PXD001225

PXD001225 is an original dataset announced via ProteomeXchange.

Title	Novel surface functionalized superparamagnetic nanoparticles with engineered cellular uptake as a means for intracellular omics
Description	Superparamagnetic nanoparticles (SPMNPs) are appealing for use in organelle isolation strategies. Yet, this potential remains largely unexplored because thus far research has focused on either physicochemical design or on their application in micron-sized beads. For their use in life sciences, the biocompatibility of SPMNPs goes beyond their chemical composition and shape, and features like their size and more importantly their surface properties are becoming more important to exploit extra- and intracellular interactions. Here we introduce thermal decomposition to manufacture iron oxide based SPMNPs (Ø10nm) and demonstrate how different surface functionalizations can lead to different types of cellular interactions. Cationic aminolipid-coated SPMNPs reside surprisingly strong at the outer cell surface. In contrast, anionic dimercaptosuccinic acid-coated SPMNPs are efficiently internalized and accumulate in a time-dependent manner in endosomal and lysosomal populations. These features allowed us to establish a standardized magnetic isolation procedure to selectively isolate plasma membranes and intracellular late endosomes/lysosomes with high yields and purities as consolidated by biochemical and ultrastructural analyses. Subsequent quantitative and qualitative proteome analysis underpins the overall high enrichment for hydrophobic (membrane) proteins as well as plasma membrane and lysosomal constituents in the respective purified fractions. This nano based technology provides therefore a breakthrough in the field of subcellular ‘omics’ as it allows the identification of subtle alterations in the biomolecular composition of different SPMNP-isolated compartments that would be otherwise not detected in total cell or tissue analysis.
HostingRepository	PRIDE
AnnounceDate	2017-02-06
AnnouncementXML	Submission_2017-02-06_04:06:37.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD001225
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Arun Kumar Tharkeshwar
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidoethyl-L-cysteine; monohydroxylated residue; acetylated residue; deaminated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2014-08-14 03:11:56	ID requested
⏵ 1	2017-02-06 04:06:38	announced

Tharkeshwar AK, Trekker J, Vermeire W, Pauwels J, Sannerud R, Priestman DA, Te Vruchte D, Vints K, Baatsen P, Decuypere JP, Lu H, Martin S, Vangheluwe P, Swinnen JV, Lagae L, Impens F, Platt FM, Gevaert K, Annaert W, A novel approach to analyze lysosomal dysfunctions through subcellular proteomics and lipidomics: the case of NPC1 deficiency. Sci Rep, 7():41408(2017) [pubmed]

curator keyword: Technical, Biomedical

submitter keyword: HeLa cells, Superparamagnetic nanoparticles, Subcellular organelles, Proteomics

Prof. Dr. Kris Gevaert
contact affiliation	Department of Medical Protein Research, VIB & Department of Biochemistry, UGent, Ghent, Belgium
contact email	kris.gevaert@vib-ugent.be
lab head
Arun Kumar Tharkeshwar
contact affiliation	VIB-KU Leuven
contact email	arun.tharkeshwar@cme.vib-kuleuven.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/2017/02/PXD001225

PRIDE project URI

• PRIDE
  1. PXD001225
     1. Label: PRIDE project
     2. Name: Novel surface functionalized superparamagnetic nanoparticles with engineered cellular uptake as a means for intracellular omics