Dataset Information

MHCquant2 refines immunopeptidomics tumor antigen discovery

ABSTRACT: The identification of human leukocyte antigen (HLA)-presented peptides as targets of anti-cancer T cell response is pivotal for the development of novel immunotherapies. Mass spectrometry (MS)-based immunopeptidomics enables the detection of these peptides, yet confident identifications and thus implementation in immunotherapy design are hampered by the high diversity and low abundance of naturally presented HLA peptides. Here, we introduce MHCquant2, a Nextflow-based open-source pipeline that leverages OpenMS tools and peptide property predictors (DeepLC, MS2PIP) for highly sensitive and scalable HLA peptide identification and quantification across various MS platforms. MHCquant2 increased peptide identifications up to 27% with significant expansion of low-abundant peptides, outperforming state-of-the-art pipelines. Using MHCquant2 we build a comprehensive benign tissue repository comprising re-analyzed data from available benign immunopeptidomes and a novel benignMHCquant2 dataset, adding more than 160,000 novel naturally presented HLA peptides. First applications of this benign repository and the MHCquant2 pipeline enabled (i) the refinement of tumor-associated antigens, (ii) as well as the detection of novel, high-frequent tumor-exclusive peptide antigens for multiple tumor entities, and (iii) the identification and quantification of mutation-derived low-abundant neoepitopes. MHCquant2 refines tumor antigen discovery in immunopeptidomics, paving the way for the implementation of off-the-shelf and personalized immunotherapy design.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Heart, Cerebellum, Testis, Spleen, Brain, Tongue, Liver, Lung, Gall Bladder, Bladder, Thyroid Gland, Kidney, Gastric Antrum, Aorta, Skin, Muscle, Pancreas, Bone Marrow, Gastric Fundus, Adrenal Gland, Small Intestine

SUBMITTER: Jonas Scheid

LAB HEAD: Juliane Sarah

PROVIDER: PXD058436 | Pride | 2025-08-22

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	241008_MW_Synpepmix01_100fmol_JS_classI_Bassani_DDA1_msms10.raw	Raw
	241008_MW_Synpepmix01_100fmol_JS_classI_Bassani_DDA2_msms16.raw	Raw
	241008_MW_Synpepmix02_100fmol_JS_classI_Bassani_DDA1_msms18.raw	Raw
	241008_MW_Synpepmix02_100fmol_JS_classI_Bassani_DDA2_msms19.raw	Raw
	241126_MW_Synpepmix03_200fmol_JS_classI_Bassani_DDA1_msms10.raw	Raw

Items per page:

1 - 5 of 2017

Similar Datasets

Project description:Various cancer immunotherapies rely on the T cell recognition of peptide antigens presented on human leukocyte antigens (HLA). However, the identification and selection of naturally presented peptide targets for the development of personalized as well as off-the-shelf immunotherapy approaches remains challenging. Here, we introduce the open-access Peptides for Cancer Immunotherapy Database (PCI-DB, https://pci-db.org/), a comprehensive resource of immunopeptidome data originating from various malignant and benign primary tissues that provides the research community with a convenient tool to facilitate the identification of peptide targets for immunotherapy development. The PCI-DB includes > 6.6 million HLA class I and > 3.4 million HLA class II peptides from over 40 tissue types and cancer entities analyzed uniformly using high-sensitive nf-core bioinformatics pipelines and applying a global peptide false discovery rate (FDR) approach. First application of the database provided insights into the representation of cancer-testis antigens (CTA) across malignant and benign tissues and enabled the identification and characterization of the cross-tumor entity and entity-specific tumor-associated antigens as well as naturally presented neoepitopes from frequent cancer mutations. Further, we used the PCI-DB to design personalized peptide vaccines for two patients suffering from metastatic cancer. PCI-DB enabled the composition of both a multi-peptide vaccine comprising non-mutated, highly frequent tumor-associated antigens matching the immunopeptidome of the individual patient´s tumor and a neoepitope-based vaccine matching the mutational profile of the cancer patient. Both vaccine approaches induced potent and long-lasting T-cell responses, accompanied by long-term survival of these advanced cancer patients. In conclusion, the PCI-DB provides a highly versatile tool to broaden the understanding of cancer-related antigen presentation and, ultimately, supports the development of novel immunotherapies.

Dataset Information

MHCquant2 refines immunopeptidomics tumor antigen discovery

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets