PXD002434

PXD002434 is an original dataset announced via ProteomeXchange.

Title	Deep Proteomic Profiling of Vasopressin-Sensitive Collecting Duct Cells
Description	The mouse mpkCCD cell line is a continuous cultured epithelial cell line with characteristics of renal collecting duct principal cells. This line is widely used to study epithelial transport and its regulation. To provide a data resource useful for experimental design and interpretation in studies using mpkCCD cells, we have carried out 'deep' proteomic profiling of these cells using three levels of fractionation (differential centrifugation, SDS-PAGE, HPLC) followed by tandem mass spectrometry to identify and quantify proteins. The use of multiple levels of fractionation increases the ability to detect low abundance proteins. As a result, we identified 6766 proteins in mpkCCD cells at a high level of stringency. These proteins are expressed over 7 orders of magnitude of protein abundance. The data are provided to users as a public data base at https://helixweb.nih.gov/ESBL/Database/mpkFractions/. The MS data were mapped back to gel slices to generate 'virtual western blots' for each protein. For most of the 6766 proteins, the apparent molecular weight from SDS-PAGE agreed closely with the calculated molecular weight. However, a substantial fraction (>15%) of proteins were found to run aberrantly, either with much higher or much lower than predicted. These proteins were analyzed to identify mechanisms responsible for altered mobility on SDS-PAGE (high or low isoelectric point, high or low hydrophobicity, physiological cleavage, residence in the lysosome, post-translational modifications and expression of alternative isoforms due to alternative exon usage). Additionally, this analysis identified a previously unrecognized isoform of aquaporin-2 with apparent molecular weight <20 kD.
HostingRepository	PRIDE
AnnounceDate	2015-10-06
AnnouncementXML	Submission_2015-10-06_06:24:55.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	CHIN-RANG YANG
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; 6x(13)C labeled residue; deaminated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2015-06-29 01:28:27	ID requested
1	2015-10-06 05:11:52	announced
⏵ 2	2015-10-06 06:24:57	announced	Updated publication reference for PubMed record(s): 26310816, 26310817.

Yang CR, Raghuram V, Emamian M, Sandoval PC, Knepper MA, Deep proteomic profiling of vasopressin-sensitive collecting duct cells. II. Bioinformatic analysis of vasopressin signaling. Am J Physiol Cell Physiol, 309(12):C799-812(2015) [pubmed]

Yang CR, Tongyoo P, Emamian M, Sandoval PC, Raghuram V, Knepper MA, Deep proteomic profiling of vasopressin-sensitive collecting duct cells. I. Virtual Western blots and molecular weight distributions. Am J Physiol Cell Physiol, 309(12):C785-98(2015) [pubmed]

curator keyword: Biomedical

submitter keyword: aquaporin-2, LC-MS/MS, mass spectrometry, differential centrifugation, SDS-PAGE, kidney cortical collection duct

Mark A. Knepper
contact affiliation	Epithelial Systems Biology Laboratory National Heart Lung and Blood Institute National Institutes of Health
contact email	mark_knepper@nih.gov
lab head
CHIN-RANG YANG
contact affiliation	National Institutes of Health, USA
contact email	chin-rang.yang@nih.gov
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/10/PXD002434

PRIDE project URI

• PRIDE
  1. PXD002434
     1. Label: PRIDE project
     2. Name: Deep Proteomic Profiling of Vasopressin-Sensitive Collecting Duct Cells