Quantitative clinical chemistry proteomics (qCCP) using mass spectrometry: General characteristics and application

Clinical Chemistry and Laboratory Medicine

Volumn 51, Issue 5, 2013, Pages 919-935

  Lehmann, Sylvain ^a   Hoofnagle, Andrew ^b   Hochstrasser, Denis ^c,d   Brede, Cato ^e   Glueckmann, Matthias ^f   Cocho, José A ^g   Ceglarek, Uta ^h   Lenz, Christof ⁱ   Vialaret, Jérôme ^a   Scherl, Alexander ^c   Hirtz, Christophe ^a  

^a HÔPITAL SAINT ELOI   (France)

^b UNIVERSITY OF WASHINGTON   (United States)

^c UNIVERSITY OF GENEVA   (Switzerland)

^d GENEVA UNIVERSITY HOSPITALS   (Switzerland)

^e STAVANGER UNIVERSITY HOSPITAL   (Norway)

^f MDS SCIEX   (Canada)

^g University Hospital of Santiago de Compostela   (Spain)

^h UNIVERSITY HOSPITAL LEIPZIG   (Germany)

ⁱ MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

Absolute quantification; Clinical Chemistry; Mass spectrometry; Peptides and proteins

Indexed keywords

ISOTOPE; PEPTIDE; PROTEIN;

ANTIBODY AFFINITY; BODY FLUID; CLINICAL CHEMISTRY; COMPUTER PROGRAM; DISEASES; ELECTROSPRAY MASS SPECTROMETRY; EXTRACTION; GENOMICS; HUMAN; IMMUNOCHEMISTRY; ION TRAP MASS SPECTROMETRY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MEASUREMENT; MEDICAL RESEARCH; MICROFLUIDICS; MONITORING; PATHOPHYSIOLOGY; PRECIPITATION; PRIORITY JOURNAL; PROGNOSIS; PROTEOMICS; QUALITY CONTROL; QUANTITATIVE CLINICAL CHEMISTRY PROTEOMICS; REVIEW; SOLID PHASE EXTRACTION; TANDEM MASS SPECTROMETRY;

BIOLOGICAL MARKERS; CHEMISTRY, CLINICAL; CHROMATOGRAPHY, LIQUID; HUMANS; PEPTIDES; PROTEINS; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 84882236106     PISSN: 14346621     EISSN: 14374331     Source Type: Journal    
DOI: 10.1515/cclm-2012-0723     Document Type: Review

References (87)

