Performance metrics for evaluating system suitability in liquid chromatography—Mass spectrometry peptide mass mapping of protein therapeutics and monoclonal antibodies

References

• Beck A, Wagner-Rousset E, Ayoub D, Van Dorsselaer A, Sanglier-Cianférani S. Characterization of therapeutic antibodies and related products. Anal Chem 2012; 85:715-36; PMID:23134362; http://dx.doi.org/10.1021/ac3032355
   PubMed Web of Science ®Google Scholar
• Zhang Z, Pan H, Chen X. Mass spectrometry for structural characterization of therapeutic antibodies. Mass Spectrom Rev 2009; 28:147-76; PMID:18720354; http://dx.doi.org/10.1002/mas.20190
   PubMed Web of Science ®Google Scholar
• Mann M, Kelleher NL. Precision proteomics: the case for high resolution and high mass accuracy. Proc Natl Acad Sci U S A 2008; 105:18132-8; PMID:18818311; http://dx.doi.org/10.1073/pnas.0800788105
   PubMed Web of Science ®Google Scholar
• Smith LM, Kelleher NL. Proteoform: a single term describing protein complexity. Nat Meth 2013; 10:186-7; http://dx.doi.org/10.1038/nmeth.2369
   PubMed Web of Science ®Google Scholar
• Gucinski AC, Boyne MT. Evaluation of intact mass spectrometry for the quantitative analysis of protein therapeutics. Anal Chem 2012; 84:8045-51; PMID:22916992; http://dx.doi.org/10.1021/ac301949j
   PubMed Web of Science ®Google Scholar
• Wang B, Gucinski AC, Keire DA, Buhse LF, Boyne Ii MT. Structural comparison of two anti-CD20 monoclonal antibody drug products using middle-down mass spectrometry. Analyst 2013; 138:3058-65; PMID:23579346; http://dx.doi.org/10.1039/c3an36524g
   PubMed Web of Science ®Google Scholar
• Ni W, Lin M, Salinas P, Savickas P, Wu S-L, Karger B. Complete mapping of a cystine knot and nested disulfides of recombinant human arylsulfatase a by multi-enzyme digestion and LC-MS analysis using CID and ETD. J Am Soc Mass Spectrom 2013; 24:125-33; PMID:23208745; http://dx.doi.org/10.1007/s13361-012-0510-z
   PubMed Web of Science ®Google Scholar
• Wiśniewski JR, Mann M. Consecutive proteolytic digestion in an enzyme reactor increases depth of proteomic and phosphoproteomic analysis. Anal Chem 2012; 84:2631-7; PMID:22324799; http://dx.doi.org/10.1021/ac300006b
   PubMed Web of Science ®Google Scholar
• Gatlin CL, Eng JK, Cross ST, Detter JC, Yates JR. Automated identification of amino acid sequence variations in proteins by hplc/microspray tandem mass spectrometry. Anal Chem 2000; 72:757-63; PMID:10701260; http://dx.doi.org/10.1021/ac991025n
   PubMed Web of Science ®Google Scholar
• Dick Jr LW, Mahon D, Qiu D, Cheng K-C. Peptide mapping of therapeutic monoclonal antibodies: Improvements for increased speed and fewer artifacts. J Chromatogr B 2009; 877:230-6; http://dx.doi.org/10.1016/j.jchromb.2008.12.009
   PubMed Web of Science ®Google Scholar
• Shah B, Jiang X, Chen L, Zhang Z. LC-MS/MS peptide mapping with automated data processing for routine profiling of N-glycans in immunoglobulins. J Am Soc Mass Spectrom 2014:1-13; PMID:24249043
   PubMed Web of Science ®Google Scholar
• Lowenthal MS, Liang Y, Phinney KW, Stein SE. Quantitative bottom-up proteomics depends on digestion conditions. Anal Chem 2014; 86:551-8; PMID:24294946; http://dx.doi.org/10.1021/ac4027274
   PubMed Web of Science ®Google Scholar
• Bakalarski C, Haas W, Dephoure N, Gygi S. The effects of mass accuracy, data acquisition speed, and search algorithm choice on peptide identification rates in phosphoproteomics. Anal Bioanal Chem 2007; 389:1409-19; PMID:17874083; http://dx.doi.org/10.1007/s00216-007-1563-x
   PubMed Web of Science ®Google Scholar
• Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham A-JL, Keshishian H, et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotech 2009; 27:633-41; http://dx.doi.org/10.1038/nbt.1546
   PubMed Web of Science ®Google Scholar
• Rudnick PA, Clauser KR, Kilpatrick LE, Tchekhovskoi DV, Neta P, Blonder N, Billheimer DD, Blackman RK, Bunk DM, Cardasis HL, et al. Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol Cell Proteomics 2010; 9:225-41; PMID:19837981; http://dx.doi.org/10.1074/mcp.M900223-MCP200
   PubMed Web of Science ®Google Scholar
• Gallien S, Bourmaud A, Domon B. A Simple protocol to routinely assess the uniformity of proteomics analyses. J Proteome Res 2014; 13:2688-95; PMID:24617767; http://dx.doi.org/10.1021/pr4011712
   PubMed Web of Science ®Google Scholar
• Abbatiello SE, Mani DR, Schilling B, MacLean B, Zimmerman LJ, Feng X, Cusack MP, Sedransk N, Hall SC, Addona T, et al. Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS). Mol Cell Proteomics 2013; 12:2623-39; PMID:23689285; http://dx.doi.org/10.1074/mcp.M112.027078
   PubMed Web of Science ®Google Scholar
• Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, uumlttenhain R, Koomen JM, et al. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics 2014; 13(3):907-17.
