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Title: An open-source computational and data resource to analyze digital maps of immunopeptidomes

Journal Article · · eLife, 4:Article No. e07661
DOI:https://doi.org/10.7554/eLife.07661· OSTI ID:1221455
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We present a novel proteomics-based workflow and an open source data and computational resource for reproducibly identifying and quantifying HLA-associated peptides at high-throughput. The provided resources support the generation of HLA allele-specific peptide assay libraries consisting of consensus fragment ion spectra and the analysis of quantitative digital maps of HLA peptidomes generated by SWATH mass spectrometry (MS). This is the first community-based study towards the development of a robust platform for the reproducible and quantitative measurement of HLA peptidomes, an essential step towards the design of efficient immunotherapies.

Research Organization:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Organization:
USDOE
DOE Contract Number:
AC05-76RL01830
OSTI ID:
1221455
Report Number(s):
PNNL-SA-108494; 48680; 400412000
Journal Information:
eLife, 4:Article No. e07661, Journal Name: eLife, 4:Article No. e07661
Country of Publication:
United States
Language:
English

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Cited By (30)

Proteogenomics from a bioinformatics angle: A growing field: PROTEOGENOMICS FROM A BIOINFORMATICS ANGLE journal December 2015
SWATH-MS as a tool for biomarker discovery: From basic research to clinical applications journal February 2017
Immunopeptidomic Profiling of HLA-A2-Positive Triple Negative Breast Cancer Identifies Potential Immunotherapy Target Antigens journal June 2018
Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE) journal June 2018
Proteogenomic-based discovery of minor histocompatibility antigens with suitable features for immunotherapy of hematologic cancers journal February 2016
Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry journal December 2018
Mass spectrometry–based identification of MHC-bound peptides for immunopeptidomics journal May 2019
Murine xenograft bioreactors for human immunopeptidome discovery journal December 2019
A tissue-based draft map of the murine MHC class I immunopeptidome journal August 2018
Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry journal October 2015
The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases journal November 2019
The SysteMHC Atlas project journal July 2017
Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry journal May 2018
A large fraction of HLA class I ligands are proteasome-generated spliced peptides journal October 2016
MHC class I–associated peptides derive from selective regions of the human genome journal November 2016
Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome journal January 2019
ProGeo-neo: a customized proteogenomic workflow for neoantigen prediction and selection journal April 2020
Detection of brain-directed autoantibodies in the serum of non-small cell lung cancer patients journal July 2017
‘Hotspots’ of Antigen Presentation Revealed by Human Leukocyte Antigen Ligandomics for Neoantigen Prioritization journal October 2017
Discrimination Between Human Leukocyte Antigen Class I-Bound and Co-Purified HIV-Derived Peptides in Immunopeptidomics Workflows journal April 2018
Determination of a Predictive Cleavage Motif for Eluted Major Histocompatibility Complex Class II Ligands journal August 2018
Autoimmunity (or Not) in Atopic Dermatitis journal September 2019
TCR Fingerprinting and Off-Target Peptide Identification journal October 2019
Unsupervised HLA Peptidome Deconvolution Improves Ligand Prediction Accuracy and Predicts Cooperative Effects in Peptide–HLA Interactions journal August 2016
Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry journal December 2015
ProGeo-neo: a Customized Proteogenomic Workflow for Neoantigen Prediction and Selection journal July 2019
Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE) text January 2018
A tissue-based draft map of the murine MHC class I immunopeptidome text January 2018
The SysteMHC Atlas project text January 2018
The SysteMHC Atlas project text January 2018

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Related Subjects

human leukocytes antigen / immunopeptidome / targeted / SWATH-MS / DIA
Environmental Molecular Sciences Laboratory