Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DIA acquisition of the immunopeptidomes of C1R-B57:01 and C1R-A02:01 cell lines

ABSTRACT: Immunopeptidomes are the peptide repertoires bound by the molecules encoded by the major histocompatibility complex (MHC) (human leukocyte antigen (HLA) in humans). These HLA-peptide complexes are presented on the cell surface for immune T cell recognition. Immunopeptidomics utilizes tandem mass spectrometry (MS/MS) to identify and quantify peptides bound to HLA molecules. Data-independent acquisition (DIA) has emerged as a powerful strategy for deep proteome-wide profiling, but DIA application to immunopeptidomics analyses has so far seen limited use. The dataset deposited here contains the DIA data of the HLA-bound peptides purified and isolated from C1R-B*57:01 and C1R-A*02:01 cell lines.

INSTRUMENT(S): Orbitrap Fusion, Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Mohammad Shahbazy

LAB HEAD: Anthony W. Purcell

PROVIDER: PXD034539 | Pride | 2023-02-13

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	F120191219_PF_C1R-B5701_w632_MS_12122019_S1_DIA.raw	Raw
	F120191219_PF_C1R-B5701_w632_MS_12122019_S2_DIA.raw	Raw
	F120191219_PF_C1R-B5701_w632_MS_12122019_S3_DIA.raw	Raw
	F120201221_PF_C1R-B5701_DIA_W632_MS_04122020_DF0-2_r1.raw	Raw
	F120201221_PF_C1R-B5701_DIA_W632_MS_04122020_DF0-2_r2.raw	Raw

Items per page:

1 - 5 of 30

Similar Datasets

DDA acquisition of the immunopeptidomes of C1R-B*57:01 and C1R-A*02:01 cell lines

Project description:Immunopeptidomes are the peptide repertoires bound by the molecules encoded by the major histocompatibility complex (MHC) (human leukocyte antigen (HLA) in humans). These HLA-peptide complexes are presented on the cell surface for immune T cell recognition. Immunopeptidomics utilizes tandem mass spectrometry (MS/MS) to identify and quantify peptides bound to HLA molecules. The dataset deposited here contains the DDA runs used to generate the spectral libraries of the HLA-bound peptides purified and isolated from C1R-B*57:01 and C1R-A*02:01 cell lines.

2023-02-13 | PXD034429 | Pride

Thermostability profiling of MHC-bound peptides: a new dimension in immunopeptidomics and design of immunotherapeutics

Project description:The features of peptide antigens that contribute to their immunogenicity are poorly understood. Although the stability of peptide-MHC (pMHC) is known to be important, current assays assess this interaction only for peptides in isolation and not in the context of natural antigen processing and presentation. Here, we present a novel method which provides a comprehensive and unbiased measure of pMHC stability for thousands of individual ligands detected simultaneously by mass spectrometry (MS). The method allows rapid assessment of intra- and inter-allelic differences in pMHC stability and reveals broader profiles of stability than previously appreciated. The additional dimensionality of the data facilitated the training of a model which improved the prediction of peptide immunogenicity, specifically of cancer neoepitopes. This assay can be applied to any cells bearing MHC or MHC-like molecules, offering insight into not only the endogenous immunopeptidome, but also that of neoepitopes and pathogen-derived sequences.

2020-11-30 | PXD017839 | Pride

Identification of HLA-B*57:01-restricted endogenous and HIV epitopes

Project description:A novel modified HLA-B*57:01-restricted epitope was identified in one of the reversed-phase fractions following immunoaffinity purification of HLA-peptide complexes from C1R cells expressing HIV envelope protein. Also includes six immunopeptidome datasets from several B57 and env transfected cell lysates.

