Classical MALDI-MS versus CE-based ESI-MS proteomic profiling in urine for clinical applications

Bioanalysis

Volumn 6, Issue 2, 2014, Pages 247-266

  Albalat, Amaya ^a,b   Husi, Holger ^b   Stalmach, Angelique ^b   Schanstra, Joost P ^c   Mischak, Harald ^b,d  

^a UNIVERSITY OF STIRLING   (United Kingdom)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

^c University Hospital of Toulouse   (France)

^d MOSAIQUES DIAGNOSTICS GMBH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; PROTEOME; TUMOR MARKER;

BILE DUCT CARCINOMA; BLADDER CANCER; CHRONIC KIDNEY DISEASE; COMPARATIVE STUDY; DIABETIC NEPHROPATHY; ELECTROSPRAY MASS SPECTROMETRY; HUMAN; MASS SPECTROMETRY; PROSTATE CANCER; PROTEIN MICROARRAY; PROTEOMIC PROFILING; PROTEOMICS; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; REVIEW; URINALYSIS;

ELECTROPHORESIS, CAPILLARY; HUMANS; NEOPLASMS; PEPTIDES; PROTEOME; PROTEOMICS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TUMOR MARKERS, BIOLOGICAL;

EID: 84892712389     PISSN: 17576180     EISSN: 17576199     Source Type: Journal    
DOI: 10.4155/bio.13.313     Document Type: Review

References (147)

1. Altelaar AF, Munoz J, Heck AJ. Next-generation proteomics: towards an integrative view of proteome dynamics. Nat. Rev. Genet. 14(1), 35-48 (2013).
2. Bakry R, Rainer M, Huck CW, Bonn GK: Protein profiling for cancer biomarker discovery using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and infrared imaging: a review. Anal. Chim. Acta 690(1), 26-34 (2011).
3. Biomarkers Definitions Working Group. Biomarkers and surrogate endpoints: preferred definitions and conceptual framework. Clin. Pharmacol. Ther. 69(3), 89-95 (2001).
4. Mischak H, Apweiler R, Banks RE et al. Clinical proteomics: a need to define the field and to begin to set adequate standards. Proteomics. Clin. Appl. 1(2), 148-156 (2007).
5. Hessels D, Schalken JA. Urinary biomarkers for prostate cancer: a review. Asian J. Androl. 15(3), 333-339 (2013).
6. Fung ET. A recipe for proteomics diagnostic test development: the OVA1 test, from biomarker discovery to FDA clearance. Clin. Chem. 56(2), 327-329 (2010).
7. Sigdel TK, Lee S, Sarwal MM. Profiling the proteome in renal transplantation. Proteomics. Clin. Appl. 5(5-6), 269-280 (2011).
8. Kondo T. Inconvenient truth: cancer biomarker development by using proteomics. Biochim. Biophys. Acta doi:10.1016/j.bbapap.2013.07.009 (2013) (Epub ahead of print).
9. Petter CH, Heigl N, Bachmann S et al. Near infrared spectroscopy compared to liquid chromatography coupled to mass spectrometry and capillary electrophoresis as a detection tool for peptide reaction monitoring. Amino. Acids 34(4), 605-616 (2008).
10. Mallia RJ, McVeigh PZ, Veilleux I, Wilson BC. Filter-based method for background removal in high-sensitivity wide-field-surface-enhanced Raman scattering imaging in vivo. J. Biomed. Opt. 17(7), 076017 (2012).
11. Tu C, Rudnick PA, Martinez MY et al. Depletion of abundant plasma proteins and limitations of plasma proteomics. J. Proteome. Res. 9(10), 4982-4991 (2010).
12. Lu J, Huang Y, Wang Y et al. Profiling plasma peptides for the identification of potential ageing biomarkers in Chinese Han adults. PLoS ONE 7(7), e39726 (2012).
13. Mateos J, Lourido L, Fernandez-Puente P et al. Differential protein profiling of synovial fluid from rheumatoid arthritis and osteoarthritis patients using LC-MALDI TOF/TOF. J. Proteomics. 75(10), 2869-2878 (2012).
14. Beer LA, Tang HY, Barnhart KT, Speicher DW. Plasma biomarker discovery using 3D protein profiling coupled with label-free quantitation. Methods Mol. Biol. 728, 3-27 (2011).
15. Silbiger VN, Luchessi AD, Hirata RD et al. Time course proteomic profiling of human myocardial infarction plasma samples: an approach to new biomarker discovery. Clin. Chim. Acta 412(11-12), 1086-1093 (2011).
16. Schiffer E, Liabeuf S, Lacroix C et al. Markers of vascular disease in plasma from patients with chronic kidney disease identified by proteomic analysis. J. Hypertens. 29(4), 783-790 (2011).
17. Albrethsen J, Bogebo R, Moller CH, Olsen JA, Raskov HH, Gammeltoft S. Candidate biomarker verification: Critical examination of a serum protein pattern for human colorectal cancer. Proteomics. Clin. Appl. 6(3-4), 182-189 (2012).
18. Simonsen AH, Bahl JM, Danborg PBet al. Pre-analytical factors influencing the stability of cerebrospinal fluid proteins. J. Neurosci. Methods 215(2), 234-240 (2013).
19. Bruegel M, Planert M, Baumann S et al. Standardized peptidome profiling of human cerebrospinal fluid by magnetic bead separation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J. Proteomics. 72(4), 608-615 (2009).
20. Albalat A, Bitsika V, Zurbig P, Siwy J, Mullen W. High-resolution proteome/peptidome analysis of body fluids by capillary electrophoresis coupled with MS. Methods Mol. Biol. 984, 153-165 (2013).
21. Huang JT, McKenna T, Hughes C, Leweke FM, Schwarz E, Bahn S. CSF biomarker discovery using label-free nano-LC-MS based proteomic profiling: technical aspects. J. Sep. Sci. 30(2), 214-225 (2007).
22. Teunissen CE, Koel-Simmelink MJ, Pham TV et al. Identification of biomarkers for diagnosis and progression of MS by MALDI-TOF mass spectrometry. Mult. Scler. 17(7), 838-850 (2011).
23. Simonsen AH, McGuire J, Hansson O et al. Novel panel of cerebrospinal fluid biomarkers for the prediction of progression to Alzheimer dementia in patients with mild cognitive impairment. Arch. Neurol. 64(3), 366-370 (2007).
24. Ditzen C, Tang N, Jastorff AM et al. Cerebrospinal fluid biomarkers for major depression confirm relevance of associated pathophysiology. Neuropsychopharmacology 37(4), 1013-1025 (2012).
25. Qualtieri A, Urso E, Le PM et al. Proteomic profiling of cerebrospinal fluid in Creutzfeldt-Jakob disease. Expert. Rev. Proteomics. 7(6), 907-917 (2010).
26. Constantinescu R, Andreasson U, Li S et al. Proteomic profiling of cerebrospinal fluid in parkinsonian disorders. Parkinsonism. Relat. Disord. 16(8), 545-549 (2010).
27. Amado FM, Ferreira RP, Vitorino R. One decade of salivary proteomics: current approaches and outstanding challenges. Clin. Biochem. 46(6), 506-517 (2013).
28. Denny P, Hagen FK, Hardt M et al. The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions. J. Proteome. Res. 7(5), 1994-2006 (2008).
29. Wilmarth PA, Riviere MA, Rustvold DL, Lauten JD, Madden TE, David LL. Two-dimensional liquid chromatography study of the human whole saliva proteome. J. Proteome. Res. 3(5), 1017-1023 (2004).
30. Hu S, Xie Y, Ramachandran P et al. Large-scale identification of proteins in human salivary proteome by liquid chromatography/mass spectrometry and two-dimensional gel electrophoresis-mass spectrometry. Proteomics 5(6), 1714-1728 (2005).
31. Spielmann N, Wong DT. Saliva: diagnostics and therapeutic perspectives. Oral Dis. 17(4), 345-354 (2011).
32. Lescuyer P, Hochstrasser D, Rabilloud T. How shall we use the proteomics toolbox for biomarker discovery? J. Proteome. Res. 6(9), 3371-3376 (2007).
33. Grau L, Luque-Garcia JL, Gonzalez-Peramato P et al. A quantitative proteomic analysis uncovers the relevance of CUL3 in bladder cancer aggressiveness. PLoS ONE 8(1), e53328 (2013).
34. Attarha S, Andersson S, Mints M, Souchelnytskyi S. Individualised proteome profiling of human endometrial tumours improves detection of new prognostic markers. Br. J. Cancer 109(3), 704-713 (2013).
35. Thongboonkerd V. Urinary proteomics: towards biomarker discovery, diagnostics and prognostics. Mol. Biosyst. 4(8), 810-815 (2008).
36. Mischak H, Massy ZA, Jankowski J. Proteomics in uremia and renal disease. Semin. Dial. 22(4), 409-416 (2009).
37. Vestergaard P, Leverett R. Constancy of urinary creatinine excretion. J. Lab. Clin. Med. 51(2), 211-218 (1958).
38. Mischak H, Kolch W, Aivaliotis M et al. Comprehensive human urine standards for comparability and standardization in clinical proteome analysis. Proteomics. Clin. Appl. 4(4), 464-478 (2010).
39. Zerefos PG, Aivaliotis M, Baumann M, Vlahou A. Analysis of the urine proteome via a combination of multi-dimensional approaches. Proteomics 12(3), 391-400 (2012).
40. Lei T, Zhao X, Jin S, Meng Q, Zhou H, Zhang M: Discovery of potential bladder cancer biomarkers by comparative urine proteomics and analysis. Clin. Genitourin. Cancer 11(1), 56-62 (2013).
41. Lamoureux L, Simon SL, Plews M et al. Urine proteins identified by two-dimensional differential gel electrophoresis facilitate the differential diagnoses of scrapie. PLoS ONE 8(5), e64044 (2013).
42. Sigdel TK, Kaushal A, Gritsenko M et al. Shotgun proteomics identifies proteins specific for acute renal transplant rejection. Proteomics. Clin. Appl. 4(1), 32-47 (2010).
43. Husi H, Stephens N, Cronshaw A et al. Proteomic analysis of urinary upper gastrointestinal cancer markers. Proteomics. Clin. Appl. 5(5-6), 289-299 (2011).
44. Albalat A, Stalmach A, Bitsika V et al. Improving peptide relative quantification in MALDI-TOF MS for biomarker assessment. Proteomics 13(20), 2967-2975 (2013).
45. Latosinska A, Frantzi M, Vlahou A, Mischak H. Clinical applications of capillary electrophoresis coupled to mass spectrometry in biomarker discovery: focus on bladder cancer. Proteomics. Clin. Appl. doi:10.1002/prca.201300038 (2013) (Epub ahead of print).
46. Mischak H, Schanstra JP. CE-MS in biomarker discovery, validation, and clinical application. Proteomics. Clin. Appl. 5(1-2), 9-23 (2011).
47. Albrethsen J, Bogebo R, Olsen J, Raskov H, Gammeltoft S. Preanalytical and analytical variation of surface-enhanced laser desorption-ionization time-of-flight mass spectrometry of human serum. Clin. Chem. Lab. Med. 44(10), 1243-1252 (2006).
48. Neuhoff N, Kaiser T, Wittke S et al. Mass spectrometry for the detection of differentially expressed proteins: a comparison of surface-enhanced laser desorption/ionization and capillary electrophoresis/mass spectrometry. Rapid Commun. Mass Spectrom. 18(2), 149-156 (2004).
49. Callesen AK, Mogensen O, Jensen AK et al. Reproducibility of mass spectrometry based protein profiles for diagnosis of ovarian cancer across clinical studies: a systematic review. J. Proteomics 75(10), 2758-2772 (2012).
50. Kulasingam V, Pavlou MP, Diamandis EP. Integrating high-throughput technologies in the quest for effective biomarkers for ovarian cancer. Nat. Rev. Cancer 10(5), 371-378 (2010).
51. Lossner C, Wee S, Ler SG et al. Expanding the zebrafish embryo proteome using multiple fractionation approaches and tandem mass spectrometry. Proteomics 12(11), 1879-1882 (2012).
