PXD004009

PXD004009 is an original dataset announced via ProteomeXchange.

Title	A whole proteome inventory of background photocrosslinker binding
Description	Affinity based protein profiling (AfBPP) is a widely applied methodology for target identification of bioactive molecules. Photocrosslinkers such as benzophenone, diazirine and aryl azide irreversibly link the molecule of interest to its dedicated target protein upon irradiation with UV light. Despite their prevalent application in chemical biology little is known about photolinker-specific off-targets affecting the reliability of results. Here we investigate background protein labelling in intact human cell lines via gel-free quantitative proteomics. Characteristic off-targets were identified for each photo-reactive group and compiled in a comprehensive inventory (photome). In a proof of principle study, H8, an established inhibitor of protein kinase A (PKA), was equipped with a diazirine moiety and revealed, by alignment with the photo-background, unprecedented insight into its in situ proteome targets. Taken together, our findings provide an experimental guideline to surmount photoprobe ambiguity and focus results on biologically relevant binders.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_06:38:27.237.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Matthias Stahl
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2016-04-19 02:19:45	ID requested
1	2016-12-06 00:43:04	announced
⏵ 2	2023-11-14 06:38:27	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

curator keyword: Technical

submitter keyword: affinity-based protein profiling,photocrosslinker, target identification

Stephan Axel Sieber
contact affiliation	Lehrstuhl Organische Chemie II, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85747 Garching b. München
contact email	stephan.sieber@tum.de
lab head
Matthias Stahl
contact affiliation	Karolinska Institutet
contact email	matthias.stahl@ki.se
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/2016/12/PXD004009

PRIDE project URI

• PRIDE
  1. PXD004009
     1. Label: PRIDE project
     2. Name: A whole proteome inventory of background photocrosslinker binding