CE-MS-based proteomics in biomarker discovery and clinical application

Proteomics - Clinical Applications

Volumn 9, Issue 3-4, 2015, Pages 322-334

  Pontillo, Claudia ^a,b   Filip, Szymon ^b,c   Borràs, Daniel M ^d,e,f   Mullen, William ^g   Vlahou, Antonia ^c,h   Mischak, Harald ^a,g  

^a MOSAIQUES DIAGNOSTICS GMBH   (Germany)

^b CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^c BIOMEDICAL RESEARCH FOUNDATION   (Greece)

^d ServiceXS ^*  (Netherlands)

^e INSERM   (France)

^f UNIVERSITÉ PAUL SABATIER   (France)

^g UNIVERSITY OF GLASGOW   (United Kingdom)

^h UNIVERSITY OF PLYMOUTH   (United Kingdom)

Author keywords

Biomarker; Capillary electrophoresis; Clinical proteomics; Mass spectrometry; Peptidomics

Indexed keywords

BIOLOGICAL MARKER;

AMINO ACID SEQUENCE; CAPILLARY ELECTROPHORESIS; HUMAN; INTERMETHOD COMPARISON; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR DYNAMICS; MOLECULAR WEIGHT; NONHUMAN; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN STABILITY; PROTEOMICS; REPRODUCIBILITY; REVIEW; SENSITIVITY AND SPECIFICITY; PROCEDURES;

BIOMARKERS; MASS SPECTROMETRY; PROTEOMICS; REPRODUCIBILITY OF RESULTS;

EID: 84928008315     PISSN: 18628346     EISSN: 18628354     Source Type: Journal    
DOI: 10.1002/prca.201400115     Document Type: Review

References (91)

