PXD039552-3

PXD039552 is an original dataset announced via ProteomeXchange.

Title	Inter-Laboratory Variability in the Madin-Darby Canine Kidney Cell ProteomeInter-Laboratory Variability in the Madin-Darby Canine Kidney Cell Proteome
Description	Madin-Darby Canine Kidney (MDCK) cells are widely used to study epithelial cell functionality. Their low endogenous drug transporter protein levels make them an amenable system to investigate trans-epithelial permeation and drug transporter protein activity after their transfection. MDCK cells display diverse phenotypic traits and as such laboratory-to-laboratory variability in drug permeability assessments are observed. Consequently, In Vitro-In Vivo extrapolation (IVIVE) approaches using permeability and/or transporter activity data require calibration. A comprehensive proteomic quantification of eleven filter-grown parental or mock-transfected MDCK monolayers from eight different pharmaceutical laboratories using the Total Protein Approach (TPA) is provided. TPA enabled estimations of key morphometric parameters such as monolayer cellularity and volume. Overall, metabolic liability to xenobiotics is likely to be limited for MDCK cell due to the low expression of required enzymes. SLC16A1 (MCT1) was the highest abundance SLC transporter linked to xenobiotic activity, while ABCC4 (MRP4) was the highest abundant ABC transporter. Our data supports existing findings that Claudin-2 levels may be linked to tight junction modulation, thus impacting trans-epithelial resistance. This unique database provides data on more than 8000 proteins copy number and concentrations, thus allowing an in-depth appraisal of the control monolayers used in each laboratory.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:56:46.806.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jacek Wisniewski
SpeciesList	scientific name: Zea mays (Maize); NCBI TaxID: 4577;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-18 16:29:17	ID requested
1	2023-07-20 11:57:45	announced
2	2023-11-14 09:03:35	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 05:56:48	announced	2024-10-22: Updated project metadata.

10.1021/acs.molpharmaceut.3c00108;

Harwood MD, Zettl K, Weinheimer M, Pilla-Reddy V, Shen H, Jacobs F, Chu X, Huth F, Nakakariya M, Chothe PP, Neuhoff S, Wi, ś, niewski JR, Interlaboratory Variability in the Madin-Darby Canine Kidney Cell Proteome. Mol Pharm, 20(7):3505-3518(2023) [pubmed]

submitter keyword: Label-free Proteomics

Total Protein Analysis (TPA)

MDCK

Epithelial Proteome

ADME Protein Abundances

Jacek R Wisniewski
contact affiliation	Max Planck Institute of Biochemisrty
contact email	jwisniew@biochem.mpg.de
lab head
Jacek Wisniewski
contact affiliation	Proteomics
contact email	jwisniew@biochem.mpg.de
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/2023/07/PXD039552

PRIDE project URI

• PRIDE
  1. PXD039552
     1. Label: PRIDE project
     2. Name: Inter-Laboratory Variability in the Madin-Darby Canine Kidney Cell ProteomeInter-Laboratory Variability in the Madin-Darby Canine Kidney Cell Proteome