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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
-
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 Proteins 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 Jul
24; 20(16):2463-2477.
-
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.
-
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.
-
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]
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