1. Mischak, H., Ioannidis, J. P., Argiles, A., Attwood, T. K. et al., Implementation of proteomic biomarkers: making it work. Eur. J. Clin. Invest. 2012, 42, 1027-1036.
2. Mischak, H., Apweiler, R., Banks, R. E., Conaway, M. et al., Clinical proteomics: a need to define the field and to begin to set adequate standards. Proteomics Clin. Appl. 2007, 1, 148-156.
3. Mullen, W., Delles, C., Mischak, H., Urinary proteomics in the assessment of chronic kidney disease. Curr. Opin. Nephrol. Hypertens. 2011, 20, 654-661.
4. Good, D. M., Zurbig, P., Argiles, A., Bauer, H. W. et al., Naturally occurring human urinary peptides for use in diagnosis of chronic kidney disease. Mol. Cell. Proteomics 2010, 9, 2424-2437.
5. Mischak, H., Schanstra, J. P., CE-MS in biomarker discovery, validation, and clinical application. Proteomics Clin. Appl. 2011, 5, 9-23.
6. Mischak, H., Coon, J. J., Novak, J., Weissinger, E. M. et al., Capillary electrophoresis-mass spectrometry as a powerful tool in biomarker discovery and clinical diagnosis: an update of recent developments. Mass Spectrom. Rev. 2009, 28, 703-724.
7. Ramautar, R., Heemskerk, A. A., Hensbergen, P. J., Deelder, A. M. et al., CE-MS for proteomics: advances in interface development and application. J. Proteomics 2012, 75, 3814-3828.
8. Ahmed, F. E., The role of capillary electrophoresis-mass spectrometry to proteome analysis and biomarker discovery. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2009, 877, 1963-1981.
9. Weissinger, E. M., Hertenstein, B., Mischak, H., Ganser, A., Online coupling of capillary electrophoresis with mass spectrometry for the identification of biomarkers for clinical diagnosis. Expert. Rev. Proteomics 2005, 2, 639-647.
10. Simpson, S. L., Jr., Quirino, J. P., Terabe, S., On-line sample preconcentration in capillary electrophoresis. Fundamentals and applications. J. Chromatogr A 2008, 1184, 504-541.
11. Jensen, P. K., Pasa-Tolic, L., Anderson, G. A., Horner, J. A. et al., Probing proteomes using capillary isoelectric focusing-electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 1999, 71, 2076-2084.
12. Pager, C., Vargova, A., Takacsi-Nagy, A., Dornyei, A., Kilar, F., Effect of electrolyte pH on CIEF with narrow pH range ampholytes. Electrophoresis 2012, 33, 3269-3275.
13. Simpson, D. C., Yates, A. J., Knox, J. H., Langridge-Smith, P. R. R. et al., A novel two-laser interface for coupling capillary electrochromatography with ion-trap time-of-flight mass spectrometry. Int. J. Mass Spectrom. 2014, 363, 8-15.
14. Coon, J. J., Zurbig, P., Dakna, M., Dominiczak, A. F. et al., CE-MS analysis of the human urinary proteome for biomarker discovery and disease diagnostics. Proteomics Clin. Appl. 2008, 2, 964-973.
15. Theodorescu, D., Fliser, D., Wittke, S., Mischak, H. et al., Pilot study of capillary electrophoresis coupled to mass spectrometry as a tool to define potential prostate cancer biomarkers in urine. Electrophoresis 2005, 26, 2797-2808.
16. Jahn, H., Wittke, S., Zurbig, P., Raedler, T. J. et al., Peptide fingerprinting of Alzheimer's disease in cerebrospinal fluid: identification and prospective evaluation of new synaptic biomarkers. PloS One 2011, 6, e26540.
17. Lankisch, T. O., Metzger, J., Negm, A. A., Vosskuhl, K. et al., Bile proteomic profiles differentiate cholangiocarcinoma from primary sclerosing cholangitis and choledocholithiasis. Hepatology 2011, 53, 875-884.
18. Schiffer, E., Liabeuf, S., Lacroix, C., Temmar, M. et al., Markers of vascular disease in plasma from patients with chronic kidney disease identified by proteomic analysis. J. Hypertens. 2011, 29, 783-790.
