PXD026103-1

PXD026103 is an original dataset announced via ProteomeXchange.

Title	Targeted mass spectrometry enables quantification of novel pharmacodynamic biomarkers of ATM kinase inhibitors
Description	ATM is a serine/threonine protein kinase that is responsible for initiation of DNA repair of double-stranded breaks and is a therapeutic target in cancer. A lack of analytically robust and multiplexed assays has hampered mechanistic studies of action and determination of optimal, robust pharmacodynamic biomarkers for clinical development of new therapies targeting ATM. Targeted mass spectrometry-based assays have been shown to be capable of enabling quantitative phosphosignaling studies and identification of novel phosphorylation sites. To identify new pharmacodynamic markers of ATM inhibition and expand the capabilities of targeted proteomics for quantitative profiling of the DNA damage response, we developed and fully analytically characterized a 51-plex assay quantifying protein expression and post-translational modification (phosphorylation) following induction of DNA damage. The linear range was over 3 orders of magnitude, the median inter-assay variability was 11% CV, and the assay is capable of being used in conjunction with other multiple reaction monitoring-based multiplexed assay panels. Proof-of-principle studies quantify signaling following DNA damage (ionizing radiation) in immortalized cell lines and primary human cells, identifying NUMA1 pS395 as a PD marker for ATM inhibition following DNA damage. Furthermore, the study shows the utility of using a quantitative multiplexed assay for studying cellular signaling dynamics, and the potential application to pharmacodynamic and mechanism of action studies, including development of new pharmacodynamic markers for clinical application.
HostingRepository	PRIDE
AnnounceDate	2021-07-29
AnnouncementXML	Submission_2021-07-29_03:04:04.353.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jacob Kennedy
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	carbamoylated residue; phosphorylated residue; isotope labeled residue; 6x(13)C labeled residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2021-05-19 22:40:03	ID requested
⏵ 1	2021-07-29 03:04:04	announced

Dataset with its publication pending

ProteomeXchange project tag: CPTAC Consortium

submitter keyword: Human, Lymphoblast, ATM, phosphorylation

Amanda Paulovich
contact affiliation	Clinical Research Division, Fred Hutchinson Cancer Research Center
contact email	apaulovi@fredhutch.org
lab head
Jacob Kennedy
contact affiliation	Fred Hutchinson Cancer Research Center
contact email	jkennedy@fhcrc.org
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD026103
     1. Label: PRIDE project
     2. Name: Targeted mass spectrometry enables quantification of novel pharmacodynamic biomarkers of ATM kinase inhibitors