PXD028088

PXD028088 is an original dataset announced via ProteomeXchange.

Title	Unsupervised mining of HLA-I peptidomes reveals unsuspected false positives and new binding motifs
Description	Modern antigen vaccine designs and studies of human leukocyte antigen (HLA)-mediated immune responses rely heavily on the knowledge of HLA allele-specific binding motifs and computational prediction of antigen-HLA binding affinity. Breakthroughs in HLA peptidomics have considerably expanded the databases of natural HLA antigens and enabled detailed characterizations of antigen-HLA binding specificity. However, cautions must be made when analyzing HLA peptidomics data because identified peptides may be contaminants or may weakly bind to the HLA molecules. Here, a hybrid de novo peptide sequencing approach was applied to large-scale mono-allelic HLA peptidomics datasets to uncover new antigens and refine current knowledge of HLA binding motifs. Up to 12-40% contaminations in the form of tryptic peptides were identified in the peptidomics data of HLA alleles whose binding motifs do not involve an arginine or a lysine at the C-terminus. Thousands of these peptides were reported in a community database as positive antigens and might be erroneously used to train prediction models. Furthermore, unsupervised clustering of identified antigens not only revealed additional binding motifs for several HLA class I alleles but also effectively isolated outliers which were confirmed to be false positives in a binding experiment. Overall, our findings expanded the knowledge of HLA binding specificity and indicated that a more careful HLA peptidomics data interpretation protocol is needed to ensure the high quality of community antigen databases.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:29:31.865.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Poorichaya Somparn
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2021-08-24 03:08:27	ID requested
1	2021-09-17 07:14:35	announced
⏵ 2	2024-10-22 05:29:32	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: SMSnet, Peptidome, HLA-I

Poorichaya somparn
contact affiliation	Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok, Thailand 10330
contact email	poorichaya.s@chula.ac.th
lab head
Poorichaya Somparn
contact affiliation	Chulalongkorn university
contact email	poorichaya.s@chula.ac.th
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD028088
     1. Label: PRIDE project
     2. Name: Unsupervised mining of HLA-I peptidomes reveals unsuspected false positives and new binding motifs