Adapting mass spectrometry-based platforms for clinical proteomics applications: The capillary electrophoresis coupled mass spectrometry paradigm

References

• Hernandez J, Thompson IM. Prostate-specific antigen: a review of the validation of the most commonly used cancer biomarker. Cancer 2004; 101: 894–904.
   PubMed Web of Science ®Google Scholar
• Mogensen CE. Systemic blood pressure and glomerular leakage with particular reference to diabetes and hypertension. J Intern Med 1994; 235: 297–316.
   PubMed Web of Science ®Google Scholar
• Rossing K. Progression and remission of nephropathy in type 2 diabetes: new strategies of treatment and monitoring. Dan Med Bull 2007; 54: 79–98.
   PubMedGoogle Scholar
• Fliser D, Novak J, Thongboonkerd V, Argiles A, Jankowski V, Girolami M, Jankowski J, Mischak H. Advances in urinary proteome analysis and biomarker discovery. J Am Soc Nephrol 2007; 18: 1057–1071.
   PubMed Web of Science ®Google Scholar
• Mischak H, Apweiler R, Banks RE, Conaway M, Coon JJ, Dominizak A, Ehrich JH, Fliser D, Girolami M, Hermjakob H, Hochstrasser DF, Jankowski V, Julian BA, Kolch W, Massy Z, Neususs C, Novak J, Peter K, Rossing K, Schanstra JP, Semmes OJ, Theodorescu D, Thongboonkerd V, Weissinger EM, Van Eyk JE, Yamamoto T. Clinical proteomics: a need to define the field and to begin to set adequate standards. Proteomics Clin Appl 2007; 1: 148–156.
   PubMed Web of Science ®Google Scholar
• Castronovo V, Kischel P, Guillonneau F, de LL, Defechereux T, De PE, Neri D, Waltregny D. Identification of specific reachable molecular targets in human breast cancer using a versatile ex vivo proteomic method. Proteomics 2007; 7: 1188–1196.
   PubMed Web of Science ®Google Scholar
• Roessler M, Rollinger W, Mantovani-Endl L, Hagmann ML, Palme S, Berndt P, Engel AM, Pfeffer M, Karl J, Bodenmueller H, Ruschoff J, Henkel T, Rohr G, Rossol S, Rosch W, Langen H, Zolg W, Tacke M. Identification of PSME3 as a novel serum tumor marker for colorectal cancer by combining two-dimensional polyacrylamide gel electrophoresis with a strictly mass spectrometry-based approach for data analysis. Mol Cell Proteomics 2006; 5: 2092–2101.
   PubMed Web of Science ®Google Scholar
• Lescuyer P, Hochstrasser D, Rabilloud T. How shall we use the proteomics toolbox for biomarker discovery? J Proteome Res 2007; 6: 3371–3376.
   PubMed Web of Science ®Google Scholar
• Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes JS, Kapp EA, Moritz RL, Chan DW, Rai AJ, Admon A, Aebersold R, Eng J, Hancock WS, Hefta SA, Meyer H, Paik YK, Yoo JS, Ping P, Pounds J, Adkins J, Qian X, Wang R, Wasinger V, Wu CY, Zhao X, Zeng R, Archakov A, Tsugita A, Beer I, Pandey A, Pisano M, Andrews P, Tammen H, Speicher DW, Hanash SM. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 2005; 5: 3226–3245.
   PubMed Web of Science ®Google Scholar
• Rai AJ, Gelfand CA, Haywood BC, Warunek DJ, Yi J, Schuchard MD, Mehigh RJ, Cockrill SL, Scott GB, Tammen H, Schulz-Knappe P, Speicher DW, Vitzthum F, Haab BB, Siest G, Chan DW. HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics 2005; 5: 3262–3277.
   PubMed Web of Science ®Google Scholar
• Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics 2002; 1: 845–867.
   PubMed Web of Science ®Google Scholar
• 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 2005; 24: 959–977.
   PubMed Web of Science ®Google Scholar
• Schaub S, Wilkins J, Weiler T, Sangster K, Rush D, Nickerson P. Urine protein profiling with surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry. Kidney Int 2004; 65: 323–332.
   PubMed Web of Science ®Google Scholar
• Hortin GL, Sviridov D. Diagnostic potential for urinary proteomics. Pharmacogenomics 2007; 8: 237–255.
   PubMed Web of Science ®Google Scholar
• Thongboonkerd V. Recent progress in urinary proteomics. Proteomics Clin Appl 2007; 1: 780–791.
   PubMed Web of Science ®Google Scholar
• Theodorescu D, Schiffer E, Bauer HW, Douwes F, Eichhorn F, Polley R, Schmidt T, Schofer W, Zuerbig P, Good DM, Coon JJ, Mischak H. Discovery and validation of urinary biomarkers for prostate cancer. Proteomics Clin Appl 2008; 2: 556–570.
   PubMed Web of Science ®Google Scholar
• Zurbig P, Decramer S, Dakna M, Jantos J, Good DM, Coon JJ, Bandin F, Mischak H, Bascands JL, Schanstra JP. A low molecular weight urinary proteome profile of human kidney aging. Proteomics Clin Appl 2009; Epub ahead of print.
   Google Scholar
• Hoang K, Tan JC, Derby G, Blouch KL, Masek M, Ma I, Lemley KV, Myers BD. Determinants of glomerular hypofiltration in aging humans. Kidney Int 2003; 64: 1417–1424.
   PubMed Web of Science ®Google Scholar
• O’Farrell PH. High resolution two-dimensional electrophoresis of proteins. J Biol Chem 1975; 250: 4007–4021.
   PubMed Web of Science ®Google Scholar
• Rose K, Kocher HP, Blumberg BM, Kolakofsky D. An improved procedure, involving mass spectrometry, for N-terminal amino acid sequence determination of proteins which are N alpha-blocked. Biochem J 1984; 217: 253–257.
   PubMed Web of Science ®Google Scholar
• Suckau D, Resemann A. T3-sequencing: targeted characterization of the N- and C-termini of undigested proteins by mass spectrometry. Anal Chem 2003; 75: 5817–5824.
   PubMed Web of Science ®Google Scholar
• Burnette WN. “Western blotting”: electrophoretic transfer of proteins from sodium dodecyl sulfate-polyacrylamide gels to unmodified nitrocellulose and radiographic detection with antibody and radioiodinated protein A. Anal Biochem 1981; 112: 195–203.
   PubMed Web of Science ®Google Scholar
• Zhu H, Snyder M. Protein chip technology. Curr Opin Chem Biol 2003; 7: 55–63.
   PubMed Web of Science ®Google Scholar
• Spisak S, Tulassay Z, Molnar B, Guttman A. Protein microchips in biomedicine and biomarker discovery. Electrophoresis 2007; 28: 4261–4273.
   PubMed Web of Science ®Google Scholar
• Wu TL. Two-dimensional difference gel electrophoresis. Methods Mol Biol 2006; 328: 71–95.
   PubMedGoogle Scholar
• Delahunty CM, Yates JR III. MudPIT: multidimensional protein identification technology. Biotechniques 2007; 43: 563, 565, 567.
   PubMed Web of Science ®Google Scholar
• Gaspari M, Verhoeckx KC, Verheij ER, van der GJ. Integration of two-dimensional LC-MS with multivariate statistics for comparative analysis of proteomic samples. Anal Chem 2006; 78: 2286–2296.
   PubMed Web of Science ®Google Scholar
• Cutillas PR, Norden AG, Cramer R, Burlingame AL, Unwin RJ. Detection and analysis of urinary peptides by on-line liquid chromatography and mass spectrometry: application to patients with renal Fanconi syndrome. Clin Sci (Lond) 2003; 104: 483–490.
   PubMed Web of Science ®Google Scholar
• Kreunin P, Zhao J, Rosser C, Urquidi V, Lubman DM, Goodison S. Bladder cancer associated glycoprotein signatures revealed by urinary proteomic profiling. J Proteome Res 2007; 6: 2631–2639.
   PubMed Web of Science ®Google Scholar
• Nagele E, Vollmer M, Horth P, Vad C. 2D-LC/MS techniques for the identification of proteins in highly complex mixtures. Expert Rev Proteomics 2004; 1: 37–46.
   PubMed Web of Science ®Google Scholar
• Qian WJ, Jacobs JM, Liu T, Camp DG, Smith RD. Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications. Mol Cell Proteomics 2006; 5: 1727–1744.
   PubMed Web of Science ®Google Scholar
• Shiwa M, Nishimura Y, Wakatabe R, Fukawa A, Arikuni H, Ota H, Kato Y, Yamori T. Rapid discovery and identification of a tissue-specific tumor biomarker from 39 human cancer cell lines using the SELDI ProteinChip platform. Biochem Biophys Res Commun 2003; 309: 18–25.
   PubMed Web of Science ®Google Scholar
• Woroniecki, RP, Orlova TN, Mendelev N, Shatat IF, Hailpern SM, Kaskel FJ, Goligorsky MS, O’Riordan E. Urinary proteome of steroid-sensitive and steroid-resistant idiopathic nephrotic syndrome of childhood. Am J Nephrol 2006; 26: 258–267.
   PubMed Web of Science ®Google Scholar
• Jahnukainen T, Malehorn D, Sun M, Lyons-Weiler J, Bigbee W, Gupta G, Shapiro R, Randhawa PS, Pelikan R, Hauskrecht M, Vats A. Proteomic analysis of urine in kidney transplant patients with BK virus nephropathy. J Am Soc Nephrol 2006; 17: 3248–3256.
   PubMed Web of Science ®Google Scholar
• Neuhoff N, Kaiser T, Wittke S, Krebs R, Pitt A, Burchard A, Sundmacher A, Schlegelberger B, Kolch W, Mischak H. 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 2004; 18: 149–156.
   PubMed Web of Science ®Google Scholar
• Rogers MA, Clarke P, Noble J, Munro NP, Paul A, Selby PJ, Banks RE. Proteomic profiling of urinary proteins in renal cancer by surface enhanced laser desorption ionization and neural-network analysis: identification of key issues affecting potential clinical utility. Cancer Res 2003; 63: 6971–6983.
   PubMed Web of Science ®Google Scholar
• 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 2006; 44: 1243–1252.
   PubMed Web of Science ®Google Scholar
• Poon TC. Opportunities and limitations of SELDI-TOF-MS in biomedical research: practical advices. Expert Rev Proteomics 2007; 4: 51–65.
   PubMed Web of Science ®Google Scholar
• Gaspar A, Englmann M, Fekete A, Harir M, Schmitt-Kopplin P. Trends in CE-MS 2005–2006. Electrophoresis 2008; 29: 66–79.
   PubMed Web of Science ®Google Scholar
• Kaiser T, Wittke S, Just I, Krebs R, Bartel S, Fliser D, Mischak H, Weissinger EM. Capillary electrophoresis coupled to mass spectrometer for automated and robust polypeptide determination in body fluids for clinical use. Electrophoresis 2004; 25: 2044–2055.
   PubMed Web of Science ®Google Scholar
• Weissinger EM, Wittke S, Kaiser T, Haller H, Bartel S, Krebs R, Golovko I, Rupprecht HD, Haubitz M, Hecker H, Mischak H, Fliser D. Proteomic patterns established with capillary electrophoresis and mass spectrometry for diagnostic purposes. Kidney Int 2004; 65: 2426–2434.
   PubMed Web of Science ®Google Scholar
• Kaiser T, Hermann A, Kielstein JT, Wittke S, Bartel S, Krebs R, Hausadel F, Hillmann M, Golovko I, Koester P, Haller H, Weissinger EM, Fliser D, Mischak H. Capillary electrophoresis coupled to mass spectrometry to establish polypeptide patterns in dialysis fluids. J Chromatogr A 2003; 1013: 157–171.
   PubMed Web of Science ®Google Scholar
• Neususs C, Pelzing M, Macht M. A robust approach for the analysis of peptides in the low femtomole range by capillary electrophoresis-tandem mass spectrometry. Electrophoresis 2002; 23: 3149–3159.
   PubMed Web of Science ®Google Scholar
• Smith RD, Olivares JA, Nguyen NT, Udseth HR. Capillary zone electrophoresis-mass spectrometry using an electrospray ionization interface. Anal Chem 1988; 60: 436–441.
   Web of Science ®Google Scholar
• Wahl JH, Gale DC, Smith RD. Sheathless capillary electrophoresis-electrospray ionization mass. J Chromatogr A 1994; 659: 217–222.
   PubMed Web of Science ®Google Scholar
• Theodorescu D, Wittke S, Ross MM, Walden M, Conaway M, Just I, Mischak H, Frierson HF. Discovery and validation of new protein biomarkers for urothelial cancer: a prospective analysis. Lancet Oncol 2006; 7: 230–240.
   PubMed Web of Science ®Google Scholar
• Wittke S, Fliser D, Haubitz M, Bartel S, Krebs R, Hausadel F, Hillmann M, Golovko I, Koester P, Haller H, Kaiser T, Mischak H, Weissinger EM. 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 2003; 1013: 173–181.
   PubMed Web of Science ®Google Scholar
• Theodorescu D, Fliser D, Wittke S, Mischak H, Krebs R, Walden M, Ross M, Eltze E, Bettendorf O, Wulfing C, Semjonow A. 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.
   PubMed Web of Science ®Google Scholar
• Shannon W, Culverhouse R, Duncan J. Analyzing microarray data using cluster analysis. Pharmacogenomics 2003; 4: 41–52.
   PubMed Web of Science ®Google Scholar
• Smola AJ, Scholkopf B. A tutorial on support vector regression. Statistics and Computing 2004; 14: 199–222.
   Web of Science ®Google Scholar
• Abdi H. Bonferroni and Sidak corrections for multiple comparisons. In Salkind NJ, (Ed.). Encyclopedia of Measurement and Statistics. Sage: Thousand Oaks CA, 2007; 103–107.
   Google Scholar
• Westfall PH, Young SS. Resampling-Based Multiple Testing: Examples and Methods for P-Value Adjustment. Wiley: New York, 1993.
   Google Scholar
• Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Stat Soc B (Methodological) 1995; 57: 125–133.
   Web of Science ®Google Scholar
• McLerran D, Grizzle WE, Feng Z, Thompson IM, Bigbee WL, Cazares LH, Chan DW, Dahlgren J, Diaz J, Kagan J, Lin DW, Malik G, Oelschlager D, Partin A, Randolph TW, Sokoll L, Srivastava S, Srivastava S, Thornquist M, Troyer D, Wright GL, Zhang Z, Zhu L, Semmes OJ. SELDI-TOF MS whole serum proteomic profiling with IMAC surface does not reliably detect prostate cancer. Clin Chem 2008; 54: 53–60.
   PubMed Web of Science ®Google Scholar
• Zweig MH, Campbell G. Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine. Clin Chem 1993; B 561–577.
   Web of Science ®Google Scholar
• Jaattela M. Escaping cell death: survival proteins in cancer. I 1999; B 30–43.
   Google Scholar
• Helmbrecht K, Zeise E, Rensing L. Chaperones in cell cycle regulation and mitogenic signal transduction: a review. I 2000; B 341–365.
   Google Scholar
• Jolly C, Morimoto RI. Role of the heat shock response and molecular chaperones in oncogenesis and cell death. J Natl Cancer Inst 2000; B 1564–1572.
   PubMedGoogle Scholar
• Lindquist S, Craig EA. The heat-shock proteins. Annu Rev Genet 1988; B 631–677.
   PubMed Web of Science ®Google Scholar
• Good DM, Thongboonkerd V, Novak J, Bascands JL, Schanstra JP, Coon JJ, Dominiczak A, Mischak H. Body fluid proteomics for biomarker discovery: lessons from the past hold the key to success in the future. J Proteome Res 2007; 6: 4549–4555.
   PubMed Web of Science ®Google Scholar
• Wa C, Cerny RL, Clarke WA, Hage DS. Characterization of glycation adducts on human serum albumin by matrix- assisted laser desorption/ionization time-of-flight mass spectrometry. Clin Chim Acta 2007; 385: 48–60.
   PubMed Web of Science ®Google Scholar
• Haubitz M, Fliser D, Rupprecht H, Floege J, Haller H, Rossing K, Walden M, Wittke S, Mischak H. Defining renal diseases based on proteom analysis. Nephrol Dial Transplant 2005; 20: V20.
   Web of Science ®Google Scholar
• Villanueva J, Shaffer DR, Philip J, Chaparro CA, Erdjument-Bromage H, Olshen AB, Fleisher M, Lilja H, Brogi E, Boyd J, Sanchez-Carbayo M, Holland EC, Cordon-Cardo C, Scher HI, Tempst P. Differential exoprotease activities confer tumor-specific serum peptidome patterns. J Clin Invest 2006; 116: 271–284.
   PubMed Web of Science ®Google Scholar
• Rossing K, Mischak H, Rossing P, Schanstra JP, Wiseman A, Maahs DM. The urinary proteome in diabetes and diabetes-associated complications: new ways to assess disease progression and evaluate therapy. Proteomics Clin Appl 2008; 2: 997–1007.
   Web of Science ®Google Scholar
• Zurbig P, Renfrow M.B., Schiffer E, Novak J, Walden M, Wittke S, Just I, Pelzing M, Neususs C, Theodorescu D, Root C, Ross M, Mischak H. Biomarker discovery by CE-MS enables sequence analysis via MS/MS with platform- independent separation. Electrophoresis 2006; 27: 2111–2125.
   PubMed Web of Science ®Google Scholar
• Righetti PG, Campostrini N, Pascali J, Hamdan M, Astner H. Quantitative proteomics: a review of different methodologies. Eur J Mass Spectrom (Chichester, Eng) 2004; 10: 335–348.
   PubMed Web of Science ®Google Scholar
• Zybailov B, Coleman MK, Florens L, Washburn MP. Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal Chem 2005; 77: 6218–6224.
   PubMed Web of Science ®Google Scholar
• Barnidge DR, Dratz EA, Martin T, Bonilla LE, Moran LB, Lindall A. Absolute quantification of the G protein-coupled receptor rhodopsin by LC/MS/MS using proteolysis product peptides and synthetic peptide standards. Anal Chem 2003; 75: 445–451.
   PubMed Web of Science ®Google Scholar
• DeKeyser SS, Li L. Matrix-assisted laser desorption/ ionization Fourier transform mass spectrometry quantitation via in cell combination. Analyst 2006; 131: 281–290.
   PubMed Web of Science ®Google Scholar
• Jantos-Siwy J, Schiffer E, Brand K, Schumann G, Rossing K, Delles C, Mischak H, Metzger J. Quantitative urinary proteome analysis for biomarker evaluation in chronic kidney disease. J Proteome Res 2009; 8: 268–281.
   PubMed Web of Science ®Google Scholar
• Holland M, Yagi H, Takahashi N, Kato K, Savage CO, Goodall DM, Jefferis R. Differential glycosylation of polyclonal IgG, IgG-Fc and IgG-Fab isolated from the sera of patients with ANCA-associated systemic vasculitis. Biochim Biophys Acta 2006; 1760: 669–677.
   PubMed Web of Science ®Google Scholar
• Soucek K, Kamaid A, Phung AD, Kubala L, Bulinski JC, Harper RW, Eiserich JP. Normal and prostate cancer cells display distinct molecular profiles of alpha-tubulin posttranslational modifications. Prostate 2006; 66: 954–965.
   PubMed Web of Science ®Google Scholar
• Uzawa K, Marshall MK, Katz EP, Tanzawa H, Yeowell HN, Yamauchi M. Altered posttranslational modifications of collagen in keloid. Biochem Biophys Res Commun 1998; 249: 652–655.
   PubMed Web of Science ®Google Scholar
• Coon JJ, Zurbig P, Dakna M, Dominiczak AF, Decramer S, Fliser D, Frommberger M, Golovko I, Good DM, Herget-Rosenthal S, Jankowski J, Julian BA, Kellmann M, Kolch W, Massy Z, Novak J, Rossing K, Schanstra JP, Schiffer E, Theodorescu D, Vanholder R, Weissinger EM, Mischak H, Schmitt-Kopplin P. CE-MS analysis of the human urinary proteome for biomarker discovery and disease diagnostics. Proteomics Clin Appl 2008; 2: 964–973.
   PubMed Web of Science ®Google Scholar
• Castagna A, Cecconi D, Sennels L, Rappsilber J, Guerrier L, Fortis F, Boschetti E, Lomas L, Righetti PG. Exploring the hidden human urinary proteome via ligand library beads. J Proteome Res 2005; 4: 1917–1930.
   PubMed Web of Science ®Google Scholar
• Adachi J, Kumar C, Zhang Y, Olsen JV, Mann M. The human urinary proteome contains more than 1500 proteins including a large proportion of membranes proteins. Genome Biol 2006; 7: R80.
   PubMed Web of Science ®Google Scholar
• Haubitz M, Wittke S, Weissinger EM, Walden M, Rupprecht HD, Floege J, Haller H, Mischak H. Urine protein patterns can serve as diagnostic tools in patients with IgA nephropathy. Kidney Int 2005; 67: 2313–2320.
   PubMed Web of Science ®Google Scholar
• Schiffer E, Mischak H, Novak J. High resolution proteome/peptidome analysis of body fluids by capillary electrophoresis coupled with MS. Proteomics 2006; 6: 5615–5627.
   PubMed Web of Science ®Google Scholar
• Julian BA, Wittke S, Novak J, Good DM, Coon JJ, Kellmann M, Zurbig P, Schiffer E, Haubitz M, Moldoveanu Z, Calcatera SM, Wyatt RJ, Sykora J, Sladkova E, Hes O, Mischak H, McGuire BM. Electrophoretic methods for analysis of urinary polypeptides in IgA-associated renal diseases. Electrophoresis 2007; 28: 4469–4483.
   PubMed Web of Science ®Google Scholar
• Julian BA, Wittke S, Haubitz M, Zurbig P, Schiffer E, McGuire BM, Wyatt RJ, Novak J. Urinary biomarkers of IgA nephropathy and other IgA-associated renal diseases. World J Urol 2007; 25: 467–476.
   PubMed Web of Science ®Google Scholar
• Rossing K, Mischak H, Parving HH, Christensen PK, Walden M, Hillmann M, Kaiser T. Impact of diabetic nephropathy and angiotensin II receptor blockade on urinary polypeptide patterns. Kidney Int 2005; 68: 193–205.
   PubMed Web of Science ®Google Scholar
• Rossing K, Mischak H, Dakna M, Zurbig P, Novak J, Julian BA, Good DM, Coon JJ, Tarnow L, Rossing P. Urinary proteomics in diabetes and CKD. J Am Soc Nephrol 2008; 19: 1283–1290.
   PubMed Web of Science ®Google Scholar
• Chalmers MJ, Mackay CL, Hendrickson CL, Wittke S, Walden M, Mischak H, Fliser D, Just I, Marshall AG. Combined top-down and bottom-up mass spectrometric approach to characterization of biomarkers for renal disease. Anal Chem 2005; 77: 7163–7171.
   PubMed Web of Science ®Google Scholar
• Comper WD, Hilliard LM, Nikolic-Paterson DJ, Russo LM. Disease-dependent mechanisms of albuminuria. an invited review. Am J Physiol Renal Physiol 2008; 295: F1589–F1600.
   PubMed Web of Science ®Google Scholar
• Birn H, Christensen EI. Renal albumin absorption in physiology and pathology. Kidney Int 2006; 69: 440–449.
   PubMed Web of Science ®Google Scholar
• Sever S, Altintas MM, Nankoe SR, Moller CC, Ko D, Wei C, Henderson J, del Re EC, Hsing L, Erickson A, Cohen CD, Kretzler M, Kerjaschki D, Rudensky A, Nikolic B, Reiser J. Proteolytic processing of dynamin by cytoplasmic cathepsin L is a mechanism for proteinuric kidney disease. J Clin Invest 2007; 117: 2095–2104.
   Web of Science ®Google Scholar
• Kafienah W, Buttle DJ, Burnett D, Hollander AP. Cleavage of native type I collagen by human neutrophil elastase. Biochem J 1998; 330(Pt 2): 897–902.
   PubMedGoogle Scholar
• Thongboonkerd V, Barati MT, McLeish KR, Benarafa C, Remold-O’Donnell E, Zheng S, Rovin BH, Pierce WM, Epstein PN, Klein JB. Alterations in the renal elastin-elastase system in type 1 diabetic nephropathy identified by proteomic analysis. J Am Soc Nephrol 2004; 15: 650–662.
   PubMed Web of Science ®Google Scholar
• Nerlich A, Schleicher E. Immunohistochemical localization of extracellular matrix components in human diabetic glomerular lesions. Am J Pathol 1991; 139: 889–899.
   PubMed Web of Science ®Google Scholar
• Kwak NJ, Heo Y, Jin DC, Cha JH, Lee KH, Yang CW, Kang CS, Choi YJ, Wang EH. Proteomic analysis of alpha-1-antitrypsin in immunoglobulin A nephropathy. Proteomics Clin Appl 2007; 1: 420–428.
   PubMed Web of Science ®Google Scholar
• Barratt J, Feehally J, Smith AC. Pathogenesis of IgA nephropathy. Semin Nephrol 2004; 24: 197–217.
   PubMed Web of Science ®Google Scholar
• Couchman JR, Beavan LA, McCarthy KJ. Glomerular matrix: synthesis, turnover and role in mesangial expansion. Kidney Int 1994; 45: 328–335.
   PubMed Web of Science ®Google Scholar
• Gauer S, Yao J, Schoecklmann HO, Sterzel RB. Adhesion molecules in the glomerular mesangium. Kidney Int 1997; 51: 1447–1453.
   PubMed Web of Science ®Google Scholar
• Rupprecht HD, Schocklmann HO, Sterzel RB. Cell-matrix interactions in the glomerular mesangium. Kidney Int 1996; 49: 1575–1582.
   PubMed Web of Science ®Google Scholar
• Mischak H, Kaiser T, Walden M, Hillmann M, Wittke S, Herrmann A, Knueppel S, Haller H, Fliser D. Proteomic analysis for the assessment of diabetic renal damage in humans. Clin Sci (Lond) 2004; 107: 485–495.
   PubMed Web of Science ®Google Scholar
• Meier M, Kaiser T, Herrmann A, Knueppel S, Hillmann M, Koester P, Danne T, Haller H, Fliser D, Mischak H. Identification of urinary protein pattern in type 1 diabetic adolescents with early diabetic nephropathy by a novel combined proteome analysis. J Diabetes Complications 2005; 19: 223–232.
   PubMed Web of Science ®Google Scholar
• Dabelea D, Kinney G, Snell-Bergeon JK, Hokanson JE, Eckel RH, Ehrlich J, Garg S, Hamman RF, Rewers M. Effect of type 1 diabetes on the gender difference in coronary artery calcification: a role for insulin resistance? The Coronary Artery Calcification in Type 1 Diabetes (CACTI) Study. Diabetes 2003; 52: 2833–2839.
   PubMedGoogle Scholar
• Snell-Bergeon JK, Maahs DM, Ogden LG, Kinney G, Hokanson JE, Schiffer E, Rewers M, Mischak H. Evaluation of urinary biomarkers for coronary artery disease, diabetes, and diabetic kidney disease. Diabetes Technol Ther 2009; 11: 1–9.
   PubMed Web of Science ®Google Scholar
• Wittke S, Haubitz M, Walden M, Rohde F, Schwarz A, Mengel M, Mischak H, Haller H, Gwinner W. Detection of acute tubulointerstitial rejection by proteomic analysis of urinary samples in renal transplant recipients. Am J Transplant 2005; 5: 2479–2488.
   PubMed Web of Science ®Google Scholar
• Jennette JC, Falk RJ. Pathogenic potential of anti-neutrophil cytoplasmic autoantibodies. Adv Exp Med Biol 1993; 336: 7–15.
   PubMedGoogle Scholar
• Decramer S, Wittke S, Mischak H, Zurbig P, Walden M, Bouissou F, Bascands JL, Schanstra JP. Predicting the clinical outcome of congenital unilateral ureteropelvic junction obstruction in newborn by urinary proteome analysis. Nat Med 2006; 12: 398–400.
   PubMed Web of Science ®Google Scholar
• Decramer S, Zurbig P, Wittke S, Mischak H, Bascands JL, Schanstra JP. Identification of urinary biomarkers by proteomics in newborns: use in obstructive nephropathy. Contrib Nephrol 2008; 160: 127–141.
   PubMed Web of Science ®Google Scholar
• Fricker LD, McKinzie AA, Sun J, Curran E, Qian Y, Yan L, Patterson SD, Courchesne PL, Richards B, Levin N, Mzhavia N, Devi LA, Douglass J. Identification and characterization of proSAAS, a granin-like neuroendocrine peptide precursor that inhibits prohormone processing. J Neurosci 2000; 20: 639–648.
   PubMed Web of Science ®Google Scholar
• Chevalier RL. Obstructive nephropathy: towards biomarker discovery and gene therapy. Nat Clin Pract Nephrol 2006; 2: 157–168.
   PubMedGoogle Scholar
• Dinney CP, McConkey DJ, Millikan RE, Wu X, Bar-Eli M, Adam L, Kamat AM, Siefker-Radtke AO, Tuziak T, Sabichi AL, Grossman HB, Benedict WF, Czerniak B. Focus on bladder cancer. Cancer Cell 2004; 6: 111–116.
   PubMed Web of Science ®Google Scholar
• Lilja H. Structure and function of prostatic- and seminal vesicle-secreted proteins involved in the gelation and liquefaction of human semen. Scand J Clin Lab Invest Suppl 1988; 191: 13–20.
   PubMedGoogle Scholar
• Lilja H. Cell biology of semenogelin. Andrologia 1990; 22(Suppl 1): S132–S141.
   PubMedGoogle Scholar
• Lodding P, Aus G, Bergdahl S, Frosing R, Lilja H, Pihl CG, Hugosson J. Characteristics of screening detected prostate cancer in men 50 to 66 years old with 3 to 4 ng./ml.prostate specific antigen. J Urol 1998; 159: 899–903.
   PubMed Web of Science ®Google Scholar
• Duran MJ, Parish LD, Pressley TA. Regulation of Na,K-ATPase in prostate cancer: a role for PKCbeta. FASEB J 2007; 21: 976.2.
   Web of Science ®Google Scholar
• Blok LJ, Chang GT, Steenbeek-Slotboom M, van Weerden WM, Swarts HG, De Pont JJ, van Steenbrugge GJ, Brinkmann AO. Regulation of expression of Na+,K+-ATPase in androgen-dependent and androgen-independent prostate cancer. Br J Cancer 1999; 81: 28–36.
   PubMed Web of Science ®Google Scholar
• Brew K, Dinakarpandian D, Nagase H. Tissue inhibitors of metalloproteinases: evolution, structure and function. Biochim Biophys Acta 2000; 1477: 267–283.
   PubMed Web of Science ®Google Scholar
• DeMuth JP, Weaver DA, Crawford EL, Jackson CM, Willey JC. Loss of spr1 expression measurable by quantitative RT-PCR in human bronchogenic carcinoma cell lines. Am J Respir Cell Mol Biol 1998; 19: 25–29.
   PubMed Web of Science ®Google Scholar
• Lau D, Guo L, Chan A, Wu R. SPR1. An early molecular marker for bronchial carcinogenesis. Methods Mol Med 2003; 75: 397–403.
   PubMedGoogle Scholar
• Kaiser T, Kamal H, Rank A, Kolb HJ, Holler E, Ganser A, Hertenstein B, Mischak H, Weissinger EM. Proteomics applied to the clinical follow-up of patients after allogeneic hematopoietic stem cell transplantation. Blood 2004; 104: 340–349.
   PubMed Web of Science ®Google Scholar
• Weissinger EM, Schiffer E, Hertenstein B, Ferrara JL, Holler E, Stadler M, Kolb HJ, Zander A, Zurbig P, Kellmann M, Ganser A. Proteomic patterns predict acute graft-versus-host disease after allogeneic hematopoietic stem cell transplantation. Blood 2007; 109: 5511–5519.