19. Ramautar, R., Somsen, G. W., deJong, G. J., Recent developments in coupled SPE-CE. Electrophoresis 2010, 31, 44-54.
20. Szabo, Z., Guttman, A., Rejtar, T., Karger, B. L., Improved sample preparation method for glycan analysis of glycoproteins by CE-LIF and CE-MS. Electrophoresis 2010, 31, 1389-1395.
21. Righetti, P. G., Sebastiano, R., Citterio, A., Capillary electrophoresis and isoelectric focusing in peptide and protein analysis. Proteomics 2013, 13, 325-340.
22. Haselberg, R., deJong, G. J., Somsen, G. W., CE-MS for the analysis of intact proteins 2010-2012. Electrophoresis 2013, 34, 99-112.
23. Huhn, C., Ramautar, R., Wuhrer, M., Somsen, G. W., Relevance and use of capillary coatings in capillary electrophoresis-mass spectrometry. Anal. Bioanal. Chem. 2010, 396, 297-314.
24. Pioch, M., Bunz, S. C., Neususs, C., Capillary electrophoresis/mass spectrometry relevant to pharmaceutical and biotechnological applications. Electrophoresis 2012, 33, 1517-1530.
25. Horvath, J., Dolnik, V., Polymer wall coatings for capillary electrophoresis. Electrophoresis 2001, 22, 644-655.
26. Taichrib, A., Pioch, M., Neususs, C., Toward a screening method for the analysis of small intact proteins by CE-ESI-TOF MS. Electrophoresis 2012, 33, 1356-1366.
27. Kolch, W., Neususs, C., Pelzing, M., Mischak, H. et al., Capillary electrophoresis-mass spectrometry as a powerful tool in clinical diagnosis and biomarker discovery. Mass Spectrom. Rev. 2005, 24, 959-977.
28. Hoffmann, T., Martin, M. M., CE-ESI-MS/MS as a rapid screening tool for the comparison of protein-ligand interactions. Electrophoresis 2010, 31, 1248-1255.
29. Wang, Y., Fonslow, B. R., Wong, C. C., Nakorchevsky, A., Yates, J. R., III, Improving the comprehensiveness and sensitivity of sheathless capillary electrophoresis-tandem mass spectrometry for proteomic analysis. Anal. Chem. 2012, 84, 8505-8513.
30. Faserl, K., Sarg, B., Kremser, L., Lindner, H. et al., Optimization and evaluation of a sheathless capillary electrophoresis-electrospray ionization mass spectrometry platform for peptide analysis: comparison to liquid chromatography-electrospray ionization mass spectrometry. Anal. Chem. 2011, 83, 7297-7305.
31. Stalmach, A., Albalat, A., Mullen, W., Mischak, H. et al., Recent advances in capillary electrophoresis coupled to mass spectrometry for clinical proteomic applications. Electrophoresis 2013, 34, 1452-1464.
32. Albalat, A., Mischak, H., Mullen, W., Clinical application of urinary proteomics/peptidomics. Exp. Rev. Proteomics 2011, 8, 615-629.
33. Latosinska, A., Frantzi, M., Vlahou, A., Mischak, H. et al., Clinical applications of capillary electrophoresis coupled to mass spectrometry in biomarker discovery: focus on bladder cancer. Proteomics Clin. Appl. 2013, 7, 779-793.
34. Metzger, J., Luppa, P. B., Good, D. M., Mischak, H. et al., Adapting mass spectrometry-based platforms for clinical proteomics applications: the capillary electrophoresis coupled mass spectrometry paradigm. Crit. Rev. Clin. Lab. Sci. 2009, 46, 129-152.
35. Mullen, W., Albalat, A., Gonzalez, J., Zerefos, P. et al., Performance of different separation methods interfaced in the same MS-reflection TOF detector: a comparison of performance between CE versus HPLC for biomarker analysis. Electrophoresis 2012, 33, 567-574.
36. Elhamili, A., Wetterhall, M., Arvidsson, B., Sebastiano, R. et al., Rapid capillary electrophoresis time-of-flight mass spectrometry separations of peptides and proteins using a monoquaternarized piperazine compound (M7C4I) for capillary coatings. Electrophoresis 2008, 29, 1619-1625.
37. Metzger, J., Luppa, P. B., Good, D. M., Mischak, H. et al., Adapting mass spectrometry-based platforms for clinical proteomics applications: the capillary electrophoresis coupled mass spectrometry paradigm. Crit. Rev. Clin. Lab. Sci. 2009, 46, 129-152.
