Seminars in Nephrology
Volume 27, Issue 6 , Pages 574-583 , November 2007

Use of Quantitative Mass Spectrometry Analysis in Kidney Research

  • Timothy D. Cummins, MS
    • ,
  • David W. Powell, PhD

      Affiliations

    • Corresponding Author InformationAddress reprint requests to David W. Powell, Department of Medicine and Biochemistry and Molecular Biology, School of Medicine, University of Louisville, Louisville, KY 40202.

References 

  1. Fleischer TC, Weaver CM, McAfee KJ, et al. Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes. Genes Dev. 2006;20:1294–1307
  2. Link AJ, Eng J, Schieltz DM, et al. Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol. 1999;17:676–682
  3. Powell DW, Weaver CM, Jennings JL, et al. Cluster analysis of mass spectrometry data reveals a novel component of SAGA. Mol Cell Biol. 2004;24:7249–7259
  4. Powell DW, Merchant ML, Link AJ. Discovery of regulatory molecular events and biomarkers using 2D capillary chromatography and mass spectrometry. Expert Rev Proteomics. 2006;3:63–74
  5. Lominadze G, Powell DW, Luerman GC, et al. Proteomic analysis of human neutrophil granules. Mol Cell Proteomics. 2005;4:1503–1521
  6. Yates JR, McCormack AL, Eng J. Mining genomes with MS. Anal Chem. 1996;68:534A–540A
  7. Craig R, Cortens JC, Fenyo D, et al. Using annotated peptide mass spectrum libraries for protein identification. J Proteome Res. 2006;5:1843–1849
  8. 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
  9. McAfee KJ, Duncan DT, Assink M, et al. Analyzing proteomes and protein function using graphical comparative analysis of tandem mass spectrometry results. Mol Cell Proteomics. 2006;5:1497–1513
  10. Nesvizhskii AI, Keller A, Kolker E, et al. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem. 2003;75:4646–4658
  11. Ong SE, Blagoev B, Kratchmarova I, et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics. 2002;1:376–386
  12. Gygi SP, Rist B, Gerber SA, et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol. 1999;17:994–999
  13. Wiener MC, Sachs JR, Deyanova EG, et al. Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures. Anal Chem. 2004;76:6085–6096
  14. Old WM, Meyer-Arendt K, Aveline-Wolf L, et al. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics. 2005;4:1487–1502
  15. Wienkoop S, Larrainzar E, Niemann M, et al. Stable isotope-free quantitative shotgun proteomics combined with sample pattern recognition for rapid diagnostics. J Sep Sci. 2006;29:2793–2801
  16. Radulovic D, Jelveh S, Ryu S, et al. Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics. 2004;3:984–997
  17. Rauch A, Bellew M, Eng J, et al. Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J Proteome Res. 2006;5:112–121
  18. Bouwmeester T, Bauch A, Ruffner H, et al. A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol. 2004;6:97–105
  19. Gavin AC, Bosche M, Krause R, et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 2002;415:141–147
  20. Sanders SL, Jennings J, Canutescu A, et al. Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry. Mol Cell Biol. 2002;22:4723–4738
  21. Collins SR, Miller KM, Maas NL, et al. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature. 2007;446:806–810
  22. Butland G, Peregrin-Alvarez JM, Li J, et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature. 2005;433:531–537
  23. Rinner O, Mueller LN, Hubalek M, et al. An integrated mass spectrometric and computational framework for the analysis of protein interaction networks. Nat Biotechnol. 2007;25:345–352
  24. Foster LJ, de Hoog CL, Zhang Y, et al. A mammalian organelle map by protein correlation profiling. Cell. 2006;125:187–199
  25. Kislinger T, Cox B, Kannan A, et al. Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell. 2006;125:173–186
  26. Taal MW, Omer SA, Nadim MK, et al. Cellular and molecular mediators in common pathway mechanisms of chronic renal disease progression. Curr Opin Nephrol Hypertens. 2000;9:323–331
  27. Lee KK, Florens L, Swanson SK, et al. The deubiquitylation activity of Ubp8 is dependent upon Sgf11 and its association with the SAGA complex. Mol Cell Biol. 2005;25:1173–1182
  28. Clauser KR, Hall SC, Smith DM, et al. Rapid mass spectrometric peptide sequencing and mass matching for characterization of human melanoma proteins isolated by two-dimensional PAGE. Proc Natl Acad Sci U S A. 1995;92:5072–5076
  29. Craig R, Beavis RC. TANDEM: matching proteins with tandem mass spectra. Bioinformatics. 2004;20:1466–1467
  30. Yates JR, Eng JK, McCormack AL, et al. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal Chem. 1995;67:1426–1436
  31. Yates JR, Eng JK, McCormack AL. Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal Chem. 1995;67:3202–3210
  32. Perkins DN, Pappin DJ, Creasy DM, et al. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis. 1999;20:3551–3567
  33. Han DK, Eng J, Zhou H, et al. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat Biotechnol. 2001;19:946–951
  34. Tabb DL, McDonald WH, Yates JR. DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res. 2002;1:21–26
  35. Elias JE, Gygi SP. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods. 2007;4:207–214
  36. Chen Y, Kwon SW, Kim SC, et al. Integrated approach for manual evaluation of peptides identified by searching protein sequence databases with tandem mass spectra. J Proteome Res. 2005;4:998–1005
  37. Gatlin CL, Eng JK, Cross ST, et al. Automated identification of amino acid sequence variations in proteins by HPLC/microspray tandem mass spectrometry. Anal Chem. 2000;72:757–763
  38. Keshamouni VG, Michailidis G, Grasso CS, et al. Differential protein expression profiling by iTRAQ-2DLC-MS/MS of lung cancer cells undergoing epithelial-mesenchymal transition reveals a migratory/invasive phenotype. J Proteome Res. 2006;5:1143–1154
  39. Liu H, Sadygov RG, Yates JR. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem. 2004;76:4193–4201
  40. Ross PL, Huang YN, Marchese JN, et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics. 2004;3:1154–1169
  41. Yi EC, Li XJ, Cooke K, et al. Increased quantitative proteome coverage with (13)C/(12)C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme. Proteomics. 2005;5:380–387
  42. Gao J, Friedrichs MS, Dongre AR, et al. Guidelines for the routine application of the peptide hits technique. J Am Soc Mass Spectrom. 205;16:1231-8.
  43. Gao J, Opiteck GJ, Friedrichs MS, et al. Changes in the protein expression of yeast as a function of carbon source. J Proteome Res. 2003;2:643–649
  44. Wang W, Zhou H, Lin H, et al. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem. 2003;75:4818–4826
  45. Hughes AL, Powell DW, Bard M, et al. Dap1/PGRMC1 binds and regulates cytochrome P450 enzymes. Cell Metab. 2007;5:143–149
  46. Samatar AA, Wang L, Mirza A, et al. Transforming growth factor-beta 2 is a transcriptional target for Akt/protein kinase B via forkhead transcription factor. J Biol Chem. 2002;277:28118–28126
  47. Perlman A, Lawsin LM, Kolachana P, et al. Angiotensin II regulation of TGF-beta in murine mesangial cells involves both PI3 kinase and MAP kinase. Ann Clin Lab Sci. 2004;34:277–286
  48. Bottinger EP, Bitzer M. TGF-beta signaling in renal disease. J Am Soc Nephrol. 2002;13:2600–2610
  49. Andersen JS, Mann M. Organellar proteomics: turning inventories into insights. EMBO Rep. 2006;7:874–879
  50. Yu MJ, Pisitkun T, Wang G, et al. LC-MS/MS analysis of apical and basolateral plasma membranes of rat renal collecting duct cells. Mol Cell Proteomics. 2006;5:2131–2145
  51. Gilbert RE, Cooper ME. The tubulointerstitium in progressive diabetic kidney disease: more than an aftermath of glomerular injury?. Kidney Int. 1999;56:1627–1637
  52. Liu Y. Renal fibrosis: new insights into the pathogenesis and therapeutics. Kidney Int. 2006;69:213–217
  53. Liu Y. Epithelial to mesenchymal transition in renal fibrogenesis: pathologic significance, molecular mechanism, and therapeutic intervention. J Am Soc Nephrol. 2004;15:1–12
  54. Rastaldi MP, Ferrario F, Giardino L, et al. Epithelial-mesenchymal transition of tubular epithelial cells in human renal biopsies. Kidney Int. 2002;62:137–146
  55. Simonson MS. Phenotypic transitions and fibrosis in diabetic nephropathy. Kidney Int. 2007;71:846–854
  56. Yang J, Liu Y. Dissection of key events in tubular epithelial to myofibroblast transition and its implications in renal interstitial fibrosis. Am J Pathol. 2001;159:1465–1475
  57. Kalluri R, Neilson EG. Epithelial-mesenchymal transition and its implications for fibrosis. J Clin Invest. 2003;112:1776–1784
  58. Lan HY. Tubular epithelial-myofibroblast transdifferentiation mechanisms in proximal tubule cells. Curr Opin Nephrol Hypertens. 2003;12:25–29
  59. Zavadil J, Bottinger EP. TGF-beta and epithelial-to-mesenchymal transitions. Oncogene. 2005;24:5764–5774
  60. Zheng S, Noonan WT, Metreveli NS, et al. Development of late-stage diabetic nephropathy in OVE26 diabetic mice. Diabetes. 2004;53:3248–3257

 Supported by funding from the office of Science Financial Assistance Programs, US Department of Energy, and the National Institutes of Health grant DK176743.

PII: S0270-9295(07)00122-2

doi: 10.1016/j.semnephrol.2007.09.008

Seminars in Nephrology
Volume 27, Issue 6 , Pages 574-583 , November 2007

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