Quantitative mass spectrometry-based assay development and validation: From small molecules to proteins

Clinical Biochemistry

Volumn 46, Issue 6, 2013, Pages 444-455

  Božović, Andrea ^a,b   Kulasingam, Vathany ^a,b  

^a TORONTO GENERAL HOSPITAL   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

Assay development; Mass spectrometry; Proteomics; Selected reaction monitoring; Small molecules

Indexed keywords

DRUG METABOLITE; ION; PEPTIDE; MOLECULAR LIBRARY; PROTEIN; DIAGNOSTIC AGENT;

ACCURACY; ANALYTICAL EQUIPMENT; COMPUTER PROGRAM; HUMAN; LABORATORY DIAGNOSIS; LIMIT OF DETECTION; LIMIT OF QUANTITATION; LIQUID CHROMATOGRAPHY; LIQUID CHROMATOGRAPHY TANDEM MASS SPECTROMETRY; MASS SPECTROMETER; MASS SPECTROMETRY; PHASE SEPARATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DETERMINATION; PROTEOMICS; REVIEW; STANDARD; VALIDATION PROCESS; VALIDATION STUDY; DIAGNOSTIC TEST; DIAGNOSTIC USE; ISOLATION AND PURIFICATION; MOLECULAR LIBRARY;

CHROMATOGRAPHY, LIQUID; DIAGNOSTIC TESTS, ROUTINE; HUMANS; MASS SPECTROMETRY; PROTEINS; PROTEOMICS; SMALL MOLECULE LIBRARIES; SOFTWARE;

EID: 84891711745     PISSN: 00099120     EISSN: 18732933     Source Type: Journal    
DOI: 10.1016/j.clinbiochem.2012.09.024     Document Type: Review

References (108)