38. Oh, E., Hasan, M. N., Jamshed, M., Park, S. H. et al., Growing trend of CE at the omics level: the frontier of systems biology. Electrophoresis 2010, 31, 74-92.
39. Haselberg, R., deJong, G. J., Somsen, G. W., Capillary electrophoresis-mass spectrometry of intact basic proteins using Polybrene-dextran sulfate-Polybrene-coated capillaries: system optimization and performance. Anal. Chim. Acta 2010, 678, 128-134.
40. Wojcik, R., Li, Y., Maccoss, M. J., Dovichi, N. J. et al., Capillary electrophoresis with Orbitrap-Velos mass spectrometry detection. Talanta 2012, 88, 324-329.
41. Haselberg, R., Ratnayake, C. K., deJong, G. J., Somsen, G. W. et al., Performance of a sheathless porous tip sprayer for capillary electrophoresis-electrospray ionization-mass spectrometry of intact proteins. J. Chromatogr. A 2010, 1217, 7605-7611.
42. Moini, M., Simplifying CE-MS operation. 2. Interfacing low-flow separation techniques to mass spectrometry using a porous tip. Anal. Chem. 2007, 79, 4241-4246.
43. Haselberg, R., deJong, G. J., Somsen, G. W., Low-flow sheathless capillary electrophoresis-mass spectrometry for sensitive glycoform profiling of intact pharmaceutical proteins. Anal. Chem. 2013, 85, 2289-2296.
44. Gahoual, R., Busnel, J. M., Wolff, P., Francois, Y. N., Leize-Wagner, E., Novel sheathless CE-MS interface as an original and powerful infusion platform for nanoESI study: from intact proteins to high molecular mass noncovalent complexes. Anal. Bioanal. Chem. 2014, 406, 1029-1038.
45. Bonvin, G., Veuthey, J. L., Rudaz, S., Schappler, J. et al., Evaluation of a sheathless nanospray interface based on a porous tip sprayer for CE-ESI-MS coupling. Electrophoresis 2012, 33, 552-562.
46. Zuberovic, A., Hanrieder, J., Hellman, U., Bergquist, J., Wetterhall, M., Proteome profiling of human cerebrospinal fluid: exploring the potential of capillary electrophoresis with surface modified capillaries for analysis of complex biological samples. Eur. J. Mass Spectrom. 2008, 14, 249-260.
47. Gaspar, A., Englmann, M., Fekete, A., Harir, M., Schmitt-Kopplin, P., Trends in CE-MS 2005-2006. Electrophoresis 2008, 29, 66-79.
48. Pantuckova, P., Gebauer, P., Bocek, P., Krivankova, L. et al., Recent advances in CE-MS: synergy of wet chemistry and instrumentation innovations. Electrophoresis 2011, 32, 43-51.
49. Maxwell, E. J., Zhong, X., Zhang, H., van, Z. N., Chen, D. D., Decoupling CE and ESI for a more robust interface with MS. Electrophoresis 2010, 31, 1130-1137.
50. Zhong, X., Maxwell, E. J., Chen, D. D., Mass transport in a micro flow-through vial of a junction-at-the-tip capillary electrophoresis-mass spectrometry interface. Anal. Chem. 2011, 83, 4916-4923.
51. Hasan, M. N., Park, S. H., Oh, E., Song, E. J. et al., Sensitivity enhancement of CE and CE-MS for the analysis of peptides by a dynamic pH junction. J. Sep. Sci. 2010, 33, 3701-3709.
52. Busnel, J. M., Josserand, J., Lion, N., Girault, H. H. et al., Iontophoretic fraction collection for coupling capillary zone electrophoresis with matrix-assisted laser desorption/ionization mass spectrometry. Anal. Chem. 2009, 81, 3867-3872.
53. Hommerson, P., Khan, A. M., deJong, G. J., Somsen, G. W. et al., Capillary electrophoresis-atmospheric pressure chemical ionization-mass spectrometry using an orthogonal interface: set-up and system parameters. J. Am. Soc. Mass Spectrom. 2009, 20, 1311-1318.
54. Tanaka, Y., Otsuka, K., Terabe, S., Evaluation of an atmospheric pressure chemical ionization interface for capillary electrophoresis-mass spectrometry. J. Pharm. Biomed. Anal. 2003, 30, 1889-1895.
