PXD059495-1

PXD059495 is an original dataset announced via ProteomeXchange.

Title	Structural surfaceomics of myeloma models to identify tumor-specific protein conformations
Description	Proteins at the cell surface are promising targets for cancer immunotherapies. While standard surface proteomics can be powerful for target discovery, even more fruitful is identifying cancer-specific surface protein features. To this end, we recently described a technology to identify cancer-specific protein three-dimensional conformations. In “structural surfaceomics”, we integrated XL-MS and surface protein biotinylation to identify the active conformation of integrin beta-2 as a promising cellular therapy target in acute myeloid leukemia (Mandal et al, Nature Cancer (2023)). However, we only applied structural surfaceomics to a single cancer model, and crosslink modeling was done manually. Here, we apply our technology to additional cancer models and implement an automated pipeline for crosslink characterization, AlphaCross-XL (Biswas et al, ASMS abstract (2023)).
HostingRepository	PRIDE
AnnounceDate	2025-10-20
AnnouncementXML	Submission_2025-10-19_18:31:20.327.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Abhilash Barpanda
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-07 00:57:32	ID requested
⏵ 1	2025-10-19 18:31:21	announced

Shenoy SV, Biswas D, Zalevsky A, Kishishita A, Verma A, Upadhay I, He Y, Sali A, Viner R, Mandal K, Srivastava S, Wiita AP, AlphaCross-XL: A Seamless Tool for Automated and Proteome-Scale Mapping of Cross-Linked Peptides Onto 3D Protein Structures. Mol Cell Proteomics, 24(10):101057(2025) [pubmed]

10.1016/j.mcpro.2025.101057;

submitter keyword: cell surface proteomics

XL-MS

crosslinking mass spectrometry

structural biology

protein structure

Arun Wiita
contact affiliation	Associate Professor, Department of Laboratory Medicine, UCSF
contact email	Arun.Wiita@ucsf.edu
lab head
Abhilash Barpanda
contact affiliation	IIT Bombay
contact email	avilash94@iitb.ac.in
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/2025/10/PXD059495

PRIDE project URI

• PRIDE
  1. PXD059495
     1. Label: PRIDE project
     2. Name: Structural surfaceomics of myeloma models to identify tumor-specific protein conformations