Recent advances in absolute quantification of peptides and proteins using LC-MS

Reviews in Analytical Chemistry

Volumn 33, Issue 1, 2014, Pages 31-47

  Zhang, Stanley Weihua ^a   Jian, Wenying ^b  

^a Ortho McNeil Pharmaceutical Incorporated   (United States)

^b JANSSEN RESEARCH AND DEVELOPMENT   (Belgium)

Author keywords

Absolute quantification; Bioanalysis; LC HRMS; LC MS MS; Protein quantification

Indexed keywords

EID: 84896789160     PISSN: 07930135     EISSN: None     Source Type: Journal    
DOI: 10.1515/revac-2013-0019     Document Type: Article

References (80)

1. Anderson, L. N.; Anderson, N. G. The human plasma proteome. Mol. Cell. Proteomics 2002, 1, 845-847.
2. Anderson, L. N.; Anderson, N. G.; Haines, L. R.; Hardie, D. B.; Olafson, R. W.; Pearson, T. W. Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J. Proteome. Res. 2004, 3, 235-244. (Pubitemid 38500990)
3. Anderson, L.; Hunter, C. L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics 2006, 5, 573-588.
4. Apffel, A.; Fischer, S.; Goldberg, G.; Goodley, P. C.; Kuhlmann, F. E. Enhanced sensitivity for peptide mapping with electrospray liquid chromatography-mass spectrometry in the presence of signal suppression due to trifluoroacetic acid-containing mobile phases. J. Chromatogr. A. 1995, 712, 177-190.
5. Barnidge, D. R.; Hall, G. D.; Stocker, J. L.; Muddiman, D. C. Evaluation of a cleavable stable isotope labeled synthetic peptide for absolute protein quantification using LC-MS/MS. J. Proteome Res. 2004, 3, 658-661. (Pubitemid 39207373)
6. Berna, M.; Ackermann, B. Increased throughput for low-abundance protein biomarker verification by liquid chromatography/ tandem mass spectrometry. Anal. Chem. 2009, 81, 3950-3956.
7. Berna, M. J.; Zhen, Y.; Watson, D. E.; Hale, J. E.; Ackermann, B. L. Strategic use of immunoprecipitation and LC/MS/MS for trace-level protein quantification: Myosin light chain 1, a biomarker of cardiac necrosis. Anal. Chem. 2007, 79, 4199-4205. (Pubitemid 46903173)
8. Beynon, R. J.; Doherty, M. K.; Pratt, J. M.; Gaskell, S. J. Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat. Method. 2005, 2, 587-589. (Pubitemid 41086849)
9. Bidlingmaier, M. Problems with GH assays and strategies toward standardization. Eur. J. Endocrinol. 2008, 159, S41-S44.
10. Bronsema, K. J.; Bischoff, R.; van de Merbel, N. C. Internal standards in the quantitative determination of protein biopharmaceuticals using liquid chromatography coupled to mass spectrometry. J. Chromatogr. B. 2012, 893-894, 1-14.
11. Brun, V.; Dupuis, A.; Adrait, A.; Marcellin, M.; Thomas, D.; Court, M.; Vandenesch, F.; Garin, J. Isotope-labeled protein standards. Mol. Cell. Proteomics 2007, 12, 2139-2149.
12. Cao, J.; Covarrubias, V. M.; Straubinger, R. M.; Wang, H.; Duan, X.; Yu, H.; Qu, J.; Blanco, J. G. A rapid, reproducible, on-the-fly orthogonal array optimization method for targeted protein quantification by LC/MS and its application for accurate and sensitive quantification of carbonyl reductases in human liver. Anal. Chem. 2010, 82, 2680-2689.