52. Kellie JF, Catherman AD, Durbin KR et al. Robust analysis of the yeast proteome under 50 kDa by molecular-mass-based fractionation and top-down mass spectrometry. Anal. Chem. 84(1), 209-215 (2012).
53. Labenski MT, Fisher AA, Monks TJ, Lau SS. Identification of chemical-adducted proteins in urine by multi-dimensional protein identification technology (LC/LC-MS/MS). Methods Mol. Biol. 691, 339-347 (2011).
54. Mullen W, Albalat A, Gonzalez J 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 33(4), 567-574 (2012).
55. Eeltink S, Dolman S, Detobel F, Swart R, Ursem M, Schoenmakers PJ. High-efficiency liquid chromatography-mass spectrometry separations with 50 mm, 250 mm, and 1 m long polymer-based monolithic capillary columns for the characterization of complex proteolytic digests. J. Chromatogr. A 1217(43), 6610-6615 (2010).
56. Peffers MJ, Beynon RJ, Clegg PD. Absolute quantification of selected proteins in the human osteoarthritic secretome. Int. J. Mol. Sci. 14(10), 20658-20681 (2013).
57. Tsai TH, Tadesse MG, Di PC et al. Multi-profile Bayesian alignment model for LC-MS data analysis with integration of internal standards. Bioinformatics 29(21), 2774-2780 (2013).
58. Beavis RC, Chait BT. Matrix-assisted laser desorption ionization mass-spectrometry of proteins. Methods Enzymol. 270, 519-551 (1996).
59. Beavis RC, Chait BT. Cinnamic acid derivatives as matrices for ultraviolet laser desorption mass spectrometry of proteins. Rapid Commun. Mass Spectrom. 3(12), 432-435 (1989).
60. Tsarbopoulos A, Karas M, Strupat K, Pramanik BN, Nagabhushan TL, Hillenkamp F. Comparative mapping of recombinant proteins and glycoproteins by plasma desorption and matrix-assisted laser desorption/ionization mass spectrometry. Anal. Chem. 66(13), 2062-2070 (1994).
61. Jaskolla TW, Lehmann WD, Karas M. 4-Chloro-alpha-cyanocinnamic acid is an advanced, rationally designed MALDI matrix. Proc. Natl Acad. Sci. USA 105(34), 12200-12205 (2008).
62. Thomas H, Havlis J, Peychl J, Shevchenko A. Dried-droplet probe preparation on AnchorChip targets for navigating the acquisition of matrix-assisted laser desorption/ionization time-of-flight spectra by fluorescence of matrix/analyte crystals. Rapid Commun. Mass Spectrom. 18(9), 923-930 (2004).
63. Karas M, Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 60(20), 2299-2301 (1988).
64. Vorm O, Mann M. Improved mass accuracy in matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry of peptides. J. Am. Soc. Mass Spectrom. 5(11), 955-958 (1994).
65. Albrethsen J. The first decade of MALDI protein profiling: a lesson in translational biomarker research. J. Proteomics 74(6), 765-773 (2011).
66. Gorka J, Bahr U, Karas M. Graphite supported preparation (GSP) of alpha-cyano-4-hydroxycinnamic acid (CHCA) for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for peptides and proteins. J. Am. Soc. Mass Spectrom. 23(11), 1949-1954 (2012).
67. Jaskolla TW, Papasotiriou DG, Karas M. Comparison between the matrices alpha-cyano-4-hydroxycinnamic acid and 4-chloro-alpha-cyanocinnamic acid for trypsin, chymotrypsin, and pepsin digestions by MALDI-TOF mass spectrometry. J. Proteome. Res. 8(7), 3588-3597 (2009).
68. Pan C, Xu S, Zhou H, Fu Y, Ye M, Zou H. Recent developments in methods and technology for analysis of biological samples by MALDI-TOF-MS. Anal. Bioanal. Chem. 387(1), 193-204 (2007).
69. Vestal ML. Modern MALDI time-of-flight mass spectrometry. J. Mass Spectrom. 44(3), 303-317 (2009).
70. Zerefos P, Prados J, Kossida S, Kalousis A, Vlahou A. Sample preparation and bioinformatics in MALDI profiling of urinary proteins. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 853(1-2), 20-30 (2007).
