PXD004040

PXD004040 is an original dataset announced via ProteomeXchange.

Title	Proteomic analysis of mouse podocytes
Description	The renal filtration barrier is critically maintained by the renal podocyte, a postmitotic, neuron-like epithelial cell type. Cultured podocyte cell lines – both in the differentiated and undifferentiated state - are a widely utilized tool to estimate cytoskeletal rearrangement processes in vitro. Here, we mapped the podocyte proteome at a depth of more than 7000 proteins. The data dissects the dynamic range of the podocyte proteome during differentiation. The data also demonstrates an absolute quantitative analysis of proteins mutated in forms of hereditary disease and demonstrates expression of several proteins not expressed in other, standard cell lines. We validated differentially regulated proteins using immunoblot and functional assays estimating lysosomal and proteasomal function. Comparison with deep mapping RNAseq data from the native podocyte, preliminary fingerprint data from the native proteome and staining intensities from the human protein atlas was performed to estimate similiarities between the cultured and native podocyte proteome, unravelling that at least 26 high-abundant native, podocyte-specific proteins, were not identified in the dataset. Notably, this data detected general perturbations in proteostatic mechanisms as a key alteration during podocyte differentiation, with increased proteasome activity in the undifferentiated state and markedly increased expression of lysosomal proteins in the differentiated state. We also performed a comparative phosphoproteomic analysis with published data from the native glomeruli, revealing a strong fuzziness of phosphorylation process as compared to the native podocyte phosphoproteome. The data also suggests a preference of phosphorylation of actin associated proteins in the differentiated state. The dataset obtained here, a valuable resource, warrants and provides the means for deep mapping of the native podocyte proteome and phosphoproteome in a similar manner.
HostingRepository	PRIDE
AnnounceDate	2016-07-04
AnnouncementXML	Submission_2016-07-04_04:36:37.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Markus Rinschen
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-04-25 00:02:50	ID requested
⏵ 1	2016-07-04 04:36:38	announced

Rinschen MM, Schroeter CB, Koehler S, Ising C, Schermer B, Kann M, Benzing T, Brinkkoetter PT, Quantitative deep mapping of the cultured podocyte proteome uncovers shifts in proteostatic mechanisms during differentiation. Am J Physiol Cell Physiol, 311(3):C404-17(2016) [pubmed]

curator keyword: Biological

submitter keyword: Mouse, podocyte, LC-MS/MS

Markus Rinschen
contact affiliation	University Hospital Cologne
contact email	markus.rinschen@uk-koeln.de
lab head
Markus Rinschen
contact affiliation	Kidney research center cologne
contact email	markus.rinschen@uk-koeln.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD004040
     1. Label: PRIDE project
     2. Name: Proteomic analysis of mouse podocytes