2018-02-19 | PXD004471 | Pride

C1R.A*01:01, C1R.A*02:01, C1R.A*24:02 MHC class I immunopeptidome LC-MSMS

Project description:Characterisation of peptide ligands of Major histocompatibility class (MHC) I isolated by immunoaffinity purification from the C1R (Class I reduced) B-lymphoblastoid cell line, transfected with the MHC class I allele HLA-A*01:01, or HLA-A*02:01, HLA-A*24:02. In addition, public mass spectrometry (MS) datasets of HLA-I and HLA-II immunopeptidome derived from patients’ samples, PBMC or cell lines, and shotgun proteomics from trypsin/elastase digestion were analysed.

2020-07-27 | PXD014754 | Pride

Unveiling the Peptide Motifs of HLA-C and HLA-G from Naturally Presented Peptides and Generation of Binding Prediction Matrices

Project description:The classical HLA-C and the nonclassical HLA-E and HLA-G molecules play important roles both in the innate and adaptive immune system. Starting already during embryogenesis and continuing throughout our lives, these three Ags exert major functions in immune tolerance, defense against infections, and anticancer immune responses. Despite these important roles, identification and characterization of the peptides presented by these molecules has been lacking behind the more abundant HLA-A and HLA-B gene products. In this study, we elucidated the peptide specificities of these HLA molecules using a comprehensive analysis of naturally presented peptides.

2018-04-20 | PXD009531 | Pride

Influenza B-derived peptide presentation by HLA-B*07:02, -B*08:01 and -B*35:01

Project description:Analysis of peptide presentation by Human Leukocyte Antigen (HLA) class I of influenza B infected C1R cells expressing HLA-B*07:02, -B*08:01 or -B*35:01.

2024-03-04 | PXD045000 | Pride

C1R.B*57:01 MHC class I immunopeptidome LC-MSMS

2018-10-24 | PXD008570 | Pride

C1R.B*58:01 MHC class I immunopeptidome LC-MSMS

2018-10-24 | PXD008572 | Pride

Thermostability profiling of MHC-bound peptides: a new dimension in immunopeptidomics and design of immunotherapeutics.

Project description:The features of peptide antigens that contribute to their immunogenicity are poorly understood. Although the stability of peptide-MHC (pMHC) is known to be important, current assays assess this interaction only for peptides in isolation and not in the context of natural antigen processing and presentation2–4. Here, we present a novel method which provides a comprehensive and unbiased measure of pMHC stability for thousands of individual ligands detected simultaneously by mass spectrometry (MS). The method allows rapid assessment of intra- and inter-allelic differences in pMHC stability and reveals broader profiles of stability than previously appreciated. The additional dimensionality of the data facilitated the training of a model which improved the prediction of peptide immunogenicity, specifically of cancer neoepitopes. This assay can be applied to any cells bearing MHC or MHC-like molecules, offering insight into not only the endogenous immunopeptidome, but also that of neoepitopes and pathogen-derived sequences.

2020-11-30 | PXD017824 | Pride

HLA-I peptidomes and phosphopeptidomes (B*40, B*27, B*07, B*39)

Project description:As aberrant phosphorylation is a hallmark of tumor cells, the display of tumor-specific phosphopeptides by Human Leukocyte Antigen (HLA) class I molecules can be exploited in the treatment of cancer by T-cell-based immunotherapy. Yet, the characterization and prediction of HLA-I phospholigands is challenging as the molecular determinants of the presentation of such post-translationally modified peptides are not fully understood. Here, we employed a peptidomic workflow to identify phosphorylated ligands associated with HLA-B*40, -B*27, -B*39 and -B*07. Remarkably, these phosphopeptides showed similar molecular features. Besides the specific anchor motifs imposed by the binding groove of each allotype, the predominance of phosphorylation at peptide position 4 (P4) became strikingly evident, as was the enrichment of basic residues at P1. This molecular understanding of the presentation of phosphopeptides by HLA-B molecules can help in predicting tumor-specific neo-antigens that arise from aberrant phosphorylation in cancer cells.

2016-12-12 | PXD005084 | Pride