71. Vitzthum F, Behrens F, Anderson NL,Shaw JH. Proteomics: from basic research to diagnostic application. A review of requirements and needs. J. Proteome. Res. 4(4), 1086-1097 (2005).
72. Szajli E, Feher T, Medzihradszky KF. Investigating the quantitative nature of MALDI-TOF MS. Mol. Cell Proteomics 7(12), 2410-2418 (2008).
73. Cohen SL, Chait BT. Influence of matrix solution conditions on the MALDI-MS analysis of peptides and proteins. Anal. Chem. 68(1), 31-37 (1996).
74. Krause E, Wenschuh H, Jungblut PR. The dominance of arginine-containing peptides in MALDI-derived tryptic mass fingerprints of proteins. Anal. Chem. 71(19), 4160-4165 (1999).
75. Amado FM, Domingues P, Graca Santana-Marques M, Ferrer-Correira AJ, Tomer KB. Discrimination effects and sensitivity variations in matrix-assisted laser desorption/ionisation. Rapid Commun. Mass Spectrom. 11, 1347-1352 (1997).
76. Fliser D, Novak J, Thongboonkerd V et al. Advances in urinary proteome analysis and biomarker discovery. J. Am. Soc. Nephrol. 18(4), 1057-1071 (2007).
77. Haselberg R, de Jong GJ, Somsen GW. Capillary electrophoresis-mass spectrometry for the analysis of intact proteins. J. Chromatogr. A 1159(1-2), 81-109 (2007).
78. Simpson DC, Smith RD. Combining capillary electrophoresis with mass spectrometry for applications in proteomics. Electrophoresis 26(7-8), 1291-1305 (2005).
79. Kolch W, Neususs C, Pelzing M, Mischak H. Capillary electrophoresis-mass spectrometry as a powerful tool in clinical diagnosis and biomarker discovery. Mass Spectrom. Rev. 24(6), 959-977 (2005).
80. Whatley H. Basic principles and modes of Capillary Electrophoresis. In: Clinical and Forensic Application of Capillary Electrophoresis. Petersen RJ, Mohammad AA (Eds.). Humana Press Inc., NY, USA 21-58 (2001).
81. Frommberger M, Zurbig P, Jantos J et al. Peptidomic analysis of rat urine using capillary electrophoresis coupled to mass spectrometry. Proteomics Clin. Appl. 1(7), 650-660 (2007).
82. Siwy J, Mullen W, Golovko I, Franke J, Zurbig P. Human urinary peptide database for multiple disease biomarker discovery. Proteomics Clin. Appl. 5(5-6), 367-374 (2011).
83. Mischak H, Coon JJ, Novak J, Weissinger EM, Schanstra JP, Dominiczak AF. Capillary electrophoresis-mass spectrometry as a powerful tool in biomarker discovery and clinical diagnosis: an update of recent developments. Mass Spectrom. Rev. 28(5), 703-724 (2009).
84. Beleslin DB, Jovanovic-Micic D, Nikolic SB, Samardzic R. Selective effect of ethanol on norepinephrine-and nicotine-induced emesis in cats. Alcohol 8(6), 499-501 (1991).
85. Maxwell EJ, Chen DD. Twenty years of interface development for capillary electrophoresis-electrospray ionization-mass spectrometry. Anal. Chim. Acta 627(1), 25-33 (2008).
86. Gahoual R, Busnel JM, Wolff P, Francois YN, 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. doi:10.1007/s00216-013-7226-1 (2013) (Epub ahead of print).
87. Zurbig P, Renfrow MB, Schiffer E et al. Biomarker discovery by CE-MS enables sequence analysis via MS/MS with platform-independent separation. Electrophoresis 27(11), 2111-2125 (2006).
88. Bakry R, Huck CW, Najam-ul-Haq M, Rainer M, Bonn GK. Recent advances in capillary electrophoresis for biomarker discovery. J. Sep. Sci. 30(2), 192-201 (2007).
89. Song EJ, Babar SM, Oh E, Hasan MN, Hong HM, Yoo YS. CE at the omics level: towards systems biology-an update. Electrophoresis 29(1), 129-142 (2008).