13. Chelius, D.; Xiao, G.; Nichols, A. C.; Vizel, A.; He, B.; Dillon, T. M.; Rehder, D. S.; Pipes, G. D.; Kraft, E.; Oroska, A.; Treuheit, M. J.; Bondarenko, P. V. Automated tryptic digestion procedure for HPLC/MS/MS peptide mapping of immunoglobulin gamma antibodies in pharmaceutics. J. Pharm. Biomed. Anal. 2008, 47, 285-294.
14. Ciccimaro, E.; Blair, I. A. Stable-isotope dilution LC-MS for quantitative biomarker analysis. Bioanalysis 2010, 2, 311-341.
15. Coon, J. J. Collisions or electrons? Protein sequence analysis in the 21st century. Anal. Chem. 2009, 81, 3208-3215.
16. Coon, J. J.; Ueberheide, B.; Syka, J. E.; Dryhurst, D. D.; Ausio, J., Shabanowitz, J.; Hunt, D. F. Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proc. Natl. Acad. Sci. USA 2005, 102, 9463-9468. (Pubitemid 40981704)
17. Dillen, L.; Cools, W.; Vereyken, L.; Lorreyne, W.; Huybrechts, T.; de Vries, R.; Ghobarah, H.; Cuyckens, F. Comparison of triple quadrupole and high-resolution TOF-MS for quantification of peptides. Bioanalysis 2012, 4, 565-579.
18. Dufield, D. R.; Radabaugh, M. R. Online immunoaffinity LC/MS/ MS. A general method to increase sensitivity and specificity: How do you do it and what do you need? Methods 2012, 56, 236-245.
19. Echan, L. A.; Tang, H.-Y.; Ali-Khan, N.; Lee, K.; Speicher, D. W. Depletion of multiple high abundance proteins improves protein profiling capability of human serum and plasma. Proteomics 2005, 5, 3292-3303. (Pubitemid 41192036)
20. Fouda, H.; Nocerini, M.; Schneider, R.; Gedutis, C. Quantitative analysis by high-performance liquid chromatagraph atmospheric pressure chemical ionization mass spectrometry: the determination of the renin inhibitor CP-80,794 in human serum. J. Am. Soc. Mass. Spectrom. 1991, 2, 164-167.
21. Furlong, M. T.; Ouyang, Z.; Wu, S.; Tamura, J.; Olah, T.; Tymiak, A.; Jemal, M. A universal surrogate peptide to enable LC-MS/MS bioanalysis of a diversity of human monoclonal antibody and human Fc-fusion protein drug candidates in pre-clinical animal studies. Biomed. Chromatogr. 2012, 26, 1024-1032.
22. Gerber, S. A.; Rush, J.; Stemman, O.; Kirschner, M. W.; Gygi, S. P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. USA. 2003, 100, 6940-6945. (Pubitemid 36706372)
23. Gilar, M.; Olivova, P.; Daly, A. E.; Gebler, J. C. Orthogonality of separation in two-dimensional liquid chromatography. Anal. Chem. 2005, 77, 6426-6434. (Pubitemid 41436983)
24. Goebel-Stengel, M.; Stengel, A.; Taché, Y.; Reeve, J. R. Jr. The importance of using the optimal plastic and glassware in studies involving peptides. Anal. Biochem. 2011, 414, 38-46.
25. Gordon, E. F.; Muddiman, D. C. Quantification of singly charged biomolecules by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry utilizing an internal standard. Rapid Commun. Mass Spectrom. 1999, 13, 164-171. (Pubitemid 29073219)
26. Gordon, E. F.; Mansoori, B. A.; Carroll, C. F.; Muddiman, D. C. Hydropathic influences on the quantification of equine heart cytochrome c using relative ion abundance measurements by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. J. Mass Spectrom. 1999, 34, 1055-1062. (Pubitemid 29473720)
27. Graumann, J.; Hubner, N. C.; Kim, J. B.; Ko, K.; Moser, M.; Kumar, C.; Cox, J.; Schöler, H.; Mann, M. Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins. Mol. Cell. Proteomics 2008, 7, 672-683. (Pubitemid 351597479)
28. Gucinski, A. C.; Boyne, M. T., II. Evaluation of intact mass spectrometry for the quantitative analysis of protein therapeutics. Anal. Chem. 2012, 84, 8045-8051.
29. Herbert, B.; Galvani, M.; Hamdan, M.; Olivieri, E.; MacCarthy, J.; Pedersen, S.; Righetti, P. G. Reduction and alkylation of proteins in preparation of two-dimensional map analysis: Why, when, and how? Electrophoresis 2001, 22, 2046-2057. (Pubitemid 32621934)
30. Heudi, O.; Barteau, S.; Zimmer, D.; Schmidt, J.; Bill, K.; Lehmann, N.; Bauer, C.; Kretz, O. Towards absolute quantification of therapeutic monoclonal antibody in serum by LC-MS/MS using isotope-labeled antibody standard and protein cleavage isotope dilution mass spectrometry. Anal. Chem. 2008, 80, 4200-4207. (Pubitemid 351812775)
31. Horn, D. M.; Ge, Y.; McLafferty, F. W. Activated ion electron capture dissociation for mass spectral sequencing of larger (42 kDa) proteins. Anal. Chem. 2000, 72, 4778-4784.
32. Huq, M. D. M.; Wei, L.-N. Protein posttranslational modification: A potential target in pharmaceutical development. In Handbook of Pharmaceutical Biotechnology. Gad, S. C. Ed. John Wiley & Sons, Inc.: Hoboken, NJ, 2006; pp. 417-442.
33. Hüttenhain, R.; Surinova, S.; Ossola, R.; Sun, Z.; Campbell, D.; Cerciello, F.; Schiess, R.; Bausch-Fluck, D.; Rosenberger, G.; Chen, J., Rinner, O.; Kusebauch, U.; Hajdúch, M., Moritz, R. L.; Wollscheid, B.; Aebersold, R. N-glycoprotein SRMAtlas: A resource of mass spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications. Mol. Cell. Proteomics 2013, 12, 1005-1016.
34. Hyenstrand, P.; Metcalf, J. S.; Beattie, K. A.; Codd, G. A. Losses of the cyanobacterial toxin microcystin-LR from aqueous solution by adsorption during laboratory manipulations. Toxicon 2001, 39, 589-594.
35. Ji, Q. C.; Gage, E. M.; Rodila, R.; Chang, M. S.; El-Shourbagy, T. A. Method development for the concentration determination of a protein in human plasma utilizing 96-well solid-phase extraction and liquid chromatography/tandem mass spectrometric detection. Rapid Commun. Mass Spectrom. 2003a, 17, 794-799. (Pubitemid 36433163)
36. Ji, Q. C.; Rodila, R.; Gage, E. M.; El-Shourbagy, T. A. A strategy of plasma protein quantitation by selective reaction monitoring of an intact protein. Anal. Chem. 2003b, 75, 7008-7014. (Pubitemid 37523603)
37. Ji, Q. C.; Rodila R.; El-Shourbagy, T. A. A sample preparation process for LC-MS/MS analysis of total protein drug concentrations in monkey plasma samples with antibody. J. Chromatogr. B. 2007, 847, 133-141. (Pubitemid 46331015)
38. Jian, W.; Edom, R.; Wang, D.; Weng, N., Zhang, W. Relative quantitation of glyco-isoforms of intact apolipoprotein C3 in human plasma by liquid chromatography high-resolution mass spectrometry. Anal. Chem. 2013, 85, 2867-2874.
39. Kamiie, J.; Ohtsuki, S.; Iwase, R.; Ohmine, K.; Katsukura, Y.; Yanai, K.; Sekine, Y.; Uchida, Y.; Ito, S.; Terasaki, T. Quantitative atlas of membrane transporter proteins: Development and application of a highly sensitive simultaneous LC/MS/MS method combined with novel in-silico peptide selection criteria. Pharm. Res. 2008, 25, 1469-1483.
40. Keshishian, H.; Addona, T.; Burgess, M.; Kuhn, E.; Carr, S. A. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics 2007, 6, 2212-2229.
