PXD035591-2

PXD035591 is an original dataset announced via ProteomeXchange.

Title	Structural surfaceomics of Nomo-1 using PhoX cross-linker with timsTOF
Description	The project aimed to profile the cell surface proteins of Nomo-1 (AML cell line) using structural surfaceomics for identification of protein conformation-based cancer antigens thereby expanding the toolkit for cancer target discovery for immunotherapeutic targeting. To achieve the goal, cell surface capture (CSC) was integrated with cross-linking mass spectrometry (XL-MS). PhoX was used as a cross-linker to freeze the structural conformations of protein in three-dimensional space, followed by biotinylation of cell surface proteins to enable enrichment of cell surface proteins to allow focused XL-MS analysis of those enriched proteins. PhoX having in-built phosphonate-based IMAC handle which allowed additional enrichment of cross-linked peptides.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:04:58.268.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kamal Mandal
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2022-07-25 11:30:25	ID requested
1	2023-10-04 04:34:13	announced
⏵ 2	2024-10-22 06:04:58	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: XL-MS, PhoX, cell surfaceome,Nomo-1, AML

Dr. Arun P. Wiita
contact affiliation	Dept. of Laboratory Medicine University of California, San Francisco, USA
contact email	arun.wiita@ucsf.edu
lab head
Kamal Mandal
contact affiliation	University of California, San Francisco
contact email	kamal.mandal@ucsf.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/2023/10/PXD035591

PRIDE project URI

• PRIDE
  1. PXD035591
     1. Label: PRIDE project
     2. Name: Structural surfaceomics of Nomo-1 using PhoX cross-linker with timsTOF