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

Deciphering the MHC-associated peptidome: a review of naturally processed ligand data

(2017) Kerrie Vaughan et al.   Expert Review of Proteomics

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

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

MHC-I Ligand Discovery Using Targeted Database Searches of Mass Spectrometry Data: Implications for T-Cell Immunotherapies

(2017) J. Patrick Murphy et al.   JOURNAL OF PROTEOME RESEARCH

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

Building proteomic tool boxes to monitor MHC class I and class II peptides

(2017) Frances-Rose Schumacher et al.   PROTEOMICS

Multi-level Strategy for Identifying Proteasome-Catalyzed Spliced Epitopes Targeted by CD8 + T Cells during Bacterial Infection

(2017) Anouk C.M. Platteel et al.   Cell Reports

The neoepitope landscape in pediatric cancers

(2017) Ti-Cheng Chang et al.   Genome Medicine

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

The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design

(2017) Ward Fleri et al.   Frontiers in Immunology

Distorted Immunodominance by Linker Sequences or other Epitopes from a Second Protein Antigen During Antigen-Processing

(2017) AeRyon Kim et al.   Scientific Reports

Mass spectrometry-based antigen discovery for cancer immunotherapy

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

Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient

(2016) Markus W. Löffler et al.   JOURNAL OF HEPATOLOGY

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

The Length Distribution of Class I–Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele–Specific Binding Preference

(2016) Thomas Trolle et al.   JOURNAL OF IMMUNOLOGY

Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial

(2016) Jonathan E Rosenberg et al.   LANCET

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

Neoantigen landscape dynamics during human melanoma–T cell interactions

(2016) Els M. E. Verdegaal et al.   NATURE

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

(2016) Juliane Liepe et al.   SCIENCE

Targeting of cancer neoantigens with donor-derived T cell receptor repertoires

(2016) E. Stronen 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

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

(2016) Shelly Kalaora et al.   Oncotarget

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

Enhanced Recognition of HIV-1 Cryptic Epitopes Restricted by HLA Class I Alleles Associated With a Favorable Clinical Outcome

(2015) Anju Bansal et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Tumor neoantigens: building a framework for personalized cancer immunotherapy

(2015) Matthew M. Gubin et al.   JOURNAL OF CLINICAL INVESTIGATION

Definition of Proteasomal Peptide Splicing Rules for High-Efficiency Spliced Peptide Presentation by MHC Class I Molecules

(2015) Celia R. Berkers et al.   JOURNAL OF IMMUNOLOGY

Peptide Splicing in the Proteasome Creates a Novel Type of Antigen with an Isopeptide Linkage

(2015) Celia R. Berkers et al.   JOURNAL OF IMMUNOLOGY

Extended O-GlcNAc on HLA Class-I-Bound Peptides

(2015) Fabio Marino et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Novor: Real-Time Peptide de Novo Sequencing Software

(2015) Bin Ma   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

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

Mutant MHC class II epitopes drive therapeutic immune responses to cancer

(2015) Sebastian Kreiter et al.   NATURE

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

(2015) Jennifer G Abelin et al.   Nature Protocols

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma

(2015) E. M. Van Allen et al.   SCIENCE

Neoantigens in cancer immunotherapy

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

The future of immune checkpoint therapy

(2015) P. Sharma et al.   SCIENCE

TCLP: an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression

(2015) Jelle Scholtalbers et al.   Genome Medicine

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

(2015) Etienne Caron et al.   eLife

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

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

The IPD and IMGT/HLA database: allele variant databases

(2014) James Robinson et al.   NUCLEIC ACIDS RESEARCH

Cryptic MHC class I-binding peptides are revealed by aminoglycoside-induced stop codon read-through into the 3' UTR

(2014) E. Goodenough et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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 tumor antigen discovery for personalized vaccine approach

(2013) Hans-Georg Rammensee et al.   Expert Review of Vaccines

NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ

(2013) Edita Karosiene et al.   IMMUNOGENETICS

Tumor Exome Analysis Reveals Neoantigen-Specific T-Cell Reactivity in an Ipilimumab-Responsive Melanoma

(2013) Nienke van Rooij et al.   JOURNAL OF CLINICAL ONCOLOGY

Increased Diversity of the HLA-B40 Ligandome by the Presentation of Peptides Phosphorylated at Their Main Anchor Residue

(2013) Miguel Marcilla et al.   MOLECULAR & CELLULAR PROTEOMICS

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells

(2013) Paul F Robbins et al.   NATURE MEDICINE

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

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

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

Getting Personal with Neoantigen-Based Therapeutic Cancer Vaccines

(2013) N. Hacohen et al.   Cancer Immunology Research

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

(2012) Valérie Dutoit et al.   BRAIN

High Immunogenicity of the Human Leukocyte Antigen Peptidomes of Melanoma Tumor Cells

(2012) Saulius Jarmalavicius et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Proteomic Study and Marker Protein Identification ofCaenorhabditis elegansLipid Droplets

(2012) Peng Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

The Human Immunopeptidome Project, a Suggestion for yet another Postgenome Next Big Thing

(2011) Arie Admon et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

Identification of tumor-associated, MHC class II-restricted phosphopeptides as targets for immunotherapy

(2009) F. R. Depontieu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NetMHCpan, a method for MHC class I binding prediction beyond humans

(2008) Ilka Hoof et al.   IMMUNOGENETICS

Identification of Breast Cancer Peptide Epitopes Presented by HLA-A*0201

(2008) Oriana E. Hawkins et al.   JOURNAL OF PROTEOME RESEARCH

Phosphorylation-dependent interaction between antigenic peptides and MHC class I: a molecular basis for the presentation of transformed self

(2008) Fiyaz Mohammed et al.   NATURE IMMUNOLOGY

NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11

(2008) Claus Lundegaard et al.   NUCLEIC ACIDS RESEARCH