41. Kirsch, S.; Widart, J.; Louette, J.; Focant, J.-F.; De Pauw, E. Development of an absolute quantification method targeting growth hormone biomarkers using liquid chromatography coupled to isotope dilution mass spectrometry. J. Chromatogr. A. 2007, 1153, 300-306. (Pubitemid 46755195)
42. Kuzyk, M. A.; Smith, D.; Yang, J.; Cross, T. J.; Jackson, A. M.; Hardie, D. B.; Anderson, L. N.; Borchers, C. H. Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma. Mol. Cell. Proteomics 2009, 8, 1860-1877.
43. Li, F.; Schmerberg, C. M.; Ji, Q. C. Accelerated tryptic digestion of proteins in plasma for absolute quantitation using a protein internal standard by liquid chromatography/tandem mass spectrometry. Rapid Commun. Mass Spectrom. 2009, 23, 729-732.
44. Li, F.; Fast, D.; Michael, S. Absolute quantitation of protein therapeutics in biological matrices by enzymatic digestion and LC-MS. Bioanalysis 2011, 3, 2459-2480.
45. Li, H.; Rose, M. J.; Holder, J. R.; Wright, M.; Miranda, L. P.; James, C. A. Direct quantitative analysis of a 20 kDa PEGylated human calcitonin gene peptide antagonist in cynomolgus monkey serum using in-source CID and UPLC-MS/MS. J. Am. Soc. Mass Spectrom. 2011, 22, 1660-1667.
46. Li, H.; Ortiz, R.; Tran. L.; Hall, M.; Spahr, C.; Walker, K.; Laudemann, J.; Miller, S.; Salimi-Moosavi, H.; Lee, J. W. General LC-MS/ MS method approach to quantify therapeutic monoclonal antibodies using a common whole antibody internal standard with application to preclinical studies. Anal. Chem. 2012, 84, 1267-1273.
47. Liu, A.; Tweed, J.; Wujcik, C. E. Investigation of an on-line two-dimensional chromatographic approach for peptide analysis in plasma by LC-MS-MS. J. Chromatogr. B 2009, 877, 1873-1881.
48. Liu, H.; Manuilov, A. V.; Chumsae, C.; Babineau, M. L.; Tarcsa, E. Quantitation of a recombinant monoclonal antibody in monkey serum by liquid chromatography-mass spectrometry. Anal. Biochem. 2011, 414, 147-153.
49. Liu, G.; Ji, Q. C.; Dodge, R.; Sun, H.; Shuster, D.; Zhao, Q.; Arnold, M. Liquid chromatography coupled with tandem mass spectrometry for the bioanalysis of proteins in drug development: Practical considerations in assay development and validation. J. Chromatogr. A. 2013, 1284, 155-162.
50. Liu, X.; Jin, Z.; O'Brien, R.; Bathon, J.; Dietz, H. C.; Grote, E.; Van Eyk, J. E. Constrained selected reaction monitoring: quantification of selected post-translational modifications and protein isoforms. Methods. 2013, 61, 304-312.
51. Lu, Q.; Zheng, X.; McIntosh, T.; Davis, H.; Nemeth, J. F.; Pendley, C.; Wu, S.-L.; Hancock, W. S. Development of different analysis platforms with LC-MS for pharmacokinetic studies of protein drugs. Anal. Chem 2009, 81, 8715-8723.
52. Mayr, B. M.; Kohlbacher, O.; Reinert, K.; Sturm, M.; Gröpl, C.; Lange, E.; Klein, C.; Huber, C. G. Absolute myoglobin quantitation in serum by combining two dimensional liquid chromatographyelectrospray ionization mass spectrometry and novel data analysis algorithms. J. Proteome Res. 2006, 5, 414-421. (Pubitemid 43222310)
53. Neubert, H.; Grace, C.; Rumpel, K.; James, I. Assessing immunogenicity in the presence of excess protein therapeutic using immunoprecipitation and quantitative mass spectrometry. Anal. Chem. 2008, 80, 6907-6914.