90. Pantuckova P, Gebauer P, Bocek P, Krivankova L. Electrolyte systems for on-line CE-MS: detection requirements and separation possibilities. Electrophoresis 30(1), 203-214 (2009).
91. Pioch M, Bunz SC, Neususs C. Capillary electrophoresis/mass spectrometry relevant to pharmaceutical and biotechnological applications. Electrophoresis 33(11), 1517-1530 (2012).
92. Kaiser T, Wittke S, Just I et al. Capillary electrophoresis coupled to mass spectrometer for automated and robust polypeptide determination in body fluids for clinical use. Electrophoresis 25(13), 2044-2055 (2004).
93. Wittke S, Fliser D, Haubitz M et al. Determination of peptides and proteins in human urine with capillary electrophoresis-mass spectrometry, a suitable tool for the establishment of new diagnostic markers. J. Chromatogr. A 1013(1-2), 173-181(2003).
94. Mischak H, Vlahou A, Ioannidis JP. Technical aspects and inter-laboratory variability in native peptide profiling: the CE-MS experience. Clin. Biochem. 46(6), 432-443 (2013).
95. Stalmach A, Albalat A, Mullen W, Mischak H. Recent advances in capillary electrophoresis coupled to mass spectrometry for clinical proteomic applications. Electrophoresis 34(11), 1452-1464 (2013).
96. Flatley B, Malone P, Cramer R. MALDI mass spectrometry in prostate cancer biomarker discovery. Biochim. Biophys. Acta doi:10.1016/j.bbapap.2013.06.015 (2013) (Epub ahead of print).
97. M'Koma AE, Blum DL, Norris JL et al. Detection of pre-neoplastic and neoplastic prostate disease by MALDI profiling of urine. Biochem. Biophys. Res. Commun. 353(3), 829-834 (2007).
98. Fiedler GM, Ceglarek U, Leichtle A, Thiery J. Standardized preprocessing of urine for proteome analysis. Methods Mol. Biol. 641, 47-63 (2010).
99. Iloro I, Gonzalez E, Gutierrez-de Juan V, Mato JM, Falcon-Perez JM, Elortza F. Non-invasive detection of drug toxicity in rats by solid-phase extraction and MALDI-TOF analysis of urine samples. Anal. Bioanal. Chem. 405(7), 2311-2320 (2013).
100. Calvano CD, Aresta A, Iacovone M et al. Optimization of analytical and pre-analytical conditions for MALDI-TOF-MS human urine protein profiles. J. Pharm. Biomed. Anal. 51(4), 907-914 (2010).
101. Malyarenko DI, Cooke WE, Adam BL et al. Enhancement of sensitivity and resolution of surface-enhanced laser desorption/ionization time-of-flight mass spectrometric records for serum peptides using time-series analysis techniques. Clin. Chem. 51(1), 65-74 (2005).
102. Ling XB, Mellins ED, Sylvester KG, Cohen HJ. Urine peptidomics for clinical biomarker discovery. Adv. Clin. Chem. 51, 181-213 (2010).
103. Penno MA, Ernst M, Hoffmann P. Optimal preparation methods for automated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling of low molecular weight proteins and peptides. Rapid Commun. Mass Spectrom. 23(17), 2656-2662 (2009).
104. Zurbig P, Schiffer E, Mischak H. Capillary electrophoresis coupled to mass spectrometry for proteomic profiling of human urine and biomarker discovery. Methods Mol.Biol. 564, 105-121 (2009).
105. Albrethsen J. Reproducibility in protein profiling by MALDI-TOF mass spectrometry. Clin. Chem. 53(5), 852-858 (2007).
106. Duncan MW, Roder H, Hunsucker SW. Quantitative matrix-assisted laser desorption/ionization mass spectrometry. Brief. Funct. Genomic. Proteomic. 7(5), 355-370 (2008).
107. Taguchi F, Solomon B, Gregorc V et al. Mass spectrometry to classify non-small-cell lung cancer patients for clinical outcome after treatment with epidermal growth factor receptor tyrosine kinase inhibitors: a multicohort cross-institutional study. J. Natl. Cancer Inst. 99(11), 838-846 (2007).