1. James P. Protein identification in the post-genome era: The rapid rise of proteomics. Q Rev Biophys 1997;30:279-331.
2. Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 2003;422:198-207.
3. Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: The long and uncertain path to clinical utility. Nat Biotechnol 2006;24:971-83.
4. Stengel F, Aebersold R, Robinson CV. Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes. Mol Cell Proteomics 2012;11:R111 014027.
5. Gingras AC, Aebersold R, Raught B. Advances in protein complex analysis using mass spectrometry. J Physiol 2005;563:11-21.
6. Thakur SS, Geiger T, Chatterjee B, Bandilla P, Frohlich F, Cox J, et al. Deep and highly sensitive proteome coverage by LC-MS/ MS without prefractionation. Mol Cell Proteomics 2011;10:M110 003699.
7. Lundgren DH, Hwang SI, Wu L, Han DK. Role of spectral counting in quantitative proteomics. Expert Rev Proteomics 2010;7:39-53.
8. Ji SQ, Evenson MA. Effects of contaminants in blood-collection devices on measurements of therapeutic drugs. Clin Chem 1983;29:456-61.
9. Craig R, Cortens JP, Beavis RC. The use of proteotypic peptide libraries for protein identification. Rapid Commun Mass Spectrom 2005;19:1844-50.
10. Ewles M, Goodwin L. Bioanalytical approaches to analyzing peptides and proteins by LC-MS/MS. Bioanalysis 2011;3: 1379-97.
11. Olsen JV, Ong SE, Mann M. Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol Cell Proteomics 2004;3:608-14.
12. Anderson L, Hunter CL. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics 2006;5:573-88.
13. Mayya V, Han DK. Proteomic applications of protein quantification by isotope-dilution mass spectrometry. Expert Rev Proteomics 2006;3:597-610.
14. Domanski D, Percy AJ, Yang J, Chambers AG, Hill JS, Freue GV, et al. MRM-based multiplexed quantitation of 67 putative cardiovascular disease biomarkers in human plasma. Proteomics 2012;12:1222-43.
15. Agger SA, Marney LC, Hoofnagle AN. Simultaneous quantification of apolipoprotein A-I and apolipoprotein B by liquid-chromatography-multiple- reaction-monitoring mass spectrometry. Clin Chem 2010;56:1804-13.
16. Bansal SS, Abbate V, Bomford A, Halket JM, Macdougall IC, Thein SL, et al. Quantitation of hepcidin in serum using ultrahigh- pressure liquid chromatography and a linear ion trap mass spectrometer. Rapid Commun Mass Spectrom 2010;24:1251-9.
17. Bystrom CE, Sheng S, Clarke NJ. Narrow mass extraction of time-of-flight data for quantitative analysis of proteins: determination of insulin-like growth factor-1. Anal Chem 2011;83:9005-10.
18. Roche S, Tiers L, Provansal M, Seveno M, Piva MT, Jouin P, et al. Depletion of one, six, twelve or twenty major blood proteins before proteomic analysis: The more the better? J Proteomics 2009;72:945-51.
19. Smith MP, Wood SL, Zougman A, Ho JT, Peng J, Jackson D, et al. A systematic analysis of the effects of increasing degrees of serum immunodepletion in terms of depth of coverage and other key aspects in top-down and bottom-up proteomic analyses. Proteomics 2011;11:2222-35.
20. Callesen AK, Madsen JS, Vach W, Kruse TA, Mogensen O, Jensen ON. Serum protein profiling by solid phase extraction and mass spectrometry: A future diagnostics tool? Proteomics 2009;9:1428-41.
21. Hawkridge AM, Heublein DM, Bergen HR 3rd, Cataliotti A, Burnett JC Jr., Muddiman DC. Quantitative mass spectral evidence for the absence of circulating brain natriuretic peptide (bnp-32) in severe human heart failure. Proc Natl Acad Sci USA 2005;102:17442-7.
22. Kuhn E, Wu J, Karl J, Liao H, Zolg W, Guild B. Quantification of c-reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13c-labeled peptide standards. Proteomics 2004;4:1175-86.
23. deWilde A, Sadilkova K, Sadilek M, Vasta V, Hahn SH. Tryptic peptide analysis of ceruloplasmin in dried blood spots using liquid chromatography- tandem mass spectrometry: application to newborn screening. Clin Chem 2008;54:1961-8.
24. Li WW, Nemirovskiy O, Fountain S, Rodney Mathews W, Szekely- Klepser G. Clinical validation of an immunoaffinity LC-MS/MS assay for the quantification of a collagen type II neoepitope peptide: A biomarker of matrix metalloproteinase activity and osteoarthritis in human urine. Anal Biochem 2007;369:41-53.