54. Olivieri, E.; Herbert, B.; Righetti, P. G. The effect of protease inhibitors on the two-dimensional electrophoresis pattern of red blood cell membranes. Electrophoresis. 2001, 22, 560-565. (Pubitemid 32166581)
55. Ong, S.-E.; Blagoev, B.; Kratchmarova, I.; Kristensen, D. B.; Steen, H.; Pandey, A.; Mann, M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1, 376-386.
56. Onisko, B.; Dynin, I.; Requena, J. R.; Silva, C. J.; Erickson, M.; Carter, J. M. Mass spectrometric detection of attomole amounts of the prion protein by nanoLC/MS/MS. J. Am. Soc. Mass Spectrom. 2007, 18, 1070-1079. (Pubitemid 46755582)
57. Ouyang, Z.; Furlong, M. T.; Wu, S.; Sleczka, B.; Tamura, J.; Wang, H.; Suchard, S.; Suri, A.; Olah, T.; Tymiak, A.; Jemal, M. Pellet digestion: a simple and efficient sample preparation technique for LC-MS/MS quantification of large therapeutic proteins in plasma. Bioanalysis 2012, 4, 17-28.
58. Padley, H. R.; Bashir, S.; Wood, T. D. Quantification of biomolecules by external electrospray ionization Fourier transform mass spectrometry. Anal. Chem. 1997, 69, 2914-2918.
59. Pailleux, F.; Beaudry, F. Internal standard strategies for relative and absolute quantitation of peptides in biological matrices by liquid chromatography tandem mass spectrometry. Biomed. Chromatogr. 2012, 26, 881-891.
60. Picotti, P.; Lam, H.; Campbell, D.; Deutsch, E.; Mirzaei, H.; Ranish, J.; Domon, B.; Aebersold, R. A database of validated assays for the targeted mass spectrometric analysis of the S. cerevisiae proteome. Nat. Methods 2008, 5, 913-914.
61. Picotti, P.; Clément-Ziza, M.; Lam, H.; Campbell, D. S.; Schmidt, A.; Deutsch, E. W.; Röst, H.; Sun, Z.; Rinner, O.; Reiter, L.; Shen, Q.; Michaelson, J. J.; Frei, A.; Alberti, S.; Kusebauch, U.; Wollscheid, B.; Moritz, R. L.; Beyer, A.; Aebersold, R. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature 2013, 494, 266-270.
62. Plumb, R. S.; Fujimoto, G.; Mather, J.; Potts, W. B.; Rainville, P. D.; Ellor, N. J.; Evans, C.; Kehler, J. R.; Szapacs, M. E. Comparison of the quantification of a therapeutic protein using nominal and accurate mass MS/MS. Bioanalysis. 2012, 4, 605-615.
63. Polaskova, V.; Kapur, A.; Khan, A.; Molloy, M. P.; Baker, M. S. High-abundance protein depletion: comparison of methods for human plasma biomarker discovery. Electrophoresis 2010, 31, 471-482.
64. Pritchard, C.; Quaglia, M.; Ashcroft, A. E.; O'Connor, G. Considering the advantages and pitfalls of the use of isotopically labeled protein standards for accurate protein quantification. Bioanalysis 2011, 3, 2797-2802.
65. Rai, A. J.; Gelfand, C. A.; Haywood, B. C.; Warunek, D. J.; Yi, J.; Schuchard, M. D.; Mehigh, R. J.; Cockrill, S. L.; Scott, G. B.; Tammen, H.; Schulz-Knappe, P.; Speicher, D. W.; Vitzthum, F.; Haab, B. B.; Siest, G.; Chan, D. W. HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics 2005, 13, 3262-3277. (Pubitemid 41192034)
66. Richardson, J.; Shah, B.; Xiao, G.; Bondarenko, P. V.; Zhang, Z. Automated in-solution protein digestion using a commonly available high-performance liquid chromatography autosampler. Anal. Biochem. 2011, 411, 284-291.