   PubMed Web of Science ®Google Scholar
• Zimmerli LU, Schiffer E, Zurbig P, Good DM, Kellmann M, Mouls L, Pitt AR, Coon JJ, Schmieder RE, Peter KH, Mischak H, Kolch W, Delles C, Dominiczak AF. Urinary proteomic biomarkers in coronary artery disease. Mol Cell Proteomics 2008; 7: 290–298.
   PubMed Web of Science ®Google Scholar
• von zur Muhlen C, Schiffer E, Kellmann M, Zurbig P, Brasse M, Meert N, Vanholder R, Dominiczak AF, Chen YC, Mischak H, Bode C, Peter K. Evaluation of urine proteome pattern analysis for its potential to reflect coronary artery atherosclerosis in symptomatic patients. J Proteome Res 2009; 8: 335–345.
   PubMed Web of Science ®Google Scholar
• Pihusch M, Wegner H, Goehring P, Salat C, Pihusch V, Andreesen R, Kolb HJ, Holler E, Pihusch R. Protein C and procollagen III peptide levels in patients with hepatic dysfunction after allogeneic hematopoietic stem cell transplantation. Bone Marrow Transplant 2005; 36: 631–637.
   PubMed Web of Science ®Google Scholar
• Bentsen KD. Type III procollagen peptide: studies on the circulating peptide as a marker of fibrinogenesis with special reference to the liver. Dan Med Bull 1993; 40: 235–246.
   PubMedGoogle Scholar
• Kalela A, Koivu TA, Sisto T, Kanervisto J, Hoyhtya M, Sillanaukee P, Lehtimaki T, Nikkari ST. Serum matrix metalloproteinase-9 concentration in angiographically assessed coronary artery disease. Scand J Clin Lab Invest 2002; 62: 337–342.
   PubMed Web of Science ®Google Scholar
• Noji Y, Kajinami K, Kawashiri MA, Todo Y, Horita T, Nohara A, Higashikata T, Inazu A, Koizumi J, Takegoshi T, Mabuchi H. Circulating matrix metalloproteinases and their inhibitors in premature coronary atherosclerosis. Clin Chem Lab Med 2001; 39: 380–384.
   PubMed Web of Science ®Google Scholar
• Tayebjee MH, Tan KT, MacFadyen RJ, Lip GY. Abnormal circulating levels of metalloprotease 9 and its tissue inhibitor 1 in angiographically proven peripheral arterial disease: relationship to disease severity. J Intern Med 2005; 257: 110–116.
   PubMed Web of Science ®Google Scholar
• Blankenberg S, Rupprecht HJ, Poirier O, Bickel C, Smieja M, Hafner G, Meyer J, Cambien F, Tiret L. Plasma concentrations and genetic variation of matrix metalloproteinase 9 and prognosis of patients with cardiovascular disease. Circulation 2003; 107: 1579–1585.
   PubMed Web of Science ®Google Scholar
• de NR, Verkleij CJ, von der Thusen JH, Jukema JW, van der Wall EE, van Berkel TJ, Baker AH, Biessen EA. Lesional overexpression of matrix metalloproteinase-9 promotes intraplaque hemorrhage in advanced lesions but not at earlier stages of atherogenesis. Arterioscler Thromb Vasc Biol 2006; 26: 340–346.
   PubMed Web of Science ®Google Scholar
• Verhave JC, Hillege HL, Burgerhof JG, Gansevoort RT, de Zeeuw D, de Jong PE, PREVEND Study Group. The association between atherosclerotic risk factors and renal function in the general population. Kidney Int 2005; 67: 1967–1973.
   PubMed Web of Science ®Google Scholar
• Comper WD, Osicka TM, Clark M, MacIsaac RJ, Jerums G. Earlier detection of microalbuminuria in diabetic patients using a new urinary albumin assay. Kidney Int 2004; 65: 1850–1855.
   PubMed Web of Science ®Google Scholar
• Nemirovskiy OV, Dufield DR, Sunyer T, Aggarwal P, Welsch DJ, Mathews WR. Discovery and development of a type II collagen neoepitope (TIINE) biomarker for matrix metalloproteinase activity: from in vitro to in vivo. Anal Biochem 2006; 361: 93–101.
   PubMed Web of Science ®Google Scholar
• Candiano G, Musante L, Bruschi M, Petretto A, Santucci L, Del BP, Pavone B, Perfumo F, Urbani A, Scolari F, Ghiggeri GM. Repetitive fragmentation products of albumin and alpha1-antitrypsin in glomerular diseases associated with nephrotic syndrome. J Am Soc Nephrol 2006; 17: 3139–3148.
   PubMed Web of Science ®Google Scholar