PXD050336-1

PXD050336 is an original dataset announced via ProteomeXchange.

Title	Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues
Description	Tissue lysis using urea buffer was adopted in our previously published CPTAC protocol for mass spectrometry (MS)-based quantitative global proteomic and phosphoproteomic analysis. Herein, we reported an update to this initial protocol by implementing a sonication step into urea-based tissue lysis. Similar to the initial CPTAC protocol, we identified >12,000 proteins and >25,000 phosphopeptides in a TMT set containing both non-sonicated and sonicated tumor tissues from patient-derived xenograft mouse models. However, an improvement in the detection of membrane-bound and DNA-binding proteins was observed by including the sonication. We also offered recommendations for optimal sonication conditions such as buffer composition, timing, and instrumentation settings, and a troubleshooting section for potential users. Additionally, the protocol is equally applicable to other biological specimens.
HostingRepository	PRIDE
AnnounceDate	2025-07-28
AnnouncementXML	Submission_2025-07-27_16:24:28.198.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yingwei HU
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-04 12:36:07	ID requested
⏵ 1	2025-07-27 16:24:30	announced

Li QK, Lih TM, Clark DJ, Chen L, Schnaubelt M, Zhang H, Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues. Nat Protoc, 20(8):2083-2099(2025) [pubmed]

10.1038/s41596-024-01113-9;

ProteomeXchange project tag: CPTAC Consortium

submitter keyword: global proteomics, phosphoproteomics, tumor-associated proteomics,sonication

Tung-Shing Mamie Lih
contact affiliation	Johns Hopkins University
contact email	tlih1@jhmi.edu
lab head
Yingwei HU
contact affiliation	Johns Hopkins University
contact email	yhu39@jhmi.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/2025/07/PXD050336

PRIDE project URI

• PRIDE
  1. PXD050336
     1. Label: PRIDE project
     2. Name: Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues