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

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

Unconventional Peptide Presentation by Major Histocompatibility Complex (MHC) Class I Allele HLA-A*02:01

(2017) Soumya G. Remesh 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

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

MHC-I peptides get out of the groove and enable a novel mechanism of HIV-1 escape

(2017) Phillip Pymm et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

GibbsCluster: unsupervised clustering and alignment of peptide sequences

(2017) Massimo Andreatta et al.   NUCLEIC ACIDS RESEARCH

MHC-I peptides get out of the groove and enable a novel mechanism of HIV-1 escape

(2017) Phillip Pymm et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Mass spectrometry-based antigen discovery for cancer immunotherapy

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

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

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

Unsupervised HLA Peptidome Deconvolution Improves Ligand Prediction Accuracy and Predicts Cooperative Effects in Peptide–HLA Interactions

(2016) Michal Bassani-Sternberg et al.   JOURNAL OF IMMUNOLOGY

Analysis of the HLA-DR peptidome from human dendritic cells reveals high affinity repertoires and nonconventional pathways of peptide generation

(2016) M. Teresa Ciudad et al.   JOURNAL OF LEUKOCYTE BIOLOGY

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

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

Approach for Identifying Human Leukocyte Antigen (HLA)-DR Bound Peptides from Scarce Clinical Samples

(2016) Tina Heyder et al.   MOLECULAR & CELLULAR PROTEOMICS

Mutations as munitions: Neoantigen vaccines get a closer look as cancer treatment

(2016) Alla Katsnelson   NATURE MEDICINE

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

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

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

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

Proteomic analysis uncovers common effects of IFN-γ and IL-27 on the HLA class I antigen presentation machinery in human cancer cells

(2016) Andrea Petretto et al.   Oncotarget

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

(2016) Shelly Kalaora et al.   Oncotarget

Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove

(2016) Curtis McMurtrey et al.   eLife

Functional Interaction of the Ankylosing Spondylitis-Associated Endoplasmic Reticulum Aminopeptidase 2 With the HLA-B*27 Peptidome in Human Cells

(2016) Adrian Martín-Esteban et al.   Arthritis & Rheumatology

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

(2016) Martin G. Klatt et al.   OncoImmunology

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

(2015) S. Walz et al.   BLOOD

Defining the HLA class I-associated viral antigen repertoire from HIV-1-infected human cells

(2015) Nicola Ternette et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification

(2015) Massimo Andreatta et al.   IMMUNOGENETICS

Pooled Analysis of Long-Term Survival Data From Phase II and Phase III Trials of Ipilimumab in Unresectable or Metastatic Melanoma

(2015) Dirk Schadendorf et al.   JOURNAL OF CLINICAL ONCOLOGY

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

Neoantigens in cancer immunotherapy

(2015) T. N. Schumacher et al.   SCIENCE

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

(2015) B. M. Carreno et al.   SCIENCE

Simplified protocol for clinical-grade tumor-infiltrating lymphocyte manufacturing with use of the Wave bioreactor

(2014) Marco Donia et al.   CYTOTHERAPY

Standard and immunoproteasomes show similar peptide degradation specificities

(2014) Damien Zanker et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Proteasome isoforms exhibit only quantitative differences in cleavage and epitope generation

(2014) Michele Mishto et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Large Scale Mass Spectrometric Profiling of Peptides Eluted from HLA Molecules Reveals N-Terminal-Extended Peptide Motifs

(2014) H. Escobar et al.   JOURNAL OF IMMUNOLOGY

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

(2014) C Berlin et al.   LEUKEMIA

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

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

The Human Leukocyte Antigen–presented Ligandome of B Lymphocytes

(2013) Chopie Hassan et al.   MOLECULAR & CELLULAR PROTEOMICS

Exploring the MHC-peptide matrix of central tolerance in the human thymus

(2013) Eleni Adamopoulou et al.   Nature Communications

Kinetics of Antigen Expression and Epitope Presentation during Virus Infection

(2013) Nathan P. Croft et al.   PLoS Pathogens

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

(2012) Valérie Dutoit et al.   BRAIN

Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

(2012) Martin Christen Frølund Thomsen et al.   NUCLEIC ACIDS RESEARCH

Class II MHC Self-Antigen Presentation in Human B and T Lymphocytes

(2012) Cristina Maria Costantino et al.   PLoS One

HLA-DR-presented Peptide Repertoires Derived From Human Monocyte-derived Dendritic Cells Pulsed With Blood Coagulation Factor VIII

(2011) Simon D. van Haren 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

Conformation of peptides bound to the transporter associated with antigen processing (TAP)

(2011) M. Herget et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CD8+ Enriched "Young" Tumor Infiltrating Lymphocytes Can Mediate Regression of Metastatic Melanoma

(2010) M. E. Dudley et al.   CLINICAL CANCER 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

Molecular Mechanisms of IFN-γ to Up-Regulate MHC Class I Antigen Processing and Presentation

(2009) Fang Zhou   INTERNATIONAL REVIEWS OF IMMUNOLOGY

Improved visualization of protein consensus sequences by iceLogo

(2009) Niklaas Colaert et al.   NATURE METHODS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY