PXD017417

PXD017417 is an original dataset announced via ProteomeXchange.

Title	Mapping physiological ADP-ribosylation using Activated Ion Electron Transfer Dissociation (AI-ETD)
Description	ADP-ribosylation (ADPr) is a post-translational modification that plays pivotal roles in a wide range of cellular processes. Mass spectrometry (MS)-based analysis of ADPr under physiological conditions, without relying on genetic or chemical perturbation, has been hindered by technical limitations. Here, we describe the applicability of activated ion electron transfer dissociation (AI-ETD) for MS-based proteomics analysis of physiological ADPr using our unbiased Af1521 enrichment strategy. To benchmark AI-ETD, we profile 9,000 ADPr peptides mapping to >5,000 unique ADPr sites from a limited number of cells exposed to oxidative stress and identify 120% and 28% more ADPr peptides compared to contemporary strategies using ETD and electron-transfer higher-energy collisional dissociation (EThcD), respectively. Under physiological conditions, AI-ETD identifies 450 ADPr sites on low-abundant proteins, including in vivo cysteine modifications on poly(ADP-ribosyl)polymerase (PARP) 8 and tyrosine modifications on PARP14, hinting at specialist enzymatic functions for these enzymes. Collectively, our data provide insights into the physiological regulation of ADPr.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:12:37.894.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sara Larsen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	adenosine diphosphoribosyl (ADP-ribosyl) modified residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-02-06 05:06:32	ID requested
1	2020-09-23 07:22:15	announced
2	2021-02-11 22:35:32	announced	2021-02-12: Updated publication reference for PubMed record(s): 32966781.
3	2023-05-14 13:59:13	announced	2023-05-14: Updated project metadata.
⏵ 4	2024-10-22 05:12:38	announced	2024-10-22: Updated project metadata.

10.1016/j.celrep.2020.108176;

Buch-Larsen SC, Hendriks IA, Lodge JM, Ryk, æ, r M, Furtw, ä, ngler B, Shishkova E, Westphall MS, Coon JJ, Nielsen ML, Mapping Physiological ADP-Ribosylation Using Activated Ion Electron Transfer Dissociation. Cell Rep, 32(12):108176(2020) [pubmed]

ProteomeXchange project tag: EPIC-XS

submitter keyword: activated ion electron transfer dissociation, post-translational modification, ADPr, PTM, PARP, AI-ETD,ADP-ribosylation

Michael Lund Nielsen
contact affiliation	Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
contact email	michael.lund.nielsen@cpr.ku.dk
lab head
Sara Larsen
contact affiliation	NNF Center for Protein Research
contact email	sara.larsen@cpr.ku.dk
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/2020/09/PXD017417

PRIDE project URI

• PRIDE
  1. PXD017417
     1. Label: PRIDE project
     2. Name: Mapping physiological ADP-ribosylation using Activated Ion Electron Transfer Dissociation (AI-ETD)