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Database of Transportation Protein in Kidney

This database reports results from proteomic profiling of subcellular fractions in cultured kidney collecting duct cells. The database was created by Chin-Rang Yang, Pumipat Tongyoo, and Mark A. Knepper in the Epithelial Systems Biology Laboratory (ESBL) in the Division of Intramural Research (DIR) of the National Heart, Lung and Blood Institute (NHLBI).

Vasopressin regulates water permeability in the renal collecting duct in part by regulating the water channel protein Aquaporin 2 (AQP2). Here, we report large-scale quantification of proteins using LC-MS/MS of subcellular fractions from differential centrifugation in vasopressin- and vehicle-treated mouse mpkCCD cells. Quantification was done by SILAC. Cells treated with the vasopressin analog dDAVP (heavy) or vehicle (light) were mixed 1:1 prior to homogenization and fractionation by differential centrifugation. Fractions were subjected to SDS-PAGE, trypsinization and quantification by LC-MS/MS. Differential centrifugation fractions: 1000 Xg pellet (1K), 4000 Xg pellet (4K), 17,000 Xg pellet (17K), 200,000 Xg pellet (200Kp), and 200,000 Xg supernatant (200Ks). A total of 8608 proteins were quantified among all the fractions.

Abundance Levels in Fraction (x1000): The sum of light(ctrl)-channel intensities (area-under-curve) from the reconstructed ion chromatograms (MS1) of all peptides mapped to a given protein. The intensities were scaled as total proteins from each fraction were loaded to Mass Spectrometry.
Median Log2 (dDAVP/Ctrl) Ratio: The median Log2 ratio of Heavy(dDAVP)/Light(Ctrl) channels from all peptides mapped to a given protein. The values of intensities were median-normalized in each channel before calculating ratios.
Virtual Western Blot: The data can be viewed as virtual western blots that map the peptide intensities to individual slices from the SDS-PAGE for a given protein. The intensities were scaled as 100ug proteins were loaded equally in each lane. **These virtual blots can be viewed by mouse over the GI Number at the left. **Clicking on the Official Gene Symbol for a given protein will reveal its NCBI RefSeq record.

The virtual western blot images show data normalized using a linear conversion scale to map peptide intensities to gray-scale levels. Using this conversion method, low-abundance peptides are generally not visible in the blot images. To visualize these, switch to logarithmic conversion scale database page.

For relative protein abundances in this cell line, please visit Relative Protein Abundances in Mouse mpkCCD Cells database page.
For apparent vs. calculated MW ratios in this cell line, please visit Apparent / Calculated MW Ratios in Mouse mpkCCD Cells database page.
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Reference I: Deep Proteomic Profiling of Vasopressin-Sensitive Collecting Duct Cells. I. Virtual Western Blots and Molecular Weight Distributions. Yang, et al. (2015), PMID: 26310816
Reference II: Deep Proteomic Profiling of Vasopressin-Sensitive Collecting Duct Cells. II. Bioinformatic Analysis of Vasopressin Signaling. Yang et al. (2015), PMID: 26310817
Note: n.v. ; no value
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