PXD018272

PXD018272 is an original dataset announced via ProteomeXchange.

Title	Fishing for newly synthesized proteins with phosphonate-handles
Description	Bioorthogonal chemistry introduces affinity-labels into biomolecules with minimal disruption to the original system and is widely applicable in a range of contexts. In proteomics, immobilized metal affinity chromatography (IMAC) enables enrichment of phosphopeptides with extreme sensitivity and selectivity. Here, we adapt and combine these superb assets in a new enrichment strategy using phosphonate-handles, which we term ‘PhosID’. In this approach, ‘click-able’ phosphonate-handles are introduced into proteins via 1,3-dipolar Huisgen-cycloaddition to azido-homo-alanine (AHA) and IMAC is then used to enrich exclusively for phosphonate-labeled peptides. In interferon-gamma (IFNγ) stimulated cells, PhosID enabled the identification of a large number of IFN responsive newly synthesized proteins (NSPs) whereby we monitored the differential synthesis of these proteins over time. Collectively, these data validate the excellent performance of PhosID with efficient analysis and quantification of hundreds of NSPs by single LC-MS/MS runs. We envision PhosID as an attractive and alternative tool for studying stimuli-sensitive proteome subsets.
HostingRepository	PRIDE
AnnounceDate	2020-11-06
AnnouncementXML	Submission_2020-11-06_08:54:26.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	wei wu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	biotinylated residue; phosphorylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-30 08:26:03	ID requested
1	2020-07-28 08:49:55	announced
2	2020-08-11 04:39:07	announced	2020-08-11: Updated publication reference for PubMed record(s): 32591520.
⏵ 3	2020-11-06 08:54:27	announced	2020-11-06: Updated project metadata.

Kleinpenning F, Steigenberger B, Wu W, Heck AJR, Fishing for newly synthesized proteins with phosphonate-handles. Nat Commun, 11(1):3244(2020) [pubmed]

ProteomeXchange project tag: EPIC-XS

submitter keyword: affinity enrichment, click chemistry, bioorthogonal, LC-MS

Wei Wu
contact affiliation	Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
contact email	w.wu1@uu.nl
lab head
wei wu
contact affiliation	Utrecht University
contact email	w.wu1@uu.nl
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/2020/07/PXD018272

PRIDE project URI

• PRIDE
  1. PXD018272
     1. Label: PRIDE project
     2. Name: Fishing for newly synthesized proteins with phosphonate-handles