Wu W, Ludwig R, Tao L, Leone A. Enhancing host-cell protein detection in protein therapeutics using HILIC enrichment and proteomic analysis. Anal Chem. 2020;92(15):10327–35. doi:10.1021/acs.analchem.0c00360.
  • Zhao B, Abdubek P, Zhang S, Xiao H, Li N. Analysis of host cell proteins in monoclonal antibody therapeutics through size exclusion chromatography. Pharm Res. 2022;39(11):3029–37. doi:10.1007/s11095-022-03381-0.
  • Mörtstedt H, Makower Å, Edlund P-O, Sjöberg K, Tjernberg A. Improved identification of host cell proteins in a protein biopharmaceutical by LC–MS/MS using the ProteoMiner™ Enrichment Kit. J Pharm Biomed Anal. 2020;185:113256. doi:10.1016/j.jpba.2020.113256.
  • Chen IH, Xiao H, Li N. Improved host cell protein analysis in monoclonal antibody products through ProteoMiner. Anal Biochem. 2020;2020:113972. doi:10.1016/j.ab.2020.113972.
  • Yang F, Walker DE, Schoenfelder J, Carver J, Zhang A, Li D, Harris R, Stults JT, Yu XC, Michels DA. A 2D LC-MS/MS strategy for reliable detection of 10-ppm level residual host cell proteins in therapeutic antibodies. Anal Chem. 2018;90(22):13365–72. doi:10.1021/acs.analchem.8b03044.
  • Johnson ROB, Greer T, Cejkov M, Zheng X, Li N. Combination of FAIMS, protein a depletion, and native digest conditions enables deep proteomic profiling of host cell proteins in monoclonal antibodies. Anal Chem. 2020;92(15):10478–84. doi:10.1021/acs.analchem.0c01175.
  • Ma J, Sensitive KG. Rapid, rOBUST, AND REPRODUCIBLE WORKFLOW FOR HOST CELL PROTEIN PROFILING IN BIOPHARMACEUTICAL PROCESS DEVELOpment. J Proteome Res. 2020;19(8):3396–404. doi:10.1021/acs.jproteome.0c00252.
  • Farrell A, Mittermayr S, Morrissey B, Mc Loughlin N, Navas Iglesias N, Marison IW, Bones J. Quantitative host cell protein analysis using two dimensional data independent LC–MSE. Anal Chem. 2015;87(18):9186–93. doi:10.1021/acs.analchem.5b01377.
  • Jawa V, Joubert MK, Zhang Q, Deshpande M, Hapuarachchi S, Hall MP, Flynn GC. Evaluating immunogenicity risk due to host cell protein impurities in antibody-based biotherapeutics. Aaps J. 2016;18(6):1439–52. doi:10.1208/s12248-016-9948-4.
  • Hansen FM, Tanzer MC, Brüning F, Bludau I, Stafford C, Schulman BA, Robles MS, Karayel O, Mann M. Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology. Nat Commun. 2021;12(1):254. doi:10.1038/s41467-020-20509-1.
  • Bache N, Geyer PE, Bekker-Jensen DB, Hoerning O, Falkenby L, Treit PV, Doll S, Paron I, Müller JB, Meier F, et al. A novel LC system embeds analytes in pre-formed gradients for rapid, ultra-robust proteomics. Molecular & Cellular Proteomics: MCP. 2018;17(11):2284–96. doi:10.1074/mcp.TIR118.000853.
  • Bian Y, Zheng R, Bayer FP, Wong C, Chang Y-C, Meng C, Zolg DP, Reinecke M, Zecha J, Wiechmann S, et al. Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC–MS/MS. Nat Commun. 2020;11(1):157. doi:10.1038/s41467-019-13973-x.
  • Christianson CC, Johnson CJ, Needham SR. The advantages of microflow LC–MS/MS compared with conventional HPLC–MS/MS for the analysis of methotrexate from human plasma. Bioanalysis. 2013;5(11):1387–96. doi:10.4155/bio.13.73.