55. Kannamkumarath, S. S., Wrobel, K., Wrobel, K., B'Hymer, C., Caruso, J. A., Capillary electrophoresis-inductively coupled plasma-mass spectrometry: an attractive complementary technique for elemental speciation analysis. J. Chromatogr. A 2002, 975, 245-266.
56. Fonslow, B. R., Yates, J. R., III, Capillary electrophoresis applied to proteomic analysis. J. Sep. Sci. 2009, 32, 1175-1188.
57. Molin, L., Seraglia, R., Lapolla, A., Ragazzi, E. et al., A comparison between MALDI-MS and CE-MS data for biomarker assessment in chronic kidney diseases. J. Proteomics 2012, 75, 5888-5897.
58. Mischak, H., Vlahou, A., Ioannidis, J. P., Technical aspects and inter-laboratory variability in native peptide profiling: the CE-MS experience. Clin. Biochem. 2013, 46, 432-443.
59. Li, Y., Champion, M. M., Sun, L., Champion, P. A. et al., Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry as an alternative proteomics platform to ultraperformance liquid chromatography-electrospray ionization-tandem mass spectrometry for samples of intermediate complexity. Anal. Chem. 2012, 84, 1617-1622.
60. Klein, J., Papadopoulos, T., Mischak, H., Mullen, W. et al., Comparison of CE-MS/MS and LC-MS/MS sequencing demonstrates significant complementarity in natural peptide identification in human urine. Electrophoresis 2014, 35, 1060-1064.
61. Mischak, H., Kolch, W., Aivaliotis, M., Bouyssie, D. et al., Comprehensive human urine standards for comparability and standardization in clinical proteome analysis. Proteomics Clin. Appl. 2010, 4, 464-478.
62. Zurbig, P., Jerums, G., Hovind, P., Macisaac, R. J. et al., Urinary proteomics for early diagnosis in diabetic nephropathy. Diabetes 2012, 61, 3304-3313.
63. Zurbig, P., Dihazi, H., Metzger, J., Thongboonkerd, V., Vlahou, A., Urine proteomics in kidney and urogenital diseases: moving towards clinical applications. Proteomics Clin. Appl. 2011, 5, 256-268.
64. Theodorescu, D., Schiffer, E., Bauer, H. W., Douwes, F. et al., Discovery and validation of urinary biomarkers for prostate cancer. Proteomics. Clin. Appl. 2008, 2, 556-570.
65. Elliott, M. H., Smith, D. S., Parker, C. E., Borchers, C. et al., Current trends in quantitative proteomics. J. Mass Spectrom. 2009, 44, 1637-1660.
66. Jantos-Siwy, J., Schiffer, E., Brand, K., Schumann, G. et al., Quantitative urinary proteome analysis for biomarker evaluation in chronic kidney disease. J. Proteome Res. 2009, 8, 268-281.
67. Zurbig, P., Decramer, S., Dakna, M., Jantos, J. et al., The human urinary proteome reveals high similarity between kidney aging and chronic kidney disease. Proteomics 2009, 9, 2108-2117.
68. Zurbig, P., Renfrow, M. B., Schiffer, E., Novak, J. et al., Biomarker discovery by CE-MS enables sequence analysis via MS/MS with platform-independent separation. Electrophoresis 2006, 27, 2111-2125.
69. Rejtar, T., Hu, P., Juhasz, P., Campbell, J. M. et al., Off-line coupling of high-resolution capillary electrophoresis to MALDI-TOF and TOF/TOF MS. J. Proteome Res. 2002, 1, 171-179.
70. Chalmers, M. J., Mackay, C. L., Hendrickson, C. L., Wittke, S. et al., Combined top-down and bottom-up mass spectrometric approach to characterization of biomarkers for renal disease. Anal. Chem. 2005, 77, 7163-7171.
71. Zhu, G., Sun, L., Yan, X., Dovichi, N. J. et al., Bottom-up proteomics of Escherichia coli using dynamic pH junction preconcentration and capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry. Anal. Chem. 2014, 86, 6331-6336.
72. Mikulikova, K., Eckhardt, A., Pataridis, S., Miksik, I. et al., Study of posttranslational non-enzymatic modifications of collagen using capillary electrophoresis/mass spectrometry and high performance liquid chromatography/mass spectrometry. J. Chromatogr. A 2007, 1155, 125-133.
