Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors

Targeting a neoantigen derived from a common TP53 mutation

(2021) Emily Han-Chung Hsiue et al.   SCIENCE

Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer

(2021) Tamara Ouspenskaia et al.   NATURE BIOTECHNOLOGY

Identification of tumor antigens with immunopeptidomics

(2021) Chloe Chong et al.   NATURE BIOTECHNOLOGY

Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly from deglycosylated precursors

(2020) Shutao Mei et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma

(2020) Michael A. Gillette et al.   CELL

Identification of modified peptides using localization-aware open search

(2020) Fengchao Yu et al.   Nature Communications

Identification of the Cryptic HLA-I Immunopeptidome

(2020) Florian Erhard et al.   Cancer Immunology Research

MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing

(2020) Timothy J. O’Donnell et al.   Cell Systems

PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results

(2020) Daniel J. Geiszler et al.   MOLECULAR & CELLULAR PROTEOMICS

Anti-tumour immunity induces aberrant peptide presentation in melanoma

(2020) Osnat Bartok et al.   NATURE

Diverse fate of ubiquitin chain moieties: The proximal is degraded with the target, and the distal protects the proximal from removal and recycles

(2019) Hao Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets

(2019) Arun Devabhