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Technique Summary for IMCD Proteome Database
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Technique Mass Spec Type* Experiment Quantitative Technique Mass Spectrometry Filter Used Reference**
1MALDI-TOFIMCD vs. non-IMCD protein amountsDIGEp-value < 0.1Hoffert, 2004
2MALDI-TOF3 day vasopressin infusion to Brattleboro ratDIGEp-value < 0.1van Balkom, 2004
3LC-MS/MS (LCQ)IMCD vs. non-IMCD protein amountsICAT2 or more peptides matchPisitkun, 2006
4LC-MS/MS (LCQ)3 day vasopressin infusion to Brattleboro ratICAT2 or more peptides matchPisitkun, 2006
5LC-MS/MS (LCQ)Isolation of AQP-2 containing intracellular vesiclesnone2 or more peptides matchBarile, 2005
6LC-MS/MS (LTQ)Flow through proteins from avidin affinity step of technique 4none2 or more peptides matchPisitkun, 2006
7MALDI-TOF/TOFVasopressin escape in ratDIGEp-value < 0.1Hoorn, 2005
8LC-MS/MS (LTQ and FT-ICR)Phosphoproteome of IMCDLabel free1 or more peptide + manual examination of FT-ICR dataHoffert, 2006
9LC-MS/MS (LTQ)IMCD vs. non-IMCD protein amountsIVICAT2 or more peptides matchSimons, 2006
10LC-MS/MS (LTQ)Perfusion-biotinylation or incubation-biotinylation of IMCDnone1 or more peptide + manual examinationYu, 2006
10aLC-MS/MS (LTQ)Fixed perfusion-biotinylationnone1 or more peptide + manual examinationYu, 2006
10bLC-MS/MS (LTQ)Fixed incubation-biotinylationnone1 or more peptide + manual examinationYu, 2006
10cLC-MS/MS (LTQ)10a or 10b without fixationnone1 or more peptide + manual examinationYu, 2006
11LC-MS/MS (LTQ)Proteome of differential centrifugation fractions of rat IMCDLabel freeFalse discovery rate < 2% by target-decoy analysisSachs, 2008
12LC-MS/MS (LTQ)Proteome of nuclei from rat IMCDnoneFalse discovery rate < 2% by target-decoy analysisTchapyjnikov, 2009
13LC-MS/MS (LTQ)IMCD samples were treated with dDAVP for 30 min.Label freeFalse discovery rate < 2% by target-decoy analysisBansal, 2010

* Mass spectrometer type

  • MALDI-TOF: EttanTM MALDI-ToF Pro MS
  • MALDI-TOF/TOF: ABI 4700 MALDI-TOF/TOF MS
  • LCQ: ThermoFinnigan 3D ion trap MS
  • LTQ: ThermoFinnigan linear ion trap MS
  • FT-ICR: ThermoFinnigan FT-ICR MS

** Reference

  1. Hoffert JD, van Balkom BW, Chou CL, Knepper MA. Application of difference gel electrophoresis to the identification of inner medullary collecting duct proteins. Am J Physiol Renal Physiol. 2004 Jan;286(1):F170-9.
  2. van Balkom BW, Hoffert JD, Chou CL, Knepper MA. Proteomic analysis of long-term vasopressin action in the inner medullary collecting duct of the Brattleboro rat. Am J Physiol Renal Physiol. 2004 Feb;286(2):F216-24.
  3. Barile M, Pisitkun T, Yu MJ, Chou CL, Verbalis MJ, Shen RF, Knepper MA. Large scale protein identification in intracellular aquaporin-2 vesicles from renal inner medullary collecting duct. Mol Cell Proteomics. 2005 Aug;4(8):1095-106.
  4. Hoorn EJ, Hoffert JD, Knepper MA. Combined proteomics and pathways analysis of collecting duct reveals a protein regulatory network activated in vasopressin escape. J Am Soc Nephrol. 2005 Oct;16(10):2852-63.
  5. Pisitkun T, Bieniek J, Tchapyjnikov D, Wang G, Wu WW, Shen RF, Knepper MA. High-throughput identification of IMCD proteins using LC-MS/MS. Physiol Genomics. 2006 Apr 13;25(2):263-76.
  6. Hoffert JD, Pisitkun T, Wang G, Shen RF, Knepper MA. Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites. Proc Natl Acad Sci U S A. 2006 May 2;103(18):7159-64.
  7. Simons BL, Wang G, Shen RF, Knepper MA. In vacuo isotope coded alkylation technique (IVICAT); an N-terminal stable isotopic label for quantitative liquid chromatography/mass spectrometry proteomics. Rapid Commun Mass Spectrom. 2006;20(16):2463-77.
  8. Yu MJ, Pisitkun T, Wang G, Shen RF, Knepper MA. LC-MS/MS analysis of apical and basolateral plasma membranes of rat renal collecting duct cells. Mol Cell Proteomics. 2006 Nov;5(11):2131-45.
  9. Sachs AN, Pisitkun T, Hoffert JD, Yu MJ, Knepper MA. LC-MS/MS analysis of differential centrifugation fractions from native inner medullary collecting duct of rat. Am J Physiol Renal Physiol. 2008 Dec;295(6):F1799-806.
  10. Tchapyjnikov D, Li Y, Pisitkun T, Hoffert JD, Yu MJ, Knepper MA. Proteomic profiling of nuclei from native renal inner medullary collecting duct cells using LC-MS/MS. Physiol Genomics. 2010 Feb 4;40(3):167-83.
  11. Bansal AD, Hoffert JD, Pisitkun T, Hwang S, Chou CL, Boja ES, Wang G, Knepper MA. Phosphoproteomic profiling reveals vasopressin-regulated phosphorylation sites in collecting duct. J Am Soc Nephrol. 2010 Feb;21(2):303-15.
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