Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry

The natural HLA ligandome of glioblastoma stem-like cells: antigen discovery for T cell-based immunotherapy

(2018) Marian Christoph Neidert et al.   ACTA NEUROPATHOLOGICA

Predicted MHC peptide binding promiscuity explains MHC class I ‘hotspots’ of antigen presentation defined by mass spectrometry eluted ligand data

(2018) Emma Christine Jappe et al.   IMMUNOLOGY

Membranal and Blood-Soluble HLA Class II Peptidome Analyses Using Data-Dependent and Independent Acquisition

(2018) Danilo Ritz et al.   PROTEOMICS

The Role of Mass Spectrometry and Proteogenomics in the Advancement of HLA Epitope Prediction

(2018) Amanda L. Creech et al.   PROTEOMICS

Comparison of the MHC I Immunopeptidome Repertoire of B-Cell Lymphoblasts Using Two Isolation Methods

(2018) Joël Lanoix et al.   PROTEOMICS

In Immunopeptidomics We Need a Sniper Instead of a Shotgun

(2018) Pouya Faridi et al.   PROTEOMICS

The Antigen ASB4 on Cancer Stem Cells Serves as a Target for CTL Immunotherapy of Colorectal Cancer

(2018) Sho Miyamoto et al.   Cancer Immunology Research

A Case for a Human Immuno-Peptidome Project Consortium

(2017) Etienne Caron et al.   IMMUNITY

Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction

(2017) Jennifer G. Abelin et al.   IMMUNITY

The major histocompatibility complex class I immunopeptidome of extracellular vesicles

(2017) Silvia A. Synowsky et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2017) Moreno Di Marco et al.   JOURNAL OF IMMUNOLOGY

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

(2017) Vanessa Jurtz et al.   JOURNAL OF IMMUNOLOGY

Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows

(2017) Kenneth Verheggen et al.   MASS SPECTROMETRY REVIEWS

The Human Leukocyte Antigen (HLA)-B27 Peptidomein Vivo, in Spondyloarthritis-susceptible HLA-B27 Transgenic Rats and the Effect of Erap1 Deletion

(2017) Eilon Barnea et al.   MOLECULAR & CELLULAR PROTEOMICS

High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome

(2017) Chloe Chong et al.   MOLECULAR & CELLULAR PROTEOMICS

Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer

(2017) Ugur Sahin et al.   NATURE

Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens

(2017) Michael S. Khodadoust et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

The SysteMHC Atlas project

(2017) Wenguang Shao et al.   NUCLEIC ACIDS RESEARCH

GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses

(2017) Zefang Tang et al.   NUCLEIC ACIDS RESEARCH

The immunopeptidomic landscape of ovarian carcinomas

(2017) Heiko Schuster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Data-Independent Acquisition of HLA Class I Peptidomes on the Q Exactive Mass Spectrometer Platform

(2017) Danilo Ritz et al.   PROTEOMICS

Post-Translational Peptide Splicing and T Cell Responses

(2017) Michele Mishto et al.   TRENDS IN IMMUNOLOGY

Soluble HLA-associated peptide from PSF1 has a cancer vaccine potency

(2017) Mari Yoshida et al.   Scientific Reports

Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity

(2017) Michal Bassani-Sternberg et al.   PLoS Computational Biology

Identification of Glycopeptides as Posttranslationally Modified Neoantigens in Leukemia

(2017) Stacy A. Malaker et al.   Cancer Immunology Research

‘Hotspots’ of Antigen Presentation Revealed by Human Leukocyte Antigen Ligandomics for Neoantigen Prioritization

(2017) Markus Müller et al.   Frontiers in Immunology

Mass spectrometry-based antigen discovery for cancer immunotherapy

(2016) Michal Bassani-Sternberg et al.   CURRENT OPINION IN IMMUNOLOGY

The prognostic impact of soluble and vesicular HLA-G and its relationship to circulating tumor cells in neoadjuvant treated breast cancer patients

(2016) Lisa König et al.   HUMAN IMMUNOLOGY

MHC class I–associated peptides derive from selective regions of the human genome

(2016) Hillary Pearson et al.   JOURNAL OF CLINICAL INVESTIGATION

Human Leukocyte Antigen (HLA) Peptides Derived from Tumor Antigens Induced by Inhibition of DNA Methylation for Development of Drug-facilitated Immunotherapy

(2016) Bracha Shraibman et al.   MOLECULAR & CELLULAR PROTEOMICS

A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens

(2016) Adán Alpízar et al.   MOLECULAR & CELLULAR PROTEOMICS

Sampling From the Proteome to the Human Leukocyte Antigen-DR (HLA-DR) Ligandome ProceedsViaHigh Specificity

(2016) Geert P. M. Mommen et al.   MOLECULAR & CELLULAR PROTEOMICS

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

(2016) Hannes L Röst et al.   NATURE METHODS

COSMIC: somatic cancer genetics at high-resolution

(2016) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

High-sensitivity HLA class I peptidome analysis enables a precise definition of peptide motifs and the identification of peptides from cell lines and patients’ sera

(2016) Danilo Ritz et al.   PROTEOMICS

Purification of soluble HLA class I complexes from human serum or plasma deliver high quality immuno peptidomes required for biomarker discovery

(2016) Danilo Ritz et al.   PROTEOMICS

Pathogenic CD4 T cells in type 1 diabetes recognize epitopes formed by peptide fusion

(2016) T. Delong et al.   SCIENCE

A large fraction of HLA class I ligands are proteasome-generated spliced peptides