108. Jantos-Siwy J, Schiffer E, Brand K et al. Quantitative urinary proteome analysis for biomarker evaluation in chronic kidney disease. J. Proteome. Res. 8(1), 268-281 (2009).
109. Molin L, Seraglia R, Lapolla A et al. A comparison between MALDI-MS and CE-MS data for biomarker assessment in chronic kidney diseases. J. Proteomics 75(18), 5888-5897 (2012).
110. Yan X, Essaka DC, Sun L, Zhu G, Dovichi NJ. Bottom-up proteome analysis of E. coli using capillary zone electrophoresis-tandem mass spectrometry with an electrokinetic sheath-flow electrospray interface. Proteomics 13(17), 2546-2551 (2013).
111. Klein J, Papadopoulos T, Mischak H, Mullen W. Comparison of CE-MS/MS and LC-MS/MS sequencing demonstrates significant complementarity in natural peptide identification in human urine. Electrophoresis doi: 10.1002/elps.201300327 (2013) (Epub ahead of print).
112. Kikkawa S, Sogawa K, Satoh M et al. Identification of a novel biomarker for biliary tract cancer using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Int. J. Proteomics, Article ID 108609 (2012).
113. Debois D, Smargiasso N, Demeure K et al. MALDI in-source decay, from sequencing to imaging. Top. Curr. Chem. 331, 117-141 (2013).
114. Jorgensen C, Locard-Paulet M: Analysing signalling networks by mass spectrometry. Amino. Acids 43(3), 1061-1074 (2012).
115. Dumas ME. Metabolome 2.0: quantitative genetics and network biology of metabolic phenotypes. Mol.Biosyst. 8(10), 2494-2502 (2012).
116. Kohl M, Megger DA, Trippler M et al. A practical data processing workflow for multi-OMICS projects. Biochim. Biophys. Acta doi:10.1016/j.bbapap.2013.02. 029 (2013) (Epub ahead of print).
117. Hood L, Balling R, Auffray C. Revolutionizing medicine in the 21st century through systems approaches. Biotechnol. J. 7(8), 992-1001 (2012).
118. Weston AD, Hood L. Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine. J. Proteome. Res. 3(2), 179-196 (2004).
119. Waters KM, Pounds JG, Thrall BD. Data merging for integrated microarray and proteomic analysis. Brief. Funct. Genomic. Proteomic. 5(4), 261-272 (2006).
120. Sefcik LS, Wilson JL, Papin JA, Botchwey EA. Harnessing systems biology approaches to engineer functional microvascular networks. Tissue Eng. Part B Rev. 16(3), 361-370 (2010).
121. Katoh M, Katoh M. Bioinformatics for cancer management in the post-genome era. Technol. Cancer Res. Treat. 5(2), 169-175 (2006).
122. Quackenbush J. Data standards for 'omic' science. Nat. Biotechnol. 22(5), 613-614 (2004).
123. Theodorescu D, Wittke S, Ross MM et al. Discovery and validation of new protein biomarkers for urothelial cancer: a prospective analysis. Lancet Oncol. 7(3), 230-240 (2006).
124. Schiffer E, Vlahou A, Petrolekas A et al. Prediction of muscle-invasive bladder cancer using urinary proteomics. Clin. Cancer Res. 15(15), 4935-4943 (2009).
125. Bryan RT, Wei W, Shimwell NJ et al. Assessment of high-throughput high-resolution MALDI-TOF-MS of urinary peptides for the detection of muscle-invasive bladder cancer. Proteomics Clin. Appl. 5(9-10), 493-503 (2011).
126. Theodorescu D, Fliser D, Wittke S et al. Pilot study of capillary electrophoresis coupled to mass spectrometry as a tool to define potential prostate cancer biomarkers in urine. Electrophoresis 26(14), 2797-2808 (2005).
127. Decramer S, Gonzalez de PA, Breuil B et al. Urine in clinical proteomics. Mol. Cell Proteomics 7(10), 1850-1862 (2008).
128. Theodorescu D, Schiffer E, Bauer HW et al. Discovery and validation of urinary biomarkers for prostate cancer. Proteomics. Clin. Appl. 2(4), 556-570 (2008).
129. Voss JS, Holtegaard LM, Kerr SE et al. Molecular profiling of cholangiocarcinoma shows potential for targeted therapy treatment decisions. Hum. Pathol. 44(7), 1216-1222 (2013).
130. Sriwanitchrak P, Viyanant V, Chaijaroenkul W et al. Proteomics analysis and evaluation of biomarkers for detection of cholangiocarcinoma. Asian Pac. J. Cancer Prev. 12(6), 1503-1510 (2011).
131. Yonglitthipagon P, Pairojkul C, Bhudhisawasdi V, Mulvenna J, Loukas A, Sripa B. Proteomics-based identification of alpha-enolase as a potential prognostic marker in cholangiocarcinoma. Clin. Biochem. 45(10-11), 827-834 (2012).
132. Metzger J, Negm AA, Plentz RR et al. Urine proteomic analysis differentiates cholangiocarcinoma from primary sclerosing cholangitis and other benign biliary disorders. Gut 62(1), 122-130 (2013).
133. Wen CP, Cheng TY, Tsai MK et al. All-cause mortality attributable to chronic kidney disease: a prospective cohort study based on 462 293 adults in Taiwan. Lancet 371(9631), 2173-2182 (2008).
134. Good DM, Zurbig P, Argiles A et al. Naturally occurring human urinary peptides for use in diagnosis of chronic kidney disease. Mol. Cell Proteomics. 9(11), 2424-2437 (2010).
135. Lapolla A, Seraglia R, Molin L et al.Low molecular weight proteins in urines from healthy subjects as well as diabetic, nephropathic and diabetic-nephropathic patients: a MALDI study. J. Mass Spectrom. 44(3), 419-425 (2009).
136. Lapolla A, Molin L, Sechi A et al. A further investigation on a MALDI-based method for evaluation of markers of renal damage. J. Mass Spectrom. 44(12), 1754-1760 (2009).
137. Molin L, Seraglia R, Lapolla A et al. A comparison between MALDI-MS and CE-MS data for biomarker assessment in chronic kidney diseases. J. Proteomics 75(18), 5888-5897 (2012).
138. Thongboonkerd V. Study of diabetic nephropathy in the proteomic era. Contrib.Nephrol. 170, 172-183 (2011).
139. Meier M, Kaiser T, Herrmann A et al. Identification of urinary protein pattern in Type 1 diabetic adolescents with early diabetic nephropathy by a novel combined proteome analysis. J. Diabetes Complications 19(4), 223-232 (2005).
140. Mischak H, Kaiser T, Walden M et al. Proteomic analysis for the assessment of diabetic renal damage in humans. Clin. Sci.(Lond) 107(5), 485-495 (2004).
141. Rossing K, Mischak H, Dakna M et al. Urinary proteomics in diabetes and CKD. J. Am. Soc. Nephrol. 19(7), 1283-1290 (2008).
142. Alkhalaf A, Zurbig P, Bakker SJ et al. Multicentric validation of proteomic biomarkers in urine specific for diabetic nephropathy. PLoS ONE 5(10), e13421 (2010).
143. Ward DG, Roberts K, Brookes MJ et al. Increased hepcidin expression in colorectal carcinogenesis. World J. Gastroenterol. 14(9), 1339-1345 (2008).
144. Zurbig P, Jerums G, Hovind P et al. Urinary proteomics for early diagnosis in diabetic nephropathy. Diabetes 61(12), 3304-3313 (2012).
145. Roscioni SS, de ZD, Hellemons ME et al. A urinary peptide biomarker set predicts worsening of albuminuria in Type 2 diabetes mellitus. Diabetologia 56(2), 259-267 (2013).
146. Metzger J, Kirsch T, Schiffer E et al. Urinary excretion of twenty peptides forms an early and accurate diagnostic pattern of acute kidney injury. Kidney Int. 78(12), 1252-1262 (2010).
147. Drube J, Schiffer E, Lau E et al. Urinary proteome analysis to exclude severe vesicoureteral reflux. Pediatrics 129(2), e356-e363 (2012).