PXD040858-2

PXD040858 is an original dataset announced via ProteomeXchange.

Title	A microfluidics-enabled automated workflow of sample preparation for MS-based immunopeptidomics
Description	Mass spectrometry (MS)-based immunopeptidomics is an attractive antigen discovery method with growing clinical implications, especially for personalized cancer immunotherapies. However, the current experimental approach to extract HLA-I-restricted peptides requires a bulky sample source, which remains a challenge for obtaining clinical tumor samples. We present an innovative streamlined workflow that requires a low sample volume. The workflow integrates the immunoaffinity purification (IP) and C18 peptide cleanup steps on a single microfluidics platform with automated liquid handling and minimal sample transfers, resulting in higher assay sensitivity. We also demonstrate how state-of-the-art data-independent acquisition (DIA) MS method further enhances the depth and reproducibility of tandem mass spectrometry (MS2) spectra-based peptide sequencing. As a result, over 4,000 and 5,000 HLA-I restricted peptides can be reliably identified from as low as 0.2 million human RA957 cells and a melanoma tissue of merely 5 mg, respectively. We also identified multiple known immunogenic tumor-associated antigens and hundreds of peptides derived from non-canonical protein sources. The presented workflow is a powerful tool for identifying the immunopeptidome of sparse samples.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:45:40.412.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michal Bassani-Sternberg
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-14 08:05:35	ID requested
1	2023-05-12 13:56:47	announced
⏵ 2	2024-10-22 05:45:40	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: mass spectrometry, immunopeptidomics, sample preparation, data-independent acquisition, automation,Microfluidics

Michal Bassani-Sternberg
contact affiliation	Department of oncology UNIL CHUV Ludwig Institute for Cancer Research Lausanne Office B25A/04/94 Rue du Bugnon 25a, CH-1005 Lausanne
contact email	michal.bassani@chuv.ch
lab head
Michal Bassani-Sternberg
contact affiliation	UNIL/CHUV
contact email	michal.bassani@chuv.ch
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/2023/05/PXD040858

PRIDE project URI

• PRIDE
  1. PXD040858
     1. Label: PRIDE project
     2. Name: A microfluidics-enabled automated workflow of sample preparation for MS-based immunopeptidomics