PXD011257

PXD011257 is an original dataset announced via ProteomeXchange.

Title	Pre-fractionation extends, but creates a bias in the detectable HLA class Ι ligandome
Description	HLA class Ι molecules on the cell surface enable CD8+ T lymphocytes to recognize cellular alterations in the form of antigens, including mutations, protein copy number alterations, aberrant post-translational modifications or pathogen proteins. At any given moment, tens of thousands of different self and foreign HLA class Ι peptide ligands may be presented on the cell surface by MHC class Ι complexes. Analysis of the HLA ligandome thrusts therefore unique challenges due to their enormous biochemical diversity and inherently wide range of abundances. Despite advances in enrichment, separation, MS instrumentation and fragmentation, it is still not achievable to cover the HLA class Ι ligandome in sufficient depth to support routine identification of e.g. viral pathogens or immuno-therapeutically important tumor neo-antigens. In this study, we evaluate two pre-fractionation techniques, high pH reversed phase and strong cation exchange for complementary analysis of HLA class Ι peptide ligands, benchmarking them against analyses circumventing pre-fractionation. We observe that pre-fractionation substantially extends the detectable HLA class Ι ligandome, but also creates an identification bias. We advocate a rational choice between no-fractionation, high pH reversed phase or strong cation exchange pre-fractionation for deeper HLA class Ι ligandome analysis depending on the targeted HLA locus, allele or peptide ligand modification
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:49:19.457.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Laura Demmers
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; L-citrulline
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2018-10-02 08:51:18	ID requested
1	2019-02-25 02:50:38	announced
⏵ 2	2024-10-22 04:49:27	announced	2024-10-22: Updated project metadata.

10.1021/acs.jproteome.8b00821;

Demmers LC, Heck AJR, Wu W, Ligandome. J Proteome Res, 18(4):1634-1643(2019) [pubmed]

ProteomeXchange project tag: Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

curator keyword: Technical

submitter keyword: HLA class Ι ligandome

HLA class Ι peptide ligands

high pH reversed phase

strong cation exchange

pre-fractionation

W. Wu
contact affiliation	Biomolecular Mass Spectrometry and Proteomics
contact email	w.wu1@uu.nl
lab head
Laura Demmers
contact affiliation	Utrecht University
contact email	l.c.demmers@uu.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD011257
     1. Label: PRIDE project
     2. Name: Pre-fractionation extends, but creates a bias in the detectable HLA class Ι ligandome