PXD005277-3

PXD005277 is an original dataset announced via ProteomeXchange.

Title	isobaric Colocalisation analysis (iCOLA) of A375P and A375M2 melanoma cells
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 identified proteins. Bootstrapped clustering is then used to match proteins with significant similarity in their localisation signatures. A variarion of this method optimised for rapid analysis of interactome dynamics using isobaric labelling (iCOLA) was developed and used to compare interactomes of A375P melanoma cells which are weakly metastatic, against a highly metastatic derivative named A375M2. Cells were fractionated using two parallel subcellular fractionation procedures, resulting in a total of 9 fractions. The first fractionation procedure uses a serial solubilisation approach, resulting in five subcellular fractions (cytosol, total membrane, nuclear lumen,chromatin-bound nuclear, and cytoskeleton). The second procedure uses centrifugation coupled with aqueous biphasic extraction resulting in four fractions (total nuclear, intracellular membranes, plasma-membrane, and cytosol + microsomes). For quantifications, fractions were TMT labelled using a TMT 10plex labelling kit (Thermo). A total cell lysate control was also included as the 10th channel, with protein intensities in each subcellular fraction being normalised to the total lysate control intensities. Three sets of samples were analysed: two biological replicates of A375P (sample sets A and B), and one A375M2 sample(sample set C). We compared A and B to assess iCOLA reproducibility, and B and C to assess interactome dynamics between A375P and A375M2 cells.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:32:59.457.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
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2016-11-04 10:04:24	ID requested
1	2016-12-21 07:01:14	announced
2	2017-10-24 03:10:34	announced	Updated project metadata.
⏵ 3	2024-10-22 04:33:07	announced	2024-10-22: 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: Biomedical

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/PXD005277

PRIDE project URI

• PRIDE
  1. PXD005277
     1. Label: PRIDE project
     2. Name: isobaric Colocalisation analysis (iCOLA) of A375P and A375M2 melanoma cells