   PubMed Web of Science ®Google Scholar
• Jenkins R, Duggan J, Aubry A-F, Zeng J, Lee J, Cojocaru L, Dufield D, Garofolo F, Kaur S, Schultz G, et al. Recommendations for validation of LC-MS/MS bioanalytical methods for protein biotherapeutics. AAPS J 2015; 17:1-16; PMID:25392238; http://dx.doi.org/10.1208/s12248-014-9685-5
   PubMed Web of Science ®Google Scholar
• Rochat B, Kottelat E, McMullen J. The future key role of LC–high-resolution-MS analyses in clinical laboratories: a focus on quantification. Bioanalysis 2012; 4:2939-58; PMID:23244284; http://dx.doi.org/10.4155/bio.12.243
   PubMed Web of Science ®Google Scholar
• Kalli A, Hess S. Effect of mass spectrometric parameters on peptide and protein identification rates for shotgun proteomic experiments on an LTQ-orbitrap mass analyzer. Proteomics 2012; 12:21-31; PMID:22065615; http://dx.doi.org/10.1002/pmic.201100464
   PubMed Web of Science ®Google Scholar
• Olsen JV, de Godoy LMF, Li G, Macek B, Mortensen P, Pesch R, Makarov A, Lange O, Horning S, Mann M. Parts per million mass accuracy on an orbitrap mass spectrometer via lock mass injection into a C-trap. Mol Cell Proteomics 2005; 4:2010-21; PMID:16249172; http://dx.doi.org/10.1074/mcp.T500030-MCP200
   PubMed Web of Science ®Google Scholar
• Makarov A, Denisov E, Lange O, Horning S. Dynamic range of mass accuracy in LTQ orbitrap hybrid mass spectrometer. J Am Soc Mass Spectrom 2006; 17:977-82; PMID:16750636; http://dx.doi.org/10.1016/j.jasms.2006.03.006
   PubMed Web of Science ®Google Scholar
• Zeng K, Geerlof-Vidavisky I, Gucinski A, Jiang X, Boyne M, II. Liquid chromatography-high resolution mass spectrometry for peptide drug quality control. AAPS J 2015; 17:643-51; PMID:25716148; http://dx.doi.org/10.1208/s12248-015-9730-z
   PubMed Web of Science ®Google Scholar
• Annesley TM. Ion suppression in mass spectrometry. Clinical Chemistry 2003; 49:1041-4; PMID:12816898; http://dx.doi.org/10.1373/49.7.1041
   PubMed Web of Science ®Google Scholar
• Trufelli H, Palma P, Famiglini G, Cappiello A. An overview of matrix effects in liquid chromatography–mass spectrometry. Mass Spectrom Rev 2011; 30:491-509; PMID:21500246; http://dx.doi.org/10.1002/mas.20298
   PubMed Web of Science ®Google Scholar
• Gallien S, Duriez E, Crone C, Kellmann M, Moehring T, Domon B. Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer. Mol Cell Proteomics 2012; 11:1709-23; PMID:22962056; http://dx.doi.org/10.1074/mcp.O112.019802
   PubMed Web of Science ®Google Scholar
• Wong RL, Xin B, Olah T. Optimization of Exactive Orbitrap™ acquisition parameters for quantitative bioanalysis. Bioanalysis 2011; 3:863-71; PMID:21510760; http://dx.doi.org/10.4155/bio.11.37
   PubMed Web of Science ®Google Scholar
• Guilhaus M, Selby D, Mlynski V. Orthogonal acceleration time-of-flight mass spectrometry. Mass Spectrom Rev 2000; 19:65-107; PMID:10795088; http://dx.doi.org/10.1002/(SICI)1098-2787(2000)19:2%3c65::AID-MAS1%3e3.0.CO;2-E
   PubMed Web of Science ®Google Scholar
• Chernushevich IV, Loboda AV, Thomson BA. An introduction to quadrupole–time-of-flight mass spectrometry. J Mass Spectrom 2001; 36:849-65; PMID:11523084; http://dx.doi.org/10.1002/jms.207
   PubMed Web of Science ®Google Scholar
• Cotter RJ. Time-of-flight mass spectrometry for the structural analysis of biological molecules. Anal Chem 1992; 64:1027A-39A; PMID:1443622; http://dx.doi.org/10.1021/ac00045a726
   PubMed Web of Science ®Google Scholar
• Randall S, Cardasis H, Muddiman D. Factorial experimental designs elucidate significant variables affecting data acquisition on a quadrupole orbitrap mass spectrometer. J Am Soc Mass Spectrom 2013; 24:1501-12; PMID:23913023; http://dx.doi.org/10.1007/s13361-013-0693-y
   PubMed Web of Science ®Google Scholar
• U.S. Department of Health and Human Services, Food and Drug Administration (FDA), Center for Drug Evaluation and Research (CDER), and Center for Biologics Evaluation and Research (CBER). Guidance for industry: Analytical procedures and methods validation for drugs and biologics. Silver Spring, MD: FDA; 2015
   Google Scholar
• U.S. Department of Health and Human Services, Food and Drug Administration, Center for Drug Evaluation and Research (CDER) and Center for Veterinary Medicine (CVM). Guidance for industry: Bioanalytical method validation. Silver Spring, MD: FDA; 2001
   Google Scholar