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Techniques Used

Technique Mass Spec Type* Experiment Quantitative Technique Mass Spectrometry Filter Used Reference**
1 MALDI-TOF IMCD vs. non-IMCD protein amounts DIGE p value < 0.1 Hoffert, 2004
2 MALDI-TOF 3 day Vasopressin infusion to Brattleboro rat DIGE p value < 0.1 van Balkom, 2004
3 LC-MS/MS (LCQ) IMCD vs. non-IMCD protein amounts ICAT 2 or more peptides match Pisitkun, 2006
4 LC-MS/MS (LCQ) 3 day Vasopressin infusion to Brattleboro rat ICAT 2 or more peptides match Pisitkun, 2006
5 LC-MS/MS (LCQ) Isolation of AQP-2 containing intracellular vesicles none 2 or more peptides match Barile, 2005
6 LC-MS/MS (LTQ) Flow through proteins from avidin affinity step of technique 4 none 2 or more peptides match Pisitkun, 2006
7 MALDI-TOF/TOF Vasopressin escape in rat DIGE p value < 0.1 Hoorn, 2005
8 LC-MS/MS (LTQ and FT-ICR) Phosphoproteome of IMCD Label free 1 or more peptide + manual examination of FT-ICR data Hoffert, 2006
9 LC-MS/MS (LTQ) IMCD vs. non-IMCD protein amounts IVICAT 2 or more peptides match Simons, 2006
10 LC-MS/MS (LTQ) Perfusion-biotinylation or incubation-biotinylation of IMCD none 1 or more peptide + manual examination Yu, 2006
10a LC-MS/MS (LTQ) Fixed perfusion-biotinylation none 1 or more peptide + manual examination Yu, 2006
10b LC-MS/MS (LTQ) Fixed incubation-biotinylation none 1 or more peptide + manual examination Yu, 2006
10c LC-MS/MS (LTQ) 10a or 10b without fixation none 1 or more peptide + manual examination Yu, 2006
11 LC-MS/MS (LTQ) Proteome of differential centrifugation fractions of rat IMCD Label free False discovery rate < 2% by target-decoy analysis Sachs, 2008
12 LC-MS/MS (LTQ) Proteome of nuclei from rat IMCD none False discovery rate < 2% by target-decoy analysis Tchapyjnikov, 2009

* Mass spectrometer type

  • MALDI-TOF: Ettan™ 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 Proteins 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 Jul 24; 20(16):2463-2477.
  8. Yu MJ, Pisitkun T, Wang G, Shen RF, Knepper MA. Proteomic 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, and 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, and Knepper MA. Proteomic profiling of nuclei from native inner medullary collecting duct cells using LC-MS/MS. Physiol Genomics. 2009 Dec 8. [Epub ahead of print]