73. Mischak, H., Allmaier, G., Apweiler, R., Attwood, T. et al., Recommendations for biomarker identification and qualification in clinical proteomics. Sci. Transl. Med. 2010, 2, 46ps42.
74. Dakna, M., Harris, K., Kalousis, A., Carpentier, S. et al., Addressing the challenge of defining valid proteomic biomarkers and classifiers. BMC Bioinformatics 2010, 11, 594.
75. Fuzery, A. K., Levin, J., Chan, M. M., Chan, D. W. et al., Translation of proteomic biomarkers into FDA approved cancer diagnostics: issues and challenges. Clin. Proteomics 2013, 10, 13.
76. Desiderio, C., Rossetti, D. V., Iavarone, F., Messana, I., Castagnola, M., Capillary electrophoresis-mass spectrometry: recent trends in clinical proteomics. J. Pharm. Biomed. Anal. 2010, 53, 1161-1169.
77. Rodriguez-Suarez, E., Siwy, J., Zurbig, P., Mischak, H. et al., Urine as a source for clinical proteome analysis: from discovery to clinical application. Biochim. Biophys. Acta 2014, 1844, 884-898.
78. Decramer, S., Gonzalez de Peredo, A., Breuil, B., Mischak, H. et al., Urine in clinical proteomics. Mol. Cell. Proteomics 2008, 7, 1850-1862.
79. Yin, P., Knolhoff, A. M., Rosenberg, H. J., Millet, L. J. et al., Peptidomic analyses of mouse astrocytic cell lines and rat primary cultured astrocytes. J. Proteome Res. 2012, 11, 3965-3973.
80. Fricker, L. D., Analysis of mouse brain peptides using mass spectrometry-based peptidomics: implications for novel functions ranging from non-classical neuropeptides to microproteins. Mol. bioSyst. 2010, 6, 1355-1365.
81. von zur Muhlen, C., Schiffer, E., Sackmann, C., Zurbig, P. et al., Urine proteome analysis reflects atherosclerotic disease in an ApoE-/- mouse model and allows the discovery of new candidate biomarkers in mouse and human atherosclerosis. Mol. Cell. Proteomics 2012, 11, M111 013847.
82. Dissard, R., Klein, J., Caubet, C., Breuil, B. et al., Long term metabolic syndrome induced by a high fat high fructose diet leads to minimal renal injury in C57BL/6 mice. PloS One 2013, 8, e76703.
83. Ongay, S., Neususs, C., Isoform differentiation of intact AGP from human serum by capillary electrophoresis-mass spectrometry. Anal. Bioanal. Chem. 2010, 398, 845-855.
84. Siwy, J., Zoja, C., Klein, J., Benigni, A. et al., Evaluation of the Zucker diabetic fatty (ZDF) rat as a model for human disease based on urinary peptidomic profiles. PloS One 2012, 7, e51334.
85. Delles, C., Schiffer, E., vonZur Muhlen, C., Peter, K. et al., Urinary proteomic diagnosis of coronary artery disease: identification and clinical validation in 623 individuals. J. Hypertens. 2010, 28, 2316-2322.
86. Sun, L., Zhu, G., Li, Y., Wojcik, R. et al., CZE-ESI-MS/MS system for analysis of subnanogram amounts of tryptic digests of a cellular homogenate. Proteomics 2012, 12, 3013-3019.
87. Wang, C., Lee, C. S., Smith, R. D., Tang, K. et al., Ultrasensitive sample quantitation via selected reaction monitoring using CITP/CZE-ESI-triple quadrupole MS. Anal. Chem. 2012, 84, 10395-10403.
88. Listgarten, J., Emili, A., Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics 2005, 4, 419-434.
89. America, A. H., Cordewener, J. H., Comparative LC-MS: a landscape of peaks and valleys. Proteomics 2008, 8, 731-749.
90. Radulovic, D., Jelveh, S., Ryu, S., Hamilton, T. G. et al., Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics 2004, 3, 984-997.
91. Weissinger, E. M., Wittke, S., Kaiser, T., Haller, H. et al., Proteomic patterns established with capillary electrophoresis and mass spectrometry for diagnostic purposes. Kidney Int. 2004, 65, 2426-2434.