25. del Castillo E, Montes-Bayon M, Anon E, Sanz-Medel A. Quantitative targeted biomarker assay for glycated haemoglobin by multidimensional LC using mass spectrometric detection. J Proteomics 2010;74:35-43.
26. Kaiser P, Akerboom T, Ohlendorf R, Reinauer H. Liquid chromatography- isotope dilution-mass spectrometry as a new basis for the reference measurement procedure for hemoglobin A1c determination. Clin Chem 2010;56:750-4.
27. Jeppsson JO, Kobold U, Barr J, Finke A, Hoelzel W, Hoshino T, et al. Approved IFCC reference method for the measurement of HbA1c in human blood. Clin Chem Lab Med 2002;40:78-89.
28. Anderson DS, Kirchner M, Kellogg M, Kalish LA, Jeong JY, Vanasse G, et al. Design and validation of a high-throughput matrix-assisted laser desorption ionization time-of-flight mass spectrometry method for quantification of hepcidin in human plasma. Anal Chem 2011;83:8357-62.
29. Bansal SS, Halket JM, Bomford A, Simpson RJ, Vasavda N, Thein SL, et al. Quantitation of hepcidin in human urine by liquid chromatography-mass spectrometry. Anal Biochem 2009;384:245-53.
30. Bansal SS, Halket JM, Fusova J, Bomford A, Simpson RJ, Vasavda N, et al. Quantification of hepcidin using matrixassisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 2009; 23:1531-42.
31. Bozzini C, Campostrini N, Trombini P, Nemeth E, Castagna A, Tenuti I, et al. Measurement of urinary hepcidin levels by SELDI-TOF-MS in HFE-hemochromatosis. Blood Cells Mol Dis 2008;40:347-52.
32. Hwang SI, Lee YY, Park JO, Norton HJ, Clemens E, Schrum LW, et al. Effects of a single dose of oral iron on hepcidin concentrations in human urine and serum analyzed by a robust LC-MS/MS method. Clin Chim Acta 2011;412:2241-7.
33. Houbart V, Cobraiville G, Lecomte F, Debrus B, Hubert P, Fillet M. Development of a nano-liquid chromatography on chip tandem mass spectrometry method for high-sensitivity hepcidin quantitation. J Chromatogr A 2011;1218:9046-54.
34. Kroot JJ, Kemna EH, Bansal SS, Busbridge M, Campostrini N, Girelli D, et al. Results of the first international round robin for the quantification of urinary and plasma hepcidin assays: need for standardization. Haematologica 2009;94:1748-52.
35. Li N, Palandra J, Nemirovskiy OV, Lai Y. LC-MS/MS mediated absolute quantification and comparison of bile salt export pump and breast cancer resistance protein in livers and hepatocytes across species. Anal Chem 2009;81:2251-9.
36. Murphy AT, Witcher DR, Luan P, Wroblewski VJ. Quantitation of hepcidin from human and mouse serum using liquid chromatography tandem mass spectrometry. Blood 2007;110:1048-54.
37. Song J, Patel M, Rosenzweig CN, Chan-Li Y, Sokoll LJ, Fung ET, et al. Quantification of fragments of human serum inter-alphatrypsin inhibitor heavy chain 4 by a surface-enhanced laser desorption/ionization-based immunoassay. Clin Chem 2006;52:1045-53.
38. van den Broek I, Sparidans RW, Schellens JH, Beijnen JH. Quantitative assay for six potential breast cancer biomarker peptides in human serum by liquid chromatography coupled to tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2010;878:590-602.
39. Winther B, Moi P, Paus E, Reubsaet JL. Targeted determination of the early stage SCLC specific biomarker pro-gastrin-releasing peptide (progrp) at clinical concentration levels in human serum using LC-MS. J Sep Sci 2007;30:2638-46.
40. Kuhn J, Prante C, Schon S, Gotting C, Kleesiek K. Measurement of fibrosis marker xylosyltransferase I activity by HPLC electrospray ionization tandem mass spectrometry. Clin Chem 2006;52:2243-9.
41. Seegmiller JC, Sviridov D, Larson TS, Borland TM, Hortin GL, Lieske JC. Comparison of urinary albumin quantification by immunoturbidimetry, competitive immunoassay, and proteincleavage liquid chromatography-tandem mass spectrometry. Clin Chem 2009;55:1991-4.
42. Kuzyk MA, Smith D, Yang J, Cross TJ, Jackson AM, Hardie DB, et al. Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma. Mol Cell Proteomics 2009;8:1860-77.
43. Lee HJ, Na K, Kwon MS, Kim H, Kim KS, Paik YK. Quantitative analysis of phosphopeptides in search of the disease biomarker from the hepatocellular carcinoma specimen. Proteomics 2009;9:3395-408.
44. Lewczuk P, Esselmann H, Groemer TW, Bibl M, Maler JM, Steinacker P, et al. Amyloid â peptides in cerebrospinal fluid as profiled with surface enhanced laser desorption/ionization time-of-flight mass spectrometry: evidence of novel biomarkers in Alzheimer ' s disease. Biol Psychiatry 2004;55:524-30.
