PXD045311

PXD045311 is an original dataset announced via ProteomeXchange.

Title	A comprehensive portrait of tissue-, age- and sex-specific DNA modifications in rodents and humans
Description	DNA damage causes genomic instability underlying many diseases, with traditional analytical approaches providing minimal insight into the spectrum of DNA lesions in vivo. Here we used untargeted chromatography-coupled tandem mass spectrometry-based adductomics (LC-MS/MS) to define the landscape of DNA modifications in rat and human tissues. A basis set of 114 putative DNA adducts was identified in heart, liver, brain, and kidney in 1-26-month-old rats and 111 in human heart and brain by “stepped MRM” LC-MS/MS. Subsequent targeted analysis of these species revealed species-, tissue-, age-, and sex-biases. Structural characterization of 10 selected adductomic signals as known DNA modifications validated the method and established confidence in the DNA origins of the signals. Along with strong tissue biases, we observed significant age-dependence for 36 adducts, including N2-CMdG, 5-HMdC, and 8-Oxo-dG in rats and 1,N6-εdA in human heart, as well as sex biases for 67 adducts in rat tissues. These results demonstrate the potential of adductomics for discovering the true spectrum of disease-driving DNA adducts. Our dataset of 114 putative adducts serves as a resource for characterizing dozens of new forms of DNA damage, defining mechanisms of their formation and repair, and developing biomarkers of aging and disease.
HostingRepository	PRIDE
AnnounceDate	2023-09-12
AnnouncementXML	Submission_2023-09-12_11:02:09.699.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	PeterDedon
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	6490 Triple Quadrupole LC/MS; 6495C Triple Quadrupole LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2023-09-12 07:52:13	ID requested
⏵ 1	2023-09-12 11:02:10	announced

Dataset with its publication pending

submitter keyword: adductomics, STRP MRM

Peter CDedon
contact affiliation	Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore
contact email	pcdedon@mit.edu
lab head
PeterDedon
contact affiliation	Massachusetts Institute of Technology
contact email	pcdedon@mit.edu
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/2023/09/PXD045311

PRIDE project URI

• PRIDE
  1. PXD045311
     1. Label: PRIDE project
     2. Name: A comprehensive portrait of tissue-, age- and sex-specific DNA modifications in rodents and humans