1. Borman S., Russell H., Siuzdak G. A Mass Spec timeline. Today's chemist at work 2003, 47-49.
2. Eldjarn L., Jellum E., Stokke O. Application of gas chromatography-mass spectrometry in routine and research in clinical chemistry. J Chromatogr 1974, 91:353-366.
3. Baldwin M.A., McLafferty F.W. Liquid Chromatography-mass spectrometry interface - I: the direct introduction of liquid solutions into a chemical ionization mass spectrometer. J Mass Spectrom 1973, 7:1111-1112.
4. Fenn J.B., Mann M., Meng C.K., Wong S.F., Whitehouse C.M. Electrospray ionization for mass spectrometry of large biomolecules. Science 1989, 246:64-71.
5. Karas M., Bachmann D., Hillenkamp F. Influence of the wavelength in high-irradiance ultraviolet laser desorption mass spectrometry of organic molecules. Anal Chem 1985, 57:2935-2939.
6. Trauger S.A., Webb W., Siuzdak G. Peptide and protein analysis with mass spectrometry. Spectroscopy 2002, 16:15-28.
7. de Hoffman E. Tandem mass spectrometry: a primer. J Mass Spectrom 1996, 31:129-137.
8. Chace D.H. Mass spectrometry in the clinical laboratory. Chem Rev 2001, 101:445-477.
9. Dooley K.C. Tandem mass spectrometry in the clinical chemistry laboratory. Clin Biochem 2003, 36:471-481.
10. Vogeser M. Liquid chromatography-tandem mass spectrometry-application in the clinical laboratory. Clin Chem Lab Med 2003, 41:117-126.
11. Vogeser M., Seger C. A decade of HPLC-MS/MS in the routine clinical laboratory - goals for further developments. Clin Biochem 2008, 41:649-662.
12. Pitt J.J. Principles and applications of liquid chromatography-mass spectrometry in clinical biochemistry. Clin Biochem Rev 2009, 30:19-34.
13. Kushnir M.M., Rockwood A.L., Bergquist J. Liquid chromatography-tandem mass spectrometry applications in endocrinology. Mass Spectrom Rev 2010, 29:480-502.
14. Vogeser M., Seger C. Pitfalls associated with the use of liquid chromatography-tandem mass spectrometry in the clinical laboratory. Clin Chem 2010, 56:1234-1244.
15. Shackleton C. Clinical steroid mass spectrometry: a 45-year history culminating in HPLC-MS/MS becoming an essential tool for patient diagnosis. J Steroid Biochem Mol Biol 2010, 121:481-490.
16. Grebe S.K., Singh R.J. LC-MS/MS in the clinical laboratory - where to from here?. Clin Biochem Rev 2011, 32:5-31.
17. Strathmann F.G., Hoofnagle A.N. Current and future applications of mass spectrometry to the clinical laboratory. Am J Clin Pathol 2011, 136:609-616.
18. Peters F.T. Recent advances of liquid chromatography-(tandem) mass spectrometry in clinical and forensic toxicology. Clin Biochem 2011, 44:54-65.
19. Chen Y., Guo Z., Wang X., Qiu C. Sample preparation. J Chromatogr A 2008, 1184:191-219.
20. Van Eeckhaut A., Lanckmans K., Sarre S., Smolders I., Michotte Y. Validation of bioanalytical LC-MS/MS assays: evaluation of matrix effects. J Chromatogr B Analyt Technol Biomed Life Sci 2009, 877:2198-2207.
21. Novakova L., Vlckova H. A review of current trends and advances in modern bio-analytical methods: chromatography and sample preparation. Anal Chim Acta 2009, 656:8-35.
22. Zwir-Ferenc A., Biziuk M. Solid phase extraction technique - trends, opportunities and applications. Pol J Environ Stud 2006, 15:677-690.
23. Beraldi R.P., Pawliszyn J. The application of chemically modified fused silica fibers in the extraction of organics from water matrix samples and their rapid transfer to capillary columns. Water Pollut Res J Can 1989, 24:179-191.
24. Arthur C.L., Pawliszyn J. Solid phase microextraction with thermal desorption using fused silica optical fibers. Anal Chem 1990, 62:2145-2148.
25. Pena-Pereira F., Lavilla I., Bendicho C. Miniaturized preconcentrated methods based on liquid-liquid extraction and their application in inorganic ultratrace analysis and speciation: a review. Spectrochim Acta B 2009, 64:1-15.
26. Pavlovic D.M., Babic S., Horvat A.L.M., Macan J.K. Sample preparation in analysis of pharmaceuticals. Trends Anal Chem 2007, 26:1062-1075.
27. Abdel-Rehim M. New trend in sample preparation: on-line microextraction in packed syringe for liquid and gas chromatography applications. I. Determination of local anaesthetics in human plasma samples using gas chromatography-mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2004, 801:317-321.