67. Robinson, N. E.; Robinson, A. B. Molecular Clocks: Deamidation of Asparaginyland Glutaminyl Residues in Peptides and Proteins; Althouse Press: Cave Junction, OR, 2004.
68. Ruan, Q.; Ji, Q. C.; Arnold, M. E.; Humphreys, W. G.; Zhu, M. Strategy and its implications of protein bioanalysis utilizing high-resolution mass spectrometric detection of intact protein. Anal. Chem. 2011, 83, 8937-8944.
69. Schubert, O. T.; Mouritsen, J.; Ludwig, C.; Röst, H. L.; Rosenberger, G.; Arthur, P. K.; Claassen, M.; Campbell, D. S.; Sun, Z.; Farrah, T.; Gengenbacher, M.; Maiolica, A.; Kaufmann, S. H.; Moritz, R. L.; Aebersold, R. The Mtb Proteome Library: A resource of assays to quantify the complete proteome of Mycobacterium tuberculosis. Cell Host Microbe 2013, 13, 602-612.
70. Schwartz, M.; Kline, W.; Matuszewski, B. Determination of a cyclic hexapeptide (L-743 872), a novel pneumocandin antifungal agent in human plasma and urine by high-performance liquid chromatography with fluorescence detection. Anal. Chim. Acta. 1997, 352, 299-307. (Pubitemid 27522832)
71. Shou, W. Z.; Weng, N. Simple means to alleviate sensitivity loss by trifluoroacetic acid (TFA) mobile phases in the hydrophilic interaction chromatography-electrospray tandem mass spectrometric (HILIC-ESI/MS/MS) bioanalysis of basic compounds. J. Chromatogr. B. 2005, 825, 186-192. (Pubitemid 41423602)
72. van Midwoud, P. M.; Rieux, L.; Bischoff, R.; Verpoorte, E.; Niederländer, H. A. Improvement of recovery and repeatability in liquid chromatography-mass spectrometry analysis of peptides. J. Proteome Res. 2007, 6, 781-791. (Pubitemid 46340181)
73. Veronese, F. M.; Mero, A. The impact of pegylation on biological therapies. BioDrugs. 2008, 22, 315-329.
74. Vlasak, J.; Ionescu, R. Fragmentation of monoclonal antibodies. MAbs. 2011, 3, 253-263.
75. Warnke, C.; Hermanrud, C.; Lundkvist, M.; Fogdell-Hahn, A. Anti-drug antibodies. Drugs. Ther. Stud. 2012, 2:e11, 56-63.
76. Wilson, S. F.; Li, H.; Rose, M. J.; Xiao, J.; Holder, J. R.; James, C. A. Development and validation of a method for the determination of a therapeutic peptide with affinity for the human B1 receptor in human plasma using HPLC-MS/MS. J. Chromatogr. B. 2010, 878, 749-757.
77. Wu, S. T.; Ouyang, Z.; Olah, T. V.; Jemal, M. A strategy for liquid chromatography/tandem mass spectrometry based quantitation of pegylated protein drugs in plasma using plasma protein precipitation with water-miscible organic solvents and subsequent trypsin digestion to generate surrogate peptides for detection. Rapid Commun. Mass Spectrom. 2011, 25, 281-290.
78. Xu, Y.; Mehl, J. T.; Bakhtiar, R.; Woolf, E. J. Immunoaffinity purification using anti-peg antibody followed by two-dimensional liquid chromatography/tandem mass spectrometry for the quantification of a pegylated therapeutic peptide in human plasma. Anal. Chem. 2010, 82, 6877-6886.
79. Yang, Z.; Hayes, M.; Fang, X.; Daley, M. P.; Ettenberg, S.; Tse, F. L. Therapeutic proteins in plasma using a protein internal standard and 2D-solid-phase extraction cleanup. Anal. Chem. 2007, 79, 9294-9301. (Pubitemid 350276306)
80. Zubarev, R.; Makarov, A. Orbitrap mass spectrometry. Anal. Chem. 2013, 85, 5288-5296.