PXD072729

PXD072729 is an original dataset announced via ProteomeXchange.

Title	Data-Independent Acquisition Enhancement of a Competitive Activity-Based Protein Profiling Platform for Kinase Inhibitor Screening
Description	Kinase inhibitors represent a vital class of therapeutic agents widely used in cancer research, immunology, and other disease areas. Mass spectrometry (MS) employing specially designed small molecule kinase-binding probes has become an essential strategy for identifying novel kinase drug targets. While traditional MS approaches often rely on targeted proteomics (e.g., multiple reaction monitoring, MRM) or data-dependent acquisition (DDA), data-independent acquisition (DIA) offers broader and more reproducible quantification, especially for low-abundance peptides. In this study, we systematically developed an activity-based protein profiling (ABPP) platform leveraging DIA, through integrated in-house informatics tools for data filtering and motif analysis, to provide an effective kinase profiling workflow. Compared to DDA, the DIA approach yielded more than a 100% increase in identified biotinylated peptides and over 40% improvement in kinase peptide coverage, while reducing the analysis time by half (90 min vs. 180 min per sample). Additionally, there was a modest improvement to the coefficient of variation (CV) in kinase peptide quantification (11.41% to 10.70%; mean CV). Shorter liquid chromatography (LC) gradient times (60, 45, and 30 min) were evaluated as a means for increasing sample analysis throughput. Notably, no significant loss in kinase peptide coverage was observed due to shorter gradients, highlighting the capability of DIA to significantly enhance the efficiency and scalability of kinase profiling workflows.
HostingRepository	PRIDE
AnnounceDate	2026-02-23
AnnouncementXML	Submission_2026-02-22_17:58:06.451.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dingyin Tao
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2026-01-06 18:23:59	ID requested
⏵ 1	2026-02-22 17:58:07	announced

Tharakan R, Qu Y, Ceribelli M, Morris PJ, Fang Y, Thomas CJ, LeClair CA, Tao D, Data-Independent Acquisition Enhancement of a Competitive Activity-Based Protein Profiling Platform for Kinase Inhibitor Screening. J Mass Spectrom, 61(3):e70038(2026) [pubmed]

10.1002/jms.70038;

submitter keyword: proteomics, mass spectrometry,Activity-based protein profiling, kinase, data-independent acquisition

Dingyin Tao
contact affiliation	National Center for Advancing Translational Sciences, National Institutes of Health
contact email	dingyin.tao@nih.gov
lab head
Dingyin Tao
contact affiliation	National Institutes of Health (NIH) National Center for Advancing Translational Sciences (NCATS)
contact email	dingyin.tao@nih.gov
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/2026/02/PXD072729

PRIDE project URI

• PRIDE
  1. PXD072729
     1. Label: PRIDE project
     2. Name: Data-Independent Acquisition Enhancement of a Competitive Activity-Based Protein Profiling Platform for Kinase Inhibitor Screening