Technology insight: Renal proteomics - At the crossroads between promise and problems

Nature Clinical Practice Nephrology

Volumn 2, Issue 8, 2006, Pages 445-458

  O'Riordan, Edmond ^a   Gross, Steven S ^b   Goligorsky, Michael S ^a  

^a NEW YORK MEDICAL COLLEGE   (United States)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

Bioinformatics; Kidney; Mass spectrometry; Proteome; Urine

Indexed keywords

UREMIC TOXIN;

BIOINFORMATICS; CAPILLARY ELECTROPHORESIS; CELL ORGANELLE; CHROMATOGRAPHY; DIAGNOSTIC PROCEDURE; DIAGNOSTIC VALUE; HUMAN; KIDNEY; KIDNEY CANCER; KIDNEY CELL; KIDNEY DISEASE; KIDNEY GRAFT; KNOWLEDGE; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NEPHROLITHIASIS; PRIORITY JOURNAL; PROGNOSIS; PROTEIN MICROARRAY; PROTEOMICS; REVIEW; SAMPLING; SEPARATION TECHNIQUE; SOLID; STANDARD; TWO DIMENSIONAL ELECTROPHORESIS; URINALYSIS; URINE; VIGNETTE;

HUMANS; KIDNEY DISEASES; PROTEINS; PROTEINURIA; PROTEOMICS; SPECIMEN HANDLING; URINALYSIS;

EID: 33746795859     PISSN: 17458323     EISSN: 17458331     Source Type: Journal    
DOI: 10.1038/ncpneph0241     Document Type: Review

References (82)

1. Aebersold R and Mann M (2003) Mass spectrometry-based proteomics. Nature 422: 198-207
2. Hachey DL and Chaurand P (2004) Proteomics in reproductive medicine: the technology for separation and identification of proteins. J Reprod Immunol 63: 61-73
3. Hirsch J et al. (2004) Proteomics: current techniques and potential applications to lung disease. Am J Physiol Lung Cell Mol Physiol 287: L1-L23
4. Gygi SP and Aebersold R (2000) Mass spectrometry and proteomics. Curr Opin Chem Biol 4: 489-494
5. Issaq HJ (2001) The role of separation science in proteomics research. Electrophoresis 22: 3629-3638
6. Venter JC et al. (2001) The sequence of the human genome. Science 291: 1304-1351
7. Lander ES et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921
8. Anderson NL et al. (2004) The human plasma proteome: a nonredundant list developed by combination of four separate sources. Mol Cell Proteomics 3: 311-326
9. Marshall AG et al. (1998) Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom Rev 17: 1-35
10. Ibarrola N et al. (2003) A proteomic approach for quantitation of phosphorylation using stable isotope labeling in cell culture. Anal Chem 75: 6043-6049
11. Liu T et al. (2005) Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. J Proteome Res 4: 2070-2080
12. Hao G et al. (2006) SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures. Proc Natl Acad Sci USA 103: 1012-1017
13. Ong SE and Mann M (2005) Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol 1: 252-262
14. Hewitt SM et al. (2004) Discovery of protein biomarkers for renal diseases. J Am Soc Nephrol 15: 1677-1689
15. Tencer J et al. (1994) Stability of albumin, protein HC, immunoglobulin G, kappa- and lambda-chain immunoreactivity, orosomucoid and alpha 1-antitrypsin in urine stored at various conditions. Scand J Clin Lab Invest 54: 199-206
16. Serafini-Cessi F et al. (2003) Tamm-Horsfall glycoprotein: biology and clinical relevance. Am J Kidney Dis 42: 658-676
17. Zolotarjova N et al. (2005) Differences among techniques for high-abundant protein depletion. Proteomics 5: 3304-3313
18. Marshall T and Williams KM (1986) Electrophoresis indicates protein loss on centrifugation of urine. Clin Chem 32: 2105-2106
19. Schaub S et al. (2004) Proteomic-based detection of urine proteins associated with acute renal allograft rejection. J Am Soc Nephrol 15: 219-227
20. Schaub S et al. (2004) Urine protein profiling with surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry. Kidney Int 65: 323-332
21. O'Riordan E et al. (2004) Bioinformatic analysis of the urine proteome of acute allograft rejection. J Am Soc Nephrol 15: 3240-3248
22. Schaub S et al. (2005) Proteomic-based identification of cleaved urinary beta2-microglobulin as a potential marker for acute tubular injury in renal allografts. Am J Transplant 5: 729-738
23. Jackson DW et al. (1993) Altered urinary excretion of lysosomal hydrolases in pregnancy. Am J Kidney Dis 22: 649-655
24. Taracha E et al. (2004) Alanine aminopeptidase activity in urine: a new marker of chronic alcohol abuse? Alcohol Clin Exp Res 28: 729-735
25. Osicka TM et al. (2000) Albuminuria in patients with type 1 diabetes is directly linked to changes in the lysosome-mediated degradation of albumin during renal passage. Diabetes 49: 1579-1584
26. Issaq HJ et al. (2005) Multidimensional separation of peptides for effective proteomic analysis. J Chromatogr B Analyt Technol Biomed Life Sci 817: 35-47
27. Liu H et al. (2002) Multidimensional separations for protein/peptide analysis in the post-genomic era. Biotechniques 32: 898, 900, 902 passim
28. Cooper JW et al. (2004) Recent advances in capillary separations for proteomics. Electrophoresis 25: 3913-3926
29. Giddings J (1987) Concepts and comparisons in multidimensional separation. J High Resolut Chromatogr Commun 10: 319-323
30. O'Farrell PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250: 4007-4021
31. Edwards JJ et al. (1982) Proteins of human urine. III. Identification and two-dimensional electrophoretic map positions of some major urinary proteins. Clin Chem 28: 941-948
32. Griffith OW and Meister A (1979) Potent and specific inhibition of glutathione synthesis by buthionine sulfoximine (S-n-butyl homocysteine sulfoximine). J Biol Chem 254: 7558-7560
33. Brookes PS et al. (2002) High throughput two-dimensional blue-native electrophoresis: a tool for functional proteomics of mitochondria and signaling complexes. Proteomics 2: 969-977
34. Mann M et al. (2002) Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol 20: 261-268
35. Weissinger EM et al. (2004) Proteomic patterns established with capillary electrophoresis and mass spectrometry for diagnostic purposes. Kidney Int 65: 2426-2434
36. Fung E et al. (2003) The use of SELDI protein chip array technology in renal disease research. In Renal Disease: Techniques and Protocols, 295-314 (Ed Goligorsky MS) Totowa: Humana Press
37. Wang Y (2004) Immunostaining with dissociable antibody microarrays. Proteomics 4: 20-26
38. Arthur JM (2003) Proteomics. Curr Opin Nephrol Hypertens 12: 423-430
39. Gygi SP et al. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17: 994-999
40. DeSouza L et al. (2005) Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cICAT with multidimensional liquid chromatography and tandem mass spectrometry. J Proteome Res 4: 377-386
41. Kiernan UA et al. (2003) Comparative urine protein phenotyping using mass spectrometric immunoassay. J Proteome Res 2: 191-197
42. Claverie J-M (2003) Bioinformatics for Dummies. New York: Wiley
43. Elias JE et al. (2005) Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat Methods 2: 667-675