28. Abdel-Rehim M., Altun Z., Blomberg L. Microextraction in packed syringe (MEPS) for liquid and gas chromatographic applications. Part II - determination of ropivacaine and its metabolites in human plasma samples using MEPS with liquid chromatography/tandem mass spectrometry. J Mass Spectrom 2004, 39:1488-1493.
29. Eisert R., Pawliszyn J. Automated in-tube solid-phase microextraction coupled to high-performance liquid chromatography. Anal Chem 1997, 69:3140-3147.
30. Walles M., Mullet W.M., Levsen K., Borlak J., Wunsch G., Pawliszyn J. Verapamil drug metabolism studies by automated in-tube solid phase microextraction. J Pharm Biomed Anal 2002, 30:307-319.
31. Burgess Ch., McDowall R.D. A question of balance? Part 2: putting principles into practice. LC GC Eur 2006, 19.
32. United States Pharmacopeia Weights and balances 2005, Rockville, Maryland, USA.
33. Markey S.P. Quantitative mass spectrometry. Biomed Mass Spectrom 1981, 8:426-430.
34. Wieling J. LC-MS-MS experiences with internal standards. Chromatographia 2002, 55:107-113.
35. Stokvis E., Rosing H., Beijnen J.H. Stable isotopically labeled internal standards in quantitative bioanalysis using liquid chromatography/mass spectrometry: necessity or not?. Rapid Commun Mass Spectrom 2005, 19:401-407.
36. Honour J.W. Development and validation of a quantitative assay based on tandem mass spectrometry. Ann Clin Biochem 2011, 48:97-111.
37. Jessome L.L., Volmer D.A. Ion suppression: a major concern in mass spectrometry. LCGC North America 2006, 24:499-510.
38. Wang S., Cyronak M., Yang E. Does a stable isotopically labeled internal standard always correct analyte response? A matrix effect study on a LC/MS/MS method for the determination of carvedilol enantiomers in human plasma. J Pharm Biomed Anal 2007, 43:701-707.
39. Jemal M., Schuster A., Whigan D.B. Liquid chromatography/tandem mass spectrometry methods for quantitation of mevalonic acid in human plasma and urine: method validation, demonstration of using a surrogate analyte, and demonstration of unacceptable matrix effect in spite of use of a stable isotope analog internal standard. Rapid Commun Mass Spectrom 2003, 17:1723-1734.
40. Berg T., Strand D.H. (1)(3)C labelled internal standards - a solution to minimize ion suppression effects in liquid chromatography-tandem mass spectrometry analyses of drugs in biological samples?. J Chromatogr A 2011, 1218:9366-9374.
41. Jian W., Shou W., Edom R.W., Weng N., Zhu M. Mass spectrometry handbook 2012, 140. John Wiley & Sons, Inc., Hoboken, NJ. M.S. Lee (Ed.).
42. Mass spectrometry handbook 2012, John Wiley & Sons, Inc.
43. Mitchum R.K., Korfmacher W.A. Atmospheric pressure ionization mass spectrometry. Anal Chem 1983, 55:1485-1499.
44. Covey T.R., Thomson B.A., Schneider B.B. Atmospheric pressure ion sources. Mass Spectrom Rev 2009, 28:870-897.
45. Kebarle P., Verkerk U.H. Electrospray: from ions in solution to ions in the gas phase, what we know now. Mass Spectrom Rev 2009, 28:898-917.
46. Vestal M.L. Methods of ion generation. Chem Rev 2001, 101:361-375.
47. Busch K.L. Desorption ionization mass spectrometry. J Mass Spectrom 1995, 30:233-240.
48. de Hoffmann E., Stroobant V. Mass spectrometry principles and applications 2007, John Wiley & Sons Inc. 3rd ed.
49. Ho C.S., Lam C.W., Chan M.H., Cheung R.C., Law L.K., Lit L.C., et al. Electrospray ionisation mass spectrometry: principles and clinical applications. Clin Biochem Rev 2003, 24:3-12.
50. Sweetman L. Newborn screening by tandem mass spectrometry: gaining experience. Clin Chem 2001, 47:1937-1938.
51. Ito T., van Kuilenburg A.B., Bootsma A.H., Haasnoot A.J., van Cruchten A., Wada Y., et al. Rapid screening of high-risk patients for disorders of purine and pyrimidine metabolism using HPLC-electrospray tandem mass spectrometry of liquid urine or urine-soaked filter paper strips. Clin Chem 2000, 46:445-452.
52. Higashi T., Shimada K. Derivatization of neutral steroids to enhance their detection characteristics in liquid chromatography-mass spectrometry. Anal Bioanal Chem 2004, 378:875-882.
53. Soldin S.J., Soldin O.P. Steroid hormone analysis by tandem mass spectrometry. Clin Chem 2009, 55:1061-1066.
