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PXD004246

PXD004246 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleiMixPro: intelligent Mixing of Proteomes for elimination of false positives in affinity purification-mass spectrometry
DescriptionProtein complexes are essential in most organizational and functional aspects of the cell. Different strategies currently exist to analyze such protein complexes by mass spectrometry, including affinity purification (AP-MS) and proximal labeling based strategies. However, the high sensitivity of current mass spectrometers typically results in extensive protein lists mainly consisting out of non-specifically co-purified proteins. Finding the true positive interactors in these lists thus remains highly challenging with proposed solutions on all levels of such experiments. Here, we report an intelligent experimental design based on differential isotopic labeling combined with non-equal mixing of control and experimental samples to discover bona fide interaction partners in AP-MS experiments. We apply this intelligent Mixing of Proteomes (iMixPro) concept to overexpression experiments where we investigate the interactomes of RAF1, RNF41 and TANK, and also to engineered cell lines expressing epitope-tagged endogenous PTPN14, JIP3 and IQGAP1. For all baits, we observed both known and novel interactions. The results for RNF41 and TANK were compared to a classical affinity purification design which clearly underscores the efficiency and the specificity of the iMixPro approach.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_04:30:01.424.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterSven Eyckerman
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentLTQ Orbitrap Velos; Q Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02016-05-31 02:00:53ID requested
12016-09-27 01:15:45announced
22024-10-22 04:30:09announced2024-10-22: Updated project metadata.
Publication List
Eyckerman S, Impens F, Van Quickelberghe E, Samyn N, Vandemoortele G, De Sutter D, Tavernier J, Gevaert K, Intelligent Mixing of Proteomes for Elimination of False Positives in Affinity Purification-Mass Spectrometry. J Proteome Res, 15(10):3929-3937(2016) [pubmed]
Keyword List
curator keyword: Technical
submitter keyword: human overexpression cell lines AP-MS SILAC
Contact List
Kris Gevaert
contact affiliationVIB Medical Biotechnology Center, VIB, A. Baertsoenkaai 3 B-9000 Ghent, Belgium Department of Biochemistry, Ghent University, A. Baertsoenkaai 3 B-9000 Ghent, Belgium
contact emailkris.gevaert@vib-ugent.be
lab head
Sven Eyckerman
contact affiliationVIB Center for Medical Biotechnology
contact emailsven.eyckerman@vib-ugent.be
dataset submitter
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Dataset FTP location
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Repository Record List
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