45. Thompson AJ, Lim TK, Barrow CJ. On-line high-performance liquid chromatography/mass spectrometric investigation of amyloid- Â peptide variants found in Alzheimer ' s disease. Rapid Commun Mass Spectrom 1999;13:2348-51.
46. Albertini V, Bruno A, Paterlini A, Lista S, Benussi L, Cereda C, et al. Optimization protocol for amyloid- Â peptides detection in human cerebrospinal fluid using SELDI TOF MS. Proteomics Clin Appl 2010;4:352-7.
47. Maddalena AS, Papassotiropoulos A, Gonzalez-Agosti C, Signorell A, Hegi T, Pasch T, et al. Cerebrospinal fluid profile of amyloid â peptides in patients with Alzheimer ' s disease determined by protein biochip technology. Neurodegener Dis 2004;1:231-5.
48. Du C, Ramaley C, McLean H, Leonard SC, Miller J. High-performance liquid chromatography coupled with tandem mass spectrometry for the detection of amyloid â peptide related with Alzheimer ' s disease. J Biomol Tech 2005;16:356-63.
49. Oe T, Ackermann BL, Inoue K, Berna MJ, Garner CO, Gelfanova V, et al. Quantitative analysis of amyloid â peptides in cerebrospinal fluid of Alzheimer ' s disease patients by immunoaffinity purification and stable isotope dilution liquid chromatography/negative electrospray ionization tandem mass spectrometry. Rapid Commun Mass Spectrom 2006;20:3723-35.
50. Ford MJ, Cantone JL, Polson C, Toyn JH, Meredith JE, Drexler DM. Qualitative and quantitative characterization of the amyloid beta peptide (A â ) population in biological matrices using an immunoprecipitation-LC/MS assay. J Neurosci Methods 2008;168:465-74.
51. Grasso G. The use of mass spectrometry to study amyloid- â peptides. Mass Spectrom Rev 2011;30:347-65.
52. Lame ME, Chambers EE, Blatnik M. Quantitation of amyloid â peptides A â in human cerebrospinal fluid by ultra-performance liquid chromatography-tandem mass spectrometry. Anal Biochem 2011;419:133-9.
53. Varesio E, Rudaz S, Krause KH, Veuthey JL. Nanoscale liquid chromatography and capillary electrophoresis coupled to electrospray mass spectrometry for the detection of amyloid- â peptide related to Alzheimer ' s disease. J Chromatogr A 2002;974:135-42.
54. Portelius E, Brinkmalm G, Tran A, Andreasson U, Zetterberg H, Westman-Brinkmalm A, et al. Identification of novel N-terminal fragments of amyloid precursor protein in cerebrospinal fluid. Exp Neurol 2010;223:351-8.
55. Wildsmith KR, Han B, Bateman RJ. Method for the simultaneous quantitation of apolipoprotein E isoforms using tandem mass spectrometry. Anal Biochem 2009;395:116-8.
56. Storme ML, Sinnaeve BA, Van Bocxlaer JF. The use of tryptic marker-peptides for the quantitative analysis of cystatin C. J Sep Sci 2005;28:1759-63.
57. Coelho Graca D, Lescuyer P, Clerici L, Tsybin YO, Hartmer R, Meyer M, et al. Electron transfer dissociation mass spectrometry of hemoglobin on clinical samples. J Am Soc Mass Spectrom 2012;23:1750-6.
58. Bredehoft M, Schanzer W, Thevis M. Quantification of human insulin-like growth factor-1 and qualitative detection of its analogues in plasma using liquid chromatography/electrospray ionisation tandem mass spectrometry. Rapid Commun Mass Spectrom 2008;22:477-85.
59. Kirsch S, Widart J, Louette J, Focant JF, 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;1153:300-6.
60. Keshishian H, Addona T, Burgess M, Mani DR, Shi X, Kuhn E, et al. Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution. Mol Cell Proteomics 2009;8:2339-49.
61. Kuhn E, Addona T, Keshishian H, Burgess M, Mani DR, Lee RT, et al. Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry. Clin Chem 2009;55:1108-17.
62. Zhang G, Zhang Y, Fast DM, Lin Z, Steenwyk R. Ultra sensitive quantitation of endogenous oxytocin in rat and human plasma using a two-dimensional liquid chromatography-tandem mass spectrometry assay. Anal Biochem 2011;416:45-52.
63. Huang HL, Stasyk T, Morandell S, Dieplinger H, Falkensammer G, Griesmacher A, et al. Biomarker discovery in breast cancer serum using 2-D differential gel electrophoresis/MALDI-TOF/TOF and data validation by routine clinical assays. Electrophoresis 2006;27:1641-50.
64. Fortin T, Salvador A, Charrier JP, 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;81:9343-52.