54. Andreoli R., Manini P., Poli D., Bergamaschi E., Mutti A., Niessen W.M. Development of a simplified method for the simultaneous determination of retinol, alpha-tocopherol, and beta-carotene in serum by liquid chromatography-tandem mass spectrometry with atmospheric pressure chemical ionization. Anal Bioanal Chem 2004, 378:987-994.
55. Eitenmiller R.R., Lin Y., Landen W.O. Vitamin analysis for the health and food sciences 2008, CRC Press, Taylor & Francis Group. 2nd ed.
56. Kamao M., Tsugawa N., Suhara Y., Okano T. Determination of fat-soluble vitamins in human plasma, breast milk and food samples: application in nutrition survey for establishment of "dietary reference intakes for Japanese". J Health Sci 2007, 53:257-262.
57. Miller P.E., Denton M.B. The quadrupole mass filter: basic operating concepts. J Chem Educ 1986, 63:617-623.
58. Kostiainen R., Kauppila T.J. Effect of eluent on the ionization process in liquid chromatography-mass spectrometry. J Chromatogr A 2009, 1216:685-699.
59. Baltussen E., Noij T.H.M. High speed and high resolution liquid chromatography in practice. Chim Oggi 2009, 27:31-33.
60. Yang Y. Stationary phases for LC separations at elevated temperatures. LCGC LC Column Technology Supplement 2006, 53-58.
61. McMaster M.C. LC/MS a practical user's guide 2005, John Wiley & Sons, Inc.
62. Temesi D., Law B. The effect of LC eluent composition on MS responses using electrospray ionization. LC GC N Am 1999, 17:626-632.
63. Truei Y.H., Gu T., Tsai G.J., Tsao G.T. Large-scale gradient elution chromatography. Advances in biochemical engineering/biotechnology 1992, 1-44. Springer-Verlag. A. Fiechter (Ed.).
64. Schellinger A.P., Carr P.W. Isocratic and gradient elution chromatography: a comparison in terms of speed, retention reproducibility and quantitation. J Chromatogr A 2006, 1109:253-266.
65. Guidance for industry: bioanalytical method validation 2001, US Department of Health and Human Services, FDA, CDER, CVM, Washington, DC.
66. Kalakuntla R.R., Kumar K.S. Bioanalytical method validation: a quality assurance auditor view point. J Pharm Sci Res 2009, 1:1-10.
67. Kushnir M.M., Rockwood A.L., Nelson G.J., Yue B., Urry F.M. Assessing analytical specificity in quantitative analysis using tandem mass spectrometry. Clin Biochem 2005, 38:319-327.
68. Karnes H.T., Shiu G., Shah V.P. Validation of bioanalytical methods. Pharm Res 1991, 8:421-426.
69. Bansal S., DeStefano A. Key elements of bioanalytical method validation for small molecules. AAPS J 2007, 9:109-114.
70. Boque R., Maroto A., Riu J., Rius F.X. Validation of analytical methods. Grasas Aceites 2002, 53:128-143.
71. Taverniers I., de Loose M., van Bockstaele E. Trends in quality in the analytical laboratory. II. Analytical method validation and quality assurance. Trends Anal Chem 2004, 23:535-552.
72. van den Ouweland J.M., Kema I.P. The role of liquid chromatography-tandem mass spectrometry in the clinical laboratory. J Chromatogr B Analyt Technol Biomed Life Sci 2012, 883-884:18-32.
73. Taylor P.J. Matrix effects: the Achilles heel of quantitative high-performance liquid chromatography-electrospray-tandem mass spectrometry. Clin Biochem 2005, 38:328-334.
74. Annesley T.M. Ion suppression in mass spectrometry. Clin Chem 2003, 49:1041-1044.
75. Chambers E., Wagrowski-Diehl D.M., Lu Z., Mazzeo J.R. Systematic and comprehensive strategy for reducing matrix effects in LC/MS/MS analyses. J Chromatogr B 2007, 852:22-34.
76. Allen K.R. Interference by venlafaxine ingestion in the detection of tramadol by liquid chromatography linked to tandem mass spectrometry for the screening of illicit drugs in human urine. Clin Toxicol (Phila) 2006, 44:147-153.
77. Lumsden J.H. Laboratory test method validation. Rev Med Vet 2000, 151:623-630.
78. Armbruster D.A., Pry T. Limit of blank, limit of detection and limit of quantitation. Clin Biochem Rev 2008, 29:49-52.
79. Wisniewski J.R. Mass spectrometry-based proteomics: principles, perspectives, and challenges. Arch Pathol Lab Med 2008, 132:1566-1569.
80. Gallien S., Duriez E., Domon B. Selected reaction monitoring applied to proteomics. J Mass Spectrom 2011, 46:298-312.
81. Stahl-Zeng J., Lange V., Ossola R., Eckhardt K., Krek W., Aebersold R., et al. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics 2007, 6:1809-1817.
82. Pawlak M., Schick E., Bopp M.A., Schneider M.J., Oroszlan P., Ehrat M. Zeptosens' protein microarrays: a novel high performance microarray platform for low abundance protein analysis. Proteomics 2002, 2:383-393.