(2016) Juliane Liepe et al.   SCIENCE

Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames

(2016) Céline M. Laumont et al.   Nature Communications

Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry

(2016) Michal Bassani-Sternberg et al.   Nature Communications

Carfilzomib alters the HLA-presented peptidome of myeloma cells and impairs presentation of peptides with aromatic C-termini

(2016) D J Kowalewski et al.   Blood Cancer Journal

Use of HLA peptidomics and whole exome sequencing to identify human immunogenic neo-antigens

(2016) Shelly Kalaora et al.   Oncotarget

Exosome-driven transfer of tumor-associated Pioneer Translation Products (TA-PTPs) for the MHC class I cross-presentation pathway

(2016) Emilie Duvallet et al.   OncoImmunology

Carcinogenesis of renal cell carcinoma reflected in HLA ligands: A novel approach for synergistic peptide vaccination design

(2016) Martin G. Klatt et al.   OncoImmunology

Proteasomes generate spliced epitopes by two different mechanisms and as efficiently as non-spliced epitopes

(2016) F. Ebstein et al.   Scientific Reports

The antigenic landscape of multiple myeloma: mass spectrometry (re)defines targets for T-cell-based immunotherapy

(2015) S. Walz et al.   BLOOD

Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

(2015) Michal Bassani-Sternberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry

(2015) Etienne Caron et al.   MOLECULAR & CELLULAR PROTEOMICS

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

(2015) Chih-Chiang Tsou et al.   NATURE METHODS

Complementary IMAC enrichment methods for HLA-associated phosphopeptide identification by mass spectrometry

(2015) Jennifer G Abelin et al.   Nature Protocols

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics

(2015) Eric W. Deutsch et al.   Proteomics Clinical Applications

A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells

(2015) B. M. Carreno et al.   SCIENCE

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

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

(2015) Etienne Caron et al.   eLife

Naturally Processed Non-canonical HLA-A*02:01 Presented Peptides

(2014) Chopie Hassan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Accurate quantitation of MHC-bound peptides by application of isotopically labeled peptide MHC complexes

(2014) Chopie Hassan et al.   Journal of Proteomics

Mapping the HLA ligandome landscape of acute myeloid leukemia: a targeted approach toward peptide-based immunotherapy

(2014) C Berlin et al.   LEUKEMIA

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing

(2014) Mahesh Yadav et al.   NATURE

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD)

(2014) G. P. M. Mommen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL)

(2014) Daniel J. Kowalewski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cancer Regression and Neurological Toxicity Following Anti-MAGE-A3 TCR Gene Therapy

(2013) Richard A. Morgan et al.   JOURNAL OF IMMUNOTHERAPY

The regulatory landscape for actively personalized cancer immunotherapies

(2013) Cedrik M Britten et al.   NATURE BIOTECHNOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Robust phosphoproteome enrichment using monodisperse microsphere–based immobilized titanium (IV) ion affinity chromatography

(2013) Houjiang Zhou et al.   Nature Protocols

MHC Class I-Associated Phosphopeptides Are the Targets of Memory-like Immunity in Leukemia

(2013) M. Cobbold et al.   Science Translational Medicine

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data

(2012) Richard N. Smith et al.   BIOINFORMATICS

Exploiting the glioblastoma peptidome to discover novel tumour-associated antigens for immunotherapy

(2012) Valérie Dutoit et al.   BRAIN

Major Histocompatibility Complex Class II+Invariant Chain Negative Breast Cancer Cells Present Unique Peptides that Activate Tumor-specific T Cells from Breast Cancer Patients

(2012) Olesya Chornoguz et al.   MOLECULAR & CELLULAR PROTEOMICS

Secreted HLA recapitulates the immunopeptidome and allows in-depth coverage of HLA A*02:01 ligands

(2012) Katherine E. Scull et al.   MOLECULAR IMMUNOLOGY

Importance of TAP-independent processing pathways

(2012) Claudia C. Oliveira et al.   MOLECULAR IMMUNOLOGY

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Multipeptide immune response to cancer vaccine IMA901 after single-dose cyclophosphamide associates with longer patient survival

(2012) Steffen Walter et al.   NATURE MEDICINE

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

(2012) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

PEAKS DB:De NovoSequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

(2011) Jing Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation

(2011) E. Caron et al.   Molecular Systems Biology

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

(2011) Bruno Aranda et al.   NATURE METHODS

Quantification of HLA class I molecules on renal cell carcinoma using Edman degradation

(2011) Juliane S Stickel et al.   BMC Urology

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

Soluble plasma HLA peptidome as a potential source for cancer biomarkers

(2010) M. Bassani-Sternberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Prioritization of Cancer Antigens: A National Cancer Institute Pilot Project for the Acceleration of Translational Research

(2009) M. A. Cheever et al.   CLINICAL CANCER RESEARCH

Identification of Natural MHC Class II Presented Phosphopeptides and Tumor-Derived MHC Class I Phospholigands

(2009) Verena S. Meyer et al.   JOURNAL OF PROTEOME RESEARCH

A Cryptic Vascular Endothelial Growth Factor T-Cell Epitope: Identification and Characterization by Mass Spectrometry and T-Cell Assays

(2008) A. O. Weinzierl et al.   CANCER RESEARCH

The MHC class I peptide repertoire is molded by the transcriptome

(2008) Marie-Hélène Fortier et al.   JOURNAL OF EXPERIMENTAL MEDICINE

CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens

(2008) L. G. Almeida et al.   NUCLEIC ACIDS RESEARCH

Tumor escape mechanisms: potential role of soluble HLA antigens and NK cells activating ligands

(2008) M. Campoli et al.   TISSUE ANTIGENS