PXD031245-2

PXD031245 is an original dataset announced via ProteomeXchange.

Title	Proximity labelling and cryomill affinity purification compared for Trypanosoma brucei proteins with unconfined, semi-confined and confined localisation
Description	Identification of protein-protein interactions is a major contributor for understanding protein function and elucidating molecular and cellular mechanisms. Two strategies are currently popular for identification of protein interaction partners directly from the cellular environment. Affinity purification (pulldown) isolates the protein of interest with the aid of a matrix that specifically captures the target and potential partners. In BioID, the protein of interest is fused to biotin ligase facilitating proximity biotinylation and biotinylated proteins are isolated under stringent conditions with streptavidin. Whilst clear that these two methods can provide insight, it is also apparent that they can reveal distinct interactomes, but the basis for these differences is less obvious. We compare these methods using four different trypanosome proteins as baits: the cytoplasmic poly(A) binding proteins PABP1 and PABP2, mRNA export receptor MEX67, that shuttles between the nucleus and the cytoplasm with predominant localisation at the nuclear pores, and the nucleoporin NUP158.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:42:33.446.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Martin Zoltner
SpeciesList	scientific name: Trypanosoma brucei; NCBI TaxID: 5691;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2022-01-25 07:35:20	ID requested
1	2022-11-30 07:02:39	announced
⏵ 2	2023-11-14 07:42:37	announced	2023-11-14: Updated project metadata.

Moreira CMDN, Kelemen CD, Obado SO, Zahedifard F, Zhang N, Holetz FB, Gauglitz L, Dallagiovanna B, Field MC, Kramer S, Zoltner M, Impact of inherent biases built into proteomic techniques: Proximity labeling and affinity capture compared. J Biol Chem, 299(1):102726(2023) [pubmed]

submitter keyword: cryomilling,Affinity purification, proteome, BioID, interactome

Martin Zoltner
contact affiliation	Head of Drug Discovery and Evaluation Center for Research of Pathogenicity and Virulence of Parasites Charles University in Prague, BIOCEV Průmyslová 595 252 50 Vestec Czech Republic phone: +420 325 873 966
contact email	zoltnerm@natur.cuni.cz
lab head
Martin Zoltner
contact affiliation	Division of Biological Chemistry & Drug Discovery School of Life Sciences University of Dundee Dundee DD1 5EH
contact email	m.zoltner@dundee.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/2022/11/PXD031245

PRIDE project URI

• PRIDE
  1. PXD031245
     1. Label: PRIDE project
     2. Name: Proximity labelling and cryomill affinity purification compared for Trypanosoma brucei proteins with unconfined, semi-confined and confined localisation