83. Carr S.A., Anderson L. Protein quantitation through targeted mass spectrometry: the way out of biomarker purgatory?. Clin Chem 2008, 54:1749-1752.
84. Rawlins M.L., Roberts W.L. Performance characteristics of six third-generation assays for thyroid-stimulating hormone. Clin Chem 2004, 50:2338-2344.
85. La'ulu S.L., Roberts W.L. Performance characteristics of five automated CA 19-9 assays. Am J Clin Pathol 2007, 127:436-440.
86. Rotmensch S., Cole L.A. False diagnosis and needless therapy of presumed malignant disease in women with false-positive human chorionic gonadotropin concentrations. Lancet 2000, 355:712-715.
87. Hoofnagle A.N., Wener M.H. The fundamental flaws of immunoassays and potential solutions using tandem mass spectrometry. J Immunol Methods 2009, 347:3-11.
88. Bereman M.S., Maclean B., Tomazela D.M., Liebler D.C., Maccoss M.J. The development of selected reaction monitoring methods for targeted proteomics via empirical refinement. Proteomics 2012, 12:1134-1141.
89. Lange V., Picotti P., Domon B., Aebersold R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol 2008, 4:222.
90. Picotti P., Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods 2012, 9:555-566.
91. Bantscheff M., Schirle M., Sweetman G., Rick J., Kuster B. Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem 2007, 389:1017-1031.
92. Wolf-Yadlin A., Hautaniemi S., Lauffenburger D.A., White F.M. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc Natl Acad Sci U S A 2007, 104:5860-5865.
93. Deutsch E.W., Lam H., Aebersold R. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep 2008, 9:429-434.
94. Craig R., Cortens J.P., Beavis R.C. Open source system for analyzing, validating, and storing protein identification data. J Proteome Res 2004, 3:1234-1242.
95. Mallick P., Schirle M., Chen S.S., Flory M.R., Lee H., Martin D., et al. Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol 2007, 25:125-131.
96. Picotti P., Lam H., Campbell D., Deutsch E.W., Mirzaei H., Ranish J., et al. A database of mass spectrometric assays for the yeast proteome. Nat Methods 2008, 5:913-914.
97. Mead J.A., Bianco L., Ottone V., Barton C., Kay R.G., Lilley K.S., et al. MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions. Mol Cell Proteomics 2009, 8:696-705.
98. Sherwood C.A., Eastham A., Lee L.W., Risler J., Vitek O., Martin D.B. Correlation between y-type ions observed in ion trap and triple quadrupole mass spectrometers. J Proteome Res 2009, 8:4243-4251.
99. Prakash A., Tomazela D.M., Frewen B., Maclean B., Merrihew G., Peterman S., et al. Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development. J Proteome Res 2009, 8:2733-2739.
100. Paizs B., Suhai S. Fragmentation pathways of protonated peptides. Mass Spectrom Rev 2005, 24:508-548.
101. Unwin R.D., Griffiths J.R., Leverentz M.K., Grallert A., Hagan I.M., Whetton A.D. Multiple reaction monitoring to identify sites of protein phosphorylation with high sensitivity. Mol Cell Proteomics 2005, 4:1134-1144.
102. 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 U S A 2003, 100:6940-6945.
103. 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 Methods 2005, 2:587-589.
104. Dupuis A., Hennekinne J.A., Garin J., Brun V. Protein standard absolute quantification (PSAQ) for improved investigation of staphylococcal food poisoning outbreaks. Proteomics 2008, 8:4633-4636.
105. Holzmann J., Pichler P., Madalinski M., Kurzbauer R., Mechtler K. Stoichiometry determination of the MP1-p14 complex using a novel and cost-efficient method to produce an equimolar mixture of standard peptides. Anal Chem 2009, 81:10254-10261.
106. Anderson L., Hunter C.L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics 2006, 5:573-588.
107. Prakash A., Rezai T., Krastins B., Sarracino D., Athanas M., Russo P., et al. Platform for establishing interlaboratory reproducibility of selected reaction monitoring-based mass spectrometry peptide assays. J Proteome Res 2010, 9:6678-6688.
108. Fortin T., Salvador A., Charrier J.P., Lenz C., Bettsworth F., Lacoux X., et al. Multiple reaction monitoring cubed for protein quantification at the low nanogram/milliliter level in nondepleted human serum. Anal Chem 2009, 81:9343-9352.