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PXD005277

PXD005277 is an original dataset announced via ProteomeXchange.

Dataset Summary
Titleisobaric Colocalisation analysis (iCOLA) of A375P and A375M2 melanoma cells
DescriptionTo 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_04:32:59.457.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterFaraz Mardakheh
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue
InstrumentOrbitrap Fusion
Dataset History
RevisionDatetimeStatusChangeLog Entry
02016-11-04 10:04:24ID requested
12016-12-21 07:01:14announced
22017-10-24 03:10:34announcedUpdated project metadata.
32024-10-22 04:33:07announced2024-10-22: Updated project metadata.
Publication List
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]
Keyword List
curator keyword: Biomedical
submitter keyword: COLA
spatial proteomics
protein-protein interactions
interactome;
Contact List
Faraz Mardakheh
contact affiliationDivision of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
contact emailmardakheh@icr.ac.uk
lab head
Faraz Mardakheh
contact affiliationInstitute of Cancer Research
contact emailMARDAKHEH@ICR.AC.UK
dataset submitter
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Dataset FTP location
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PRIDE project URI
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