PXD069119

PXD069119 is an original dataset announced via ProteomeXchange.

Title	HigH-ratiO partiaL proteolysiS with carriER proteome (HOLSER) Enables Global Structure Profiling and Site-resolved Elucidation of Ligand-Protein Interactions
Description	Understanding how cellular proteins interact with their environment, including endogenous and exogeneous molecules, is critical for elucidating mechanisms of cellular regulation and drug action. Partial proteolysis-based techniques offer peptide-level resolution of ligand-induced conformational changes but are limited by modest proteome coverage and depth, as well as sensitivity to the experimental conditions. To overcome these limitations, we developed higH ratiO partiaL proteolysiS with carriER proteome (HOLSER), an efficient workflow that features extended digestion time for low peptide yield variability and tandem mass tag (TMT)-based multiplexing that includes full digests for enhanced proteome depth and sequence coverage as well as higher precision of abundance measurements. We demonstrate HOLSER capabilities across diverse usage cases, including global proteome structure profiling, kinase target mapping, and structural mapping of the FKBP-mTOR complex in response to rapamycin. HOLSER reveals domain-specific stabilization and identifies peptides in direct contact with ligands, providing a powerful and scalable platform for simultaneous probing structural changes at the scale of the whole proteome, individual protein domains and specific binding sites.
HostingRepository	PRIDE
AnnounceDate	2026-06-08
AnnouncementXML	Submission_2026-06-07_18:43:40.452.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Massimiliano Gaetani
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-03 06:35:34	ID requested
⏵ 1	2026-06-07 18:43:41	announced

Lyu H, Gharibi H, Meng Z, Sokolova B, Lundstr, ö, m S, Zhang X, Zubarev RA, Peptide-to-Protein Data Aggregation Using Fisher's Method Improves Target Identification in Chemical Proteomics. Anal Chem, 98(17):12596-12602(2026) [pubmed]

10.1021/acs.analchem.5c08021;

submitter keyword: proteomics, TMT,Drug Traget deconvolution, LC-MS, machanism of action, partial proteolysis

Massimiliano Gaetani
contact affiliation	Chemical Proteomics, Division of Chemistry I, Department of Medical Biochemistry and Biophysics Karolinska Institutet, Stockholm, Sweden
contact email	massimiliano.gaetani@ki.se
lab head
Massimiliano Gaetani
contact affiliation	Karolinska Institutet
contact email	massimiliano.gaetani@ki.se
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/2026/06/PXD069119

PRIDE project URI

• PRIDE
  1. PXD069119
     1. Label: PRIDE project
     2. Name: HigH-ratiO partiaL proteolysiS with carriER proteome (HOLSER) Enables Global Structure Profiling and Site-resolved Elucidation of Ligand-Protein Interactions