  • Satkunanathan S, Wheeler J, Thorpe R, Zhao Y. Establishment of a novel cell line for the enhanced production of recombinant adeno-associated virus vectors for gene therapy. Hum Gene Ther. 2014;25(11):929–41. doi:10.1089/hum.2014.041.
  • Strobel B, Miller FD, Rist W, Lamla T. Comparative analysis of cesium chloride- and iodixanol-based purification of recombinant adeno-associated viral vectors for preclinical applications. Hum Gene Ther Methods. 2015;26(4):147–57. doi:10.1089/hgtb.2015.051.
  • Vialaret J, Picas A, Delaby C, Bros P, Lehmann S, Hirtz C. Nano-flow vs standard-flow: which is the more suitable LC/MS method for quantifying hepcidin-25 in human serum in routine clinical settings? J Chromatogr B. 2018;1086:110–17. doi:10.1016/j.jchromb.2018.04.003.
  • Zhang M, An B, Qu Y, Shen S, Fu W, Chen YJ, Wang X, Young R, Canty JM, Balthasar JP, et al. Sensitive, high-throughput, and robust trapping-micro-LC-MS strategy for the quantification of biomarkers and antibody biotherapeutics. Anal Chem. 2018;90(3):1870–80. doi:10.1021/acs.analchem.7b03949.
  • Qu M, An B, Shen S, Zhang M, Shen X, Duan X, Balthasar JP, Qu J. Qualitative and quantitative characterization of protein biotherapeutics with liquid chromatography mass spectrometry. Mass Spectrom Rev. 2017;36(6):734–54. doi:10.1002/mas.21500.
  • FDA. ICH Q2B validation of analytical procedures: methodology. FDA-1996-D-0169 1997.
  • Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R. 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: MCP. 2012;11(6):11. doi:10.1074/mcp.O111.016717.
  • Ludwig C, Gillet L, Rosenberger G, Amon S, Collins BC, Aebersold R. Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial. Mol Syst Biol. 2018;14(8):e8126. doi:10.15252/msb.20178126.
  • Zhang F, Ge W, Ruan G, Cai X, Guo T. Data-independent acquisition mass spectrometry-based proteomics and software tools: a glimpse in 2020. Proteomics. 2020;20(17–18):1900276. doi:10.1002/pmic.201900276.
  • Silva JC, Gorenstein MV, Li G-Z, Vissers JPC, Geromanos SJ. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Molecular & Cellular Proteomics: MCP. 2006;5(1):144. doi:10.1074/mcp.M500230-MCP200.
  • Kreimer S, Gao Y, Ray S, Jin M, Tan Z, Mussa NA, Tao L, Li Z, Ivanov AR, Karger BL. Host cell protein profiling by targeted and untargeted analysis of data independent acquisition mass spectrometry data with parallel reaction monitoring verification. Anal Chem. 2017;89(10):5294–302. doi:10.1021/acs.analchem.6b04892.
  • Heissel S, Bunkenborg J, Kristiansen MP, Holmbjerg AF, Grimstrup M, Mørtz E, Kofoed T, Højrup P. Evaluation of spectral libraries and sample preparation for DIA-LC-MS analysis of host cell proteins: a case study of a bacterially expressed recombinant biopharmaceutical protein. Protein Expr Purif. 2018;147:69–77. doi:10.1016/j.pep.2018.03.002.
  • Husson G, Delangle A, O’Hara J, Cianferani S, Gervais A, Van Dorsselaer A, Bracewell D, Carapito C. Dual data-independent acquisition approach combining global HCP Profiling and absolute quantification of key impurities during bioprocess development. Anal Chem. 2018;90(2):1241–47. doi:10.1021/acs.analchem.7b03965.
  • Pythoud N, Bons J, Mijola G, Beck A, Cianférani S, Carapito C. Optimized sample preparation and data processing of data-independent acquisition methods for the robust quantification of trace-level host cell protein impurities in antibody drug products. J Proteomics Res. 2021;20(1):923–31. doi:10.1021/acs.jproteome.0c00664.
  • Picotti P, Aebersold R. Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions. Nat Methods. 2012;9(6):555–66. doi:10.1038/nmeth.2015.
