PXD062352-1

PXD062352 is an original dataset announced via ProteomeXchange.

Title	Higher-throughput and sensitive immunopeptidomics profiling
Description	We developed a refined sample preparation workflow that is fully optimized to process low-input and crude samples in 96-well plates, aiming to combine high-throughput with maximal sensitivity. We implemented a miniaturized and automated workflow in a 96-well format using the Tecan Resolvex® A200 liquid handling positive pressure device. We optimized lysis in small volumes to achieve more sensitive and efficient IPs in 96-well plates under static conditions, to minimize peptide losses due to surface contact, and to eliminate the need for plate rotation and unnecessary sample transfers. Additionally, using an appropriate pore-size for the 96-well filter plate for IP prevented sample leakage and ensured efficient processing. This workflow reduces the required sample input from 500 million to as few as 16 million cells for routine experiments, and is compatible with input amounts going down to 20,000 cells. It minimizes reagent volumes, accommodates up to 96 samples simultaneously, and enables the ultrasensitive pull down from low input samples with near-complete capture of MHC peptides. Furthermore, we achieved high sensitivity by combining the sample preparation with advanced ion mobility mass spectrometry using a timsTOF SCP. This improved workflow achieves robust immunopeptidome coverage from as few as 20,000 JY cells, identifying approximately 13,000 distinct MHC-I peptides and over 5,000 MHC-II peptides from 16 million JY cells by injecting only 25% of the enriched peptides into the mass spectrometer.
HostingRepository	PRIDE
AnnounceDate	2026-04-03
AnnouncementXML	Submission_2026-04-03_08:19:03.690.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Patrick Willems
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue
Instrument	timsTOF SCP

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-28 09:05:14	ID requested
⏵ 1	2026-04-03 08:19:04	announced

Dataset with its publication pending

submitter keyword: Immunopeptidomics, bacterial infection

Francis Impens
contact affiliation	VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
contact email	Francis.Impens@UGent.be
lab head
Patrick Willems
contact affiliation	Ghent University
contact email	patwille.willems@ugent.be
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/2026/04/PXD062352

PRIDE project URI

• PRIDE
  1. PXD062352
     1. Label: PRIDE project
     2. Name: Higher-throughput and sensitive immunopeptidomics profiling