44. Li J et al. (2002) Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem 48: 1296-1304
45. Adam BL et al. (2002) Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res 62: 3609-3614
46. Granger CB et al. (2004) National Heart, Lung, And Blood Institute Clinical Proteomics Working Group report. Circulation 109: 1697-1703
47. Oh J et al. (2004) Establishment of a near-standard two-dimensional human urine proteomic map. Proteomics 4: 3485-3497
48. Pieper R et al. (2004) Characterization of the human urinary proteome: a method for high-resolution display of urinary proteins on two-dimensional electrophoresis gels with a yield of nearly 1400 distinct protein spots. Proteomics 4: 1159-1174
49. Smith G et al. (2005) Development of a high-throughput method for preparing human urine for two-dimensional electrophoresis. Proteomics 5: 2315-2318
50. Lafitte D et al. (2002) Optimized preparation of urine samples for two-dimensional electrophoresis and initial application to patient samples. Clin Biochem 35: 581-589
51. Thongboonkerd V et al. (2002) Proteomic analysis of normal human urinary proteins isolated by acetone precipitation or ultracentrifugation. Kidney Int 62: 1461-1469
52. Celis JE et al. (1999) A comprehensive protein resource for the study of bladder cancer: http://biobase.dk/cgi-bin/celis. Electrophoresis 20: 300-309
53. Spahr CS et al. (2001) Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. I. Profiling an unfractionated tryptic digest. Proteomics 1: 93-107
54. Pisitkun T et al. (2004) Identification and proteomic profiling of exosomes in human urine. Proc Natl Acad Sci USA 101: 13368-13373
55. Norden AG et al. (2004) Quantitative amino acid and proteomic analysis: very low excretion of polypeptides >750 Da in normal urine. Kidney Int 66: 1994-2003
56. Cutillas PR et al. (2004) The urinary proteome in Fanconi syndrome implies specificity in the reabsorption of proteins by renal proximal tubule cells. Am J Physiol Renal Physiol 287: F353-F364
57. Clarke W et al. (2003) Characterization of renal allograft rejection by urinary proteomic analysis. Ann Surg 237: 660-664
58. Weissinger EM et al. (2004) Proteomics: a novel tool to unravel the patho-physiology of uraemia. Nephrol Dial Transplant 19: 3068-3077
59. Mischak H et al. (2004) Proteomic analysis for the assessment of diabetic renal damage in humans. Clin Sci (Lond) 107: 485-495
60. Haubitz M et al. (2005) Urine protein patterns can serve as diagnostic tools in patients with IgA nephropathy. Kidney Int 67: 2313-2320
61. Hampel DJ et al. (2001) Toward proteomics in uroscopy: urinary protein profiles after radiocontrast medium administration. J Am Soc Nephrol 12: 1026-1035
62. Cadieux PA et al. (2004) Surface-enhanced laser desorption/ionization- time of flight-mass spectrometry (SELDI-TOF-MS): a new proteomic urinary test for patients with urolithiasis. J Clin Lab Anal 18: 170-175
63. Rogers MA et al. (2003) 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 63: 6971-6983
64. Thongboonkerd V et al. (2004) Alterations in the renal elastin-elastase system in type 1 diabetic nephropathy identified by proteomic analysis. J Am Soc Nephrol 15: 650-662
65. Kwapiszewska G et al. (2004) Identification of proteins in laser-microdissected small cell numbers by SELDITOF and Tandem MS. BMC Biotechnol 4: 30
66. Chaurand P et al. (2004) Proteomics in diagnostic pathology: profiling and imaging proteins directly in tissue sections. Am J Pathol 165: 1057-1068
67. Bagshaw RD et al. (2005) A proteomic analysis of lysosomal integral membrane proteins reveals the diverse composition of the organelle. Mol Cell Proteomics 4: 133-143
68. Molina H et al. (2005) A proteomic analysis of human hemodialysis fluid. Mol Cell Proteomics 4: 637-650
69. Carr S et al. (2004) The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol Cell Proteomics 3: 531-533
70. Orchard S et al. (2005) Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3rd annual congress, Beijing 25-27th October, 2004. Proteomics 5: 337-339
71. Hanash S (2004) HUPO initiatives relevant to clinical proteomics. Mol Cell Proteomics 3: 298-301
72. Marouga R et al. (2005) The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal Bioanal Chem 382: 669-678
73. Campostrini N et al. (2005) Spot overlapping in two-dimensional maps: a serious problem ignored for much too long. Proteomics 5: 2385-2395
74. Cho A and Normile D (2002) Nobel Prize in Chemistry. Mastering macromolecules. Science 298: 527-528
75. Breiman L et al. (1984) Classification and Regression Trees. Belmont: Wadsworth International Group
76. Breiman L (2001) Random Forests. Machine Learning 45: 5-32
77. Qu Y et al. (2002) Boosted decision tree analysis of surface-enhanced laser desorption/ionization mass spectral serum profiles discriminates prostate cancer from noncancer patients. Clin Chem 48: 1835-1843
78. Woroniecki R et al. (2006) Urinary proteome of steroid-sensitive and steroid-resistant idiopathic nephrotic syndrome of childhood. Am J Nephrol 26: 258-267
79. Wagner M et al. (2004) Computational protein biomarker prediction: a case study for prostate cancer. BMC Bioinformatics 5: 26
80. Yu JK et al. (2004) An integrated approach to the detection of colorectal cancer utilizing proteomics and bioinformatics. World J Gastroenterol 10: 3127-3131
81. Vapnik V (1995) The Nature of Statistical Learning Theory. New York: Springer
82. Ball G et al. (2002) An integrated approach utilizing artificial neural networks and SELDI mass spectrometry for the classification of human tumours and rapid identification of potential biomarkers. Bioinformatics 18: 395-404