Experimental Details for IMCD Proteome Database

Expt.	Mass Spec Type*	Experiment Description	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 vasopresson 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 vasopresson 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 (LCQ)	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	4 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
14	LC-MS/MS (LTQ-Orbitrap XL)	Large-scale phosphotyrosine proteomic profiling	none	False discovery rate <1% by target-decoy analysis	Zhao, 2012
15	LC-MS/MS (LTQ-Orbitrap Velos)	Phosphoproteomics of rat IMCD: response to vasopressin	iTRAQ	False discovery rate <1% by target-decoy analysis	Hoffert, 2012
16	LC-MS/MS (LTQ-Orbitrap Velos)	Phosphoproteomics of rat IMCD: response to vasopressin antagonist satavaptan	iTRAQ	False discovery rate <1% by target-decoy analysis	Hoffert, 2014
17	LC-MS/MS (LTQ-Orbitrap)	IMCD phosphoproteome after 9 hour lithium administration	Label free	False discovery rate <2% by target-decoy analysis	Trepiccione, 2014
18	LC-MS/MS (LTQ-Orbitrap Velos)	In vitro phosphorylation of proteins in IMCD suspensions	Label free	False discovery rate <1% by target-decoy analysis	Bradford, 2014
19	LC-MS/MS (LTQ-Orbitrap Velos)	Proteomic profiling of cellular fractions enriched in nuclear proteins from native IMCD cells	Label free	False discovery rate <1% by target-decoy analysis	Pickering, 2016
20	LC-MS/MS (LTQ-Orbitrap Velos)	Proteomic profiling of cellular fractions enriched in cytoplasmic proteins from native IMCD cells	Label free	False discovery rate <1% by target-decoy analysis	LeMaire, 2016

* Mass spectrometer type

MALDI-TOF: Ettan^TM 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
LTQ-Orbitrap Velos: ThermoFinnigan linear ion trap MS
LTQ-Orbitrap XL: ThermoFinnigan linear ion trap MS

**References

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.
Zhao B, Knepper MA, Chou CL, Pisitkun T. Large-scale phosphotyrosine proteomic profiling of rat renal collecting duct epithelium reveals predominance of proteins involved in cell polarity determination. Am J Physiol Cell Physiol. 2012 Jan 1;302(1):C27-45. doi: 10.1152/ajpcell.00300.2011. Epub 2011 Sep 21. PubMed PMID: 21940666; PubMed Central PMCID: PMC3328908.
Hoffert JD, Pisitkun T, Saeed F, Song JH, Chou CL, Knepper MA. Dynamics of the G protein-coupled vasopressin V2 receptor signaling network revealed by quantitative phosphoproteomics. Mol Cell Proteomics. 2012 Feb;11(2): M111.014613.
Hoffert JD, Pisitkun T, Saeed F, Wilson JL, Knepper MA. Global analysis of the effects of the V2 receptor antagonist satavaptan on protein phosphorylation in collecting duct. Am J Physiol Renal Physiol. 2014 Feb 15;306(4):410-21.
Trepiccione F, Pisitkun T, Hoffert JD, Poulsen SB, Capasso G, Nielsen S, Knepper MA, Fenton RA, Christensen BM. Early targets of lithium in rat kidney inner medullary collecting duct include p38 and ERK1/2. Kidney Int. 2014 Apr 30.
Bradford D, Raghuram V, Wilson JL, Chou CL, Hoffert JD, Knepper MA, Pisitkun T. Use of LC-MS/MS and Bayes' Theorem to Identify Protein Kinases That Phosphorylate Aquaporin-2 at Ser256. Am J Physiol Cell Physiol. 2014 Mar 5.
Pickering CM, Grady C, Medvar B, Emamian M, Sandoval PC, Zhao Y, Yang CR, Jung HJ, Chou CL, Knepper MA. Proteomic profiling of nuclear fractions from native renal inner medullary collecting duct cells. Am J Physiol Physiol Genomics. 2016 Feb 1.
LeMaire S, Raghuram V, Grady CR, Pickering CM, Chou CL, Umejiego EN, Knepper MA. Serine/Threonine Phosphatases and Aquaporin-2 Regulation in Renal Collecting Duct. Am J Physiol Renal Physiol 2016 Oct 26.