65. Fortin T, Salvador A, Charrier JP, Lenz C, Lacoux X, Morla A, et al. Clinical quantitation of prostate-specific antigen biomarker in the low nanogram/milliliter range by conventional bore liquid chromatography-tandem mass spectrometry (multiple reaction monitoring) coupling and correlation with ELISA tests. Mol Cell Proteomics 2009;8:1006-15.
66. Bondar OP, Barnidge DR, Klee EW, Davis BJ, Klee GG. LC-MS/ MS quantification of Zn- á 2 glycoprotein: A potential serum biomarker for prostate cancer. Clin Chem 2007;53:673-8.
67. Anderson NL, Anderson NG, Haines LR, Hardie DB, Olafson RW, Pearson TW. Mass spectrometric quantitation of peptides and proteins using stable isotope standards and capture by anti-peptide antibodies (SISCAPA). J Proteome Res 2004;3: 235-44.
68. Hoofnagle AN, Wener MH. The fundamental flaws of immunoassays and potential solutions using tandem mass spectrometry. J Immunol Methods 2009;347:3-11.
69. Portelius E, Zetterberg H, Gobom J, Andreasson U, Blennow K. Targeted proteomics in Alzheimer ' s disease: focus on amyloid- â . Expert Rev Proteomics 2008;5:225-37.
70. Sen JW, Bergen HR 3rd, Heegaard NH. On-line immunoaffinityliquid chromatography-mass spectrometry for identification of amyloid disease markers in biological fluids. Anal Chem 2003;75:1196-202.
71. Gam LH, Tham SY, Latiff A. Immunoaffinity extraction and tandem mass spectrometric analysis of human chorionic gonadotropin in doping analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2003;792:187-96.
72. Rathore R, Corr JJ, Lebre DT, Seibel WL, Greis KD. Extending matrix-assisted laser desorption/ionization triple quadrupole mass spectrometry enzyme screening assays to targets with small molecule substrates. Rapid Commun Mass Spectrom 2009;23:3293-300.
73. Portelius E, Dean RA, Gustavsson MK, Andreasson U, Zetterberg H, Siemers E, et al. A novel A â isoform pattern in CSF reflects ã -secretase inhibition in Alzheimer disease. Alzheimers Res Ther 2010;2:7.
74. Merchant M, Weinberger SR. Recent advancements in surfaceenhanced laser desorption/ionization-time of flight-mass spectrometry. Electrophoresis 2000;21:1164-77.
75. Ward DG, Roberts K, Stonelake P, Goon P, Zampronio CG, Martin A, et al. SELDI-TOF-MS determination of hepcidin in clinical samples using stable isotope labelled hepcidin as an internal standard. Proteome Sci 2008;6:28.
76. Scherl A, Shaffer SA, Taylor GK, Kulasekara HD, Miller SI, Goodlett DR. Genome-specific gas-phase fractionation strategy for improved shotgun proteomic profiling of proteotypic peptides. Anal Chem 2008;80:1182-91.
77. Lange V, Picotti P, Domon B, Aebersold R. Selected reaction monitoring for quantitative proteomics: A tutorial. Mol Syst Biol 2008;4:222.
78. Brewis IA, Brennan P. Proteomics technologies for the global identification and quantification of proteins. Adv Protein Chem Struct Biol 2010;80:1-44.
79. Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B. Quantitative mass spectrometry in proteomics: A critical review. Anal Bioanal Chem 2007;389:1017-31.
80. MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, et al. Skyline: An open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 2010;26:966-8.
81. Schilling B, Rardin MJ, MacLean BX, Zawadzka AM, Frewen BE, Cusack MP, et al. Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromato grams in skyline: application to protein acetylation and phosphorylation. Mol Cell Proteomics 2012;11:202-14.
82. Prakash A, Tomazela DM, 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;8:2733-9.
83. Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci USA 2003;100:6940-5.
84. Beynon RJ, Doherty MK, Pratt JM, Gaskell SJ. Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat Methods 2005;2:587-9.
85. Wehr AY, Hwang WT, Blair IA, Yu KH. Relative quantification of serum proteins from pancreatic ductal adenocarcinoma patients by stable isotope dilution liquid chromatography-mass spectrometry. J Proteome Res 2012;11:1749-58.
86. Brun V, Dupuis A, Adrait A, Marcellin M, Thomas D, Court M, et al. Isotope-labeled protein standards: toward absolute quantitative proteomics. Mol Cell Proteomics 2007;6:2139-49.
87. Bland JM, Altman DG. Statistical methods for assessing agreement between two methods of clinical measurement. Lancet 1986;1:307-10.