PXD064740

PXD064740 is an original dataset announced via ProteomeXchange.

Title	Phosphoproteomics Characterization of 12 Syngeneic Mouse Models
Description	Mouse syngeneic models serve as indispensable tools for elucidating tumor-immune interactions and assessing immunotherapy efficacy. In this study, we first conducted a comprehensive evaluation of six label-free protein quantification pipelines across 12 mouse syngeneic models, revealing that data-independent acquisition (DIA) significantly outperforms data-dependent acquisition (DDA) in terms of data coverage, reproducibility, and inter-model discrimination. We next performed an integrative multi-omics analysis to uncover molecular mechanisms associated with treatment response. Our analysis identified Dnmt3a and Igf2r, which are correlated with resistance to immune checkpoint inhibitors (ICIs), and highlighted key pathways including interferon signaling and oxidative phosphorylation that distinguish responders from non-responders. To facilitate broader research applications, we have developed an interactive web resource that shares our multi-omics datasets and analytical results, equipped with user-friendly tools for further exploration. It is freely accessible at https://muscreen.crownbio.com/syngeneic_omics. This resource aims to accelerate preclinical research and contribute to the development of personalized cancer therapies.
HostingRepository	PRIDE
AnnounceDate	2025-07-28
AnnouncementXML	Submission_2025-07-27_18:57:45.485.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zihan Xu
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	phosphorylated residue
Instrument	maXis

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-07 10:16:48	ID requested
⏵ 1	2025-07-27 18:57:46	announced

Xu Z, Mao B, Liu H, Wang S, Chen X, Guo S, Integrative multi-omics characterization of 12 syngeneic mouse models. iScience, 28(8):113024(2025) [pubmed]

10.1016/j.isci.2025.113024;

submitter keyword: Phosphoproteomics Characterization of 12 Syngeneic Mouse Models

Zihan Xu
contact affiliation	Crown Bioscience
contact email	zihan.xu@crownbio.com
lab head
Zihan Xu
contact affiliation	Crown Bioscience
contact email	zihan.xu@crownbio.com
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/2025/07/PXD064740

PRIDE project URI

• PRIDE
  1. PXD064740
     1. Label: PRIDE project
     2. Name: Phosphoproteomics Characterization of 12 Syngeneic Mouse Models