PXD011690

PXD011690 is an original dataset announced via ProteomeXchange.

Title	A study into the ADP-ribosylome of IFN--stimulated THP-1 human macrophage-like cells identifies ARTD8/PARP14 and ARTD9/PARP9 ADP-ribosylation
Description	ADP-ribosylation is a post-translational modification that, until recently, has remained elusive to study at the cellular level. Previously dependent on radioactive tracers to identify ADP-ribosylation targets, several advances in mass spectrometric workflows now permit global identification of ADP-ribosylated substrates. In this study, we capitalized on two ADP-ribosylation enrichment strategies, and multiple activation methods performed on the Orbitrap Fusion Lumos, to identify IFN--induced ADP-ribosylation substrates in macrophages. The ADP-ribosyl binding protein, Af1521, was used to enrich ADP-ribosylated peptides, and the anti-poly-ADP-ribosyl antibody, 10H, was used to enrich ADP-ribosylated proteins. ADP-ribosyl-specific mass spectra were further enriched by an ADP-ribose product ion triggered EThcD and HCD activation strategy, in combination with multiple acquisitions that segmented the survey scan into smaller ranges. HCD and EThcD resulted in overlapping and unique ADP-ribosyl peptide identifications, with HCD providing more peptide identifications but EThcD providing more reliable ADP-ribosyl acceptor sites. Our acquisition strategies also resulted in the first ever characterization of ADP-ribosyl on three poly-ADP-ribose polymerases, ARTD9/PARP9, ARTD10/PARP10, and ARTD8/PARP14. IFN- increased the ADP-ribosylation status of ARTD9/PARP9, ARTD8/PARP14, and proteins involved in RNA processes. This study therefore summarizes specific molecular pathways at the intersection of IFN- and ADP-ribosylation signaling pathways.
HostingRepository	PRIDE
AnnounceDate	2020-01-27
AnnouncementXML	Submission_2020-01-27_03:57:49.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sasha Singh
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	2018-11-13 08:16:16	ID requested
1	2019-08-22 07:12:02	announced
2	2019-08-26 23:43:45	announced	Updated publication reference for PubMed record(s): 30848916.
⏵ 3	2020-01-27 03:57:51	announced	2020-01-27: Updated publication reference for PubMed record(s): 30848916.

Higashi H, Maejima T, Lee LH, Yamazaki Y, Hottiger MO, Singh SA, Aikawa M, -Stimulated THP-1 Human Macrophage-like Cells Identifies ARTD8/PARP14 and ARTD9/PARP9 ADP-Ribosylation. J Proteome Res, 18(4):1607-1622(2019) [pubmed]

submitter keyword: higher-energy collision dissociation (HCD), electron transfer higher-energy collision dissociation (EThcD), Orbitrap Fusion Lumos, gas phase segmentation, parallel reaction monitoring (PRM), proteomics, post-translational modification (PTM)

SASHA SINGH
contact affiliation	BRIGHAM AND WOMEN'S HOSPITAL, HARVARD MEDICAL SCHOOL
contact email	SASINGH@BWH.HARVARD.EDU
lab head
Sasha Singh
contact affiliation	Brigham and Women's Hospital, Harvard Medical School
contact email	sasingh@partners.org
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/2020/01/PXD011690

PRIDE project URI

• PRIDE
  1. PXD011690
     1. Label: PRIDE project
     2. Name: A study into the ADP-ribosylome of IFN--stimulated THP-1 human macrophage-like cells identifies ARTD8/PARP14 and ARTD9/PARP9 ADP-ribosylation