| 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 |
| 13 | LC-MS/MS (LTQ) | IMCD samples were treated with dDAVP for 30 min. | Label free | False discovery rate < 2% by target-decoy analysis | Bansal, 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
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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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