PXD004246

PXD004246 is an original dataset announced via ProteomeXchange.

Title	iMixPro: intelligent Mixing of Proteomes for elimination of false positives in affinity purification-mass spectrometry
Description	Protein 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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:30:01.424.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sven Eyckerman
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-05-31 02:00:53	ID requested
1	2016-09-27 01:15:45	announced
⏵ 2	2024-10-22 04:30:09	announced	2024-10-22: Updated project metadata.

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]

curator keyword: Technical

submitter keyword: human overexpression cell lines AP-MS SILAC

Kris Gevaert
contact affiliation	VIB Medical Biotechnology Center, VIB, A. Baertsoenkaai 3 B-9000 Ghent, Belgium Department of Biochemistry, Ghent University, A. Baertsoenkaai 3 B-9000 Ghent, Belgium
contact email	kris.gevaert@vib-ugent.be
lab head
Sven Eyckerman
contact affiliation	VIB Center for Medical Biotechnology
contact email	sven.eyckerman@vib-ugent.be
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/2016/09/PXD004246

PRIDE project URI

• PRIDE
  1. PXD004246
     1. Label: PRIDE project
     2. Name: iMixPro: intelligent Mixing of Proteomes for elimination of false positives in affinity purification-mass spectrometry