PXD005272

PXD005272 is an original dataset announced via ProteomeXchange.

Title	Colocalisation (COLA) analysis of RPE cells untreated or treated with Blebbistatin
Description	To analyse protein-protein interactions on a global scale, we devised a methodology termed COLA, which uses subcellular fractionation combined with quantitative proteomics to generate multivariate subcellular localisation signatures for cellular proteins. Bootstrapped clustering was then used to match proteins with significant similarity in their localisation signatures. We utilised SILAC labeled human Retinal Pigment Epithelial-1 (RPE1) cells. Heavy and light labelled cells were fractionated using 4 parallel subcellular fractionation procedures, resulting in a total of 12 fractions. The majority of fractions come from two procedures, one using serial solubilisation (resulting in fractions for cytosol, total membrane, nuclear lumen,chromatin-bound nuclear, as well as two cytoskeletal fractions) and the other using centrifugation coupled with aqueous biphasic extraction (resulting in a total nuclear fraction, intracellular membranes fraction, plasma-membrane fraction, and a cytosol + microsomes fraction). The third fractionation procedure separated cellular protrusions using porous transwell membranes, and finally the fourth procedure separated the extracellular compartment by collecting conditioned media. Fractions from each SILAC label were then mixed with equal amounts of total cell lysate from the oposite label to generate fraction/lysate SILAC SILAC mixes. Two repicrocally labelled biological replicate experiments were performed. In addition to untreated RPE1 cells, we also analysed RPE1 cells pre-teated with the Myosin-II inhibitor Blebbistatin for 4 hours prior to fractionation to reveal changes in the protein localisation profiles upon Myosin-II inhibition, as Myosin-II is a key regulator of the cytoskeleton as well as intra-cellular trafficking (Note that the blebbistatin set is not included in the associated manuscript).
HostingRepository	PRIDE
AnnounceDate	2017-10-24
AnnouncementXML	Submission_2017-10-24_03:11:20.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Faraz Mardakheh
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2016-11-04 05:09:19	ID requested
1	2016-12-21 08:10:04	announced
⏵ 2	2017-10-24 03:11:21	announced	Updated project metadata.

Mardakheh FK, Sailem HZ, K, ü, mper S, Tape CJ, McCully RR, Paul A, Anjomani-Virmouni S, J, ø, rgensen C, Poulogiannis G, Marshall CJ, Bakal C, Proteomics profiling of interactome dynamics by colocalisation analysis (COLA). Mol Biosyst, 13(1):92-105(2016) [pubmed]

curator keyword: Biological

submitter keyword: COLA

spatial proteomics

protein-protein interactions

interactome;

Faraz Mardakheh
contact affiliation	Division of Cancer Biology, Institute of Cancer Research, 237 Fulham road, London SW3 6JB, UK.
contact email	mardakheh@icr.ac.uk
lab head
Faraz Mardakheh
contact affiliation	Institute of Cancer Research
contact email	MARDAKHEH@ICR.AC.UK
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/2016/12/PXD005272

PRIDE project URI

• PRIDE
  1. PXD005272
     1. Label: PRIDE project
     2. Name: Colocalisation (COLA) analysis of RPE cells untreated or treated with Blebbistatin