  • Peterson AC, Russell JD, Bailey DJ, Westphall MS, Coon JJ. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol Cell Proteom. 2012;11(11):1475–88. doi:https://doi.org/10.1074/mcp.O112.020131.
  • Vidova V, Spacil Z. A review on mass spectrometry-based quantitative proteomics: targeted and data independent acquisition. Anal Chim Acta. 2017;964:7–23. doi:10.1016/j.aca.2017.01.059.
  • Gallien S, Duriez E, Crone C, Kellmann M, Moehring T, Domon B. Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer. Molecular & Cellular Proteomics: MCP. 2012;11(12):1709–23. doi:10.1074/mcp.O112.019802.
  • Rauniyar N. Parallel reaction monitoring: a targeted experiment performed using high resolution and high mass accuracy mass spectrometry. Int J Mol Sci. 2015;16(12):28566–81. doi:10.3390/ijms161226120.
  • Ronsein GE, Pamir N, von Haller PD, Kim DS, Oda MN, Jarvik GP, Vaisar T, Heinecke JW. Parallel reaction monitoring (PRM) and selected reaction monitoring (SRM) exhibit comparable linearity, dynamic range and precision for targeted quantitative HDL proteomics. J Proteomics. 2015;113:388–99. doi:10.1016/j.jprot.2014.10.017.
  • Schiffmann C, Hansen R, Baumann S, Kublik A, Nielsen PH, Adrian L, von Bergen M, Jehmlich N, Seifert J. Comparison of targeted peptide quantification assays for reductive dehalogenases by selective reaction monitoring (SRM) and precursor reaction monitoring (PRM). Anal Bioanal Chem. 2014;406(1):283–91. doi:10.1007/s00216-013-7451-7.
  • Gao X, Rawal B, Wang Y, Li X, Wylie D, Liu Y-H, Breunig L, Driscoll D, Wang F, Richardson DD. Targeted host cell protein quantification by LC–MRM enables biologics processing and product characterization. Anal Chem. 2020;92(1):1007–15. doi:10.1021/acs.analchem.9b03952.
  • Nesvizhskii AI, Vitek O, Aebersold R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods. 2007;4(10):787–97. doi:10.1038/nmeth1088.
  • Valente KN, Lenhoff AM, Lee KH. Expression of difficult-to-remove host cell protein impurities during extended Chinese hamster ovary cell culture and their impact on continuous bioprocessing. Biotechnol Bioeng. 2015;112(6):1232–42. doi:https://doi.org/10.1002/bit.25515.
  • Sim KH, Liu L-Y, Tan HT, Tan K, Ng D, Zhang W, Yang Y, Tate S, Bi X. A comprehensive CHO SWATH-MS spectral library for robust quantitative profiling of 10,000 proteins. Sci Data. 2020;7(1):263. doi:10.1038/s41597-020-00594-z.
  • Joucla G, Le Senechal C, Begorre M, Garbay B, Santarelli X, Cabanne C. Cation exchange versus multimodal cation exchange resins for antibody capture from CHO supernatants: identification of contaminating host cell proteins by mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2013;942-943:126–33. doi:10.1016/j.jchromb.2013.10.033.
  • Liu X, Chen Y, Zhao Y, Liu-Compton V, Chen W, Payne G, Lazar AC. Identification and characterization of co-purifying CHO host cell proteins in monoclonal antibody purification process. J Pharm Biomed Anal. 2019;174:500–08. doi:10.1016/j.jpba.2019.06.021.
  • Müller B, Heinrich C, Jabs W, Kaspar-Schönefeld S, Schmidt A, Rodrigues de Carvalho N, Albaum SP, Baessmann C, Noll T, Hoffrogge R. Label-free protein quantification of sodium butyrate treated CHO cells by ESI-UHR-TOF-MS. J Biotechnol. 2017;257:87–98. doi:10.1016/j.jbiotec.2017.03.032.
  • Zhang S, Xiao H, Molden R, Qiu H, Li N. Rapid polysorbate 80 degradation by liver carboxylesterase in a monoclonal antibody formulated drug substance at early stage development. J Pharm Sci. 2020;109(11):3300–07. doi:10.1016/j.xphs.2020.07.018.
  • Chiverton LM, Evans C, Pandhal J, Landels AR, Rees BJ, Levison PR, Wright PC, Smales CM. Quantitative definition and monitoring of the host cell protein proteome using iTRAQ – a study of an industrial mAb producing CHO-S cell line. Biotechnol J. 2016;11(8):1014–24. doi:10.1002/biot.201500550.
  • Elias JE, Gygi SP. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods. 2007;4(3):207–14. doi:10.1038/nmeth1019.
  • He K, Fu Y, Zeng W-F, Luo L, Chi H, Liu C, Qing L-Y, Sun R-X, He S-M. A theoretical foundation of the target-decoy search strategy for false discovery rate control in proteomics. arXiv. 2015. doi:10.48550/arXiv.1501.00537.
  • Midha MK, Kusebauch U, Shteynberg D, Kapil C, Bader SL, Reddy PJ, Campbell DS, Baliga NS, Moritz RL. A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS. Sci Data. 2020;7(1):389. doi:10.1038/s41597-020-00724-7.
  • Blattmann P, Stutz V, Lizzo G, Richard J, Gut P, Aebersold R. Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins. Sci Data. 2019;6(1):190011. doi:10.1038/sdata.2019.11.
  • Rosenberger G, Bludau I, Schmitt U, Heusel M, Hunter CL, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, et al. Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nat Methods. 2017;14(9):921–27. doi:10.1038/nmeth.4398.
  • Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou C-C, Reiter L, Distler U, et al. A multicenter study benchmarks software tools for label-free proteome quantification. Nat Biotechnol. 2016;34:1130–36. doi:10.1038/nbt.3685.
  • MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, Kern R, Tabb DL, Liebler DC, McCoss MJ. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics. 2010;26:966–68. doi:10.1093/bioinformatics/btq054.
  • Bruderer R, Bernhardt OM, Gandhi T, Miladinović SM, Cheng LY, Messner S, Ehrenberger T, Zanotelli V, Butscheid Y, Escher C, et al. Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues. Molecular & Cellular Proteomics: MCP. 2015;14:1400–10. doi:10.1074/mcp.M114.044305.
  • Colangelo C, Chung L, Bruce C, Cheung K. Review of software tools for design and analysis of large scale MRM proteomic datasets. Methods (San Diego, Calif). 2013:61. doi:10.1016/j.ymeth.2013.05.004.
  • Briscoe CJ, Stiles MR, Hage DS. System suitability in bioanalytical LC/MS/MS. J Pharm Biomed Anal. 2007;44:484–91. doi:10.1016/j.jpba.2007.03.003.
  • FDA. Guidance for industry: analytical procedures and methods validation for drugs and biologics. 2015: FDA-2015-N-0007.
  • Thompson M, Wood R. Harmonized guidelines for internal quality control in analytical chemistry laboratories (Technical Report). Pure Appl Chem. 1995;67:649–66. doi:10.1351/pac199567040649.
  • Trauchessec M, Hesse AM, Kraut A, Berard Y, Herment L, Fortin T, Bruley C, Ferro M, Manin C. An innovative standard for LC-MS-based HCP profiling and accurate quantity assessment: application to batch consistency in viral vaccine samples. PROTEOMICS. 2021;21:2000152. doi:10.1002/pmic.202000152.
  • Bereman MS, Beri J, Sharma V, Nathe C, Eckels J, MacLean B, McCoss MJ. An automated pipeline to monitor system performance in liquid chromatography–tandem mass spectrometry proteomic experiments. J Proteome Res. 2016;15:4763–69. doi:10.1021/acs.jproteome.6b00744.
  • Li X, Chandra D, Letarte S, Adam GC, Welch J, Yang RS, Rivera S, Bodea S, Dow A, Chi A, et al. Profiling active enzymes for polysorbate degradation in biotherapeutics by activity-based protein profiling. Anal Chem. 2021;93:8161–69. doi:10.1021/acs.analchem.1c00042.
  • Ren D. Advancing mass spectrometry technology in cGMP environments. Trends Biotechnol. 2020;38:1051–53. doi:10.1016/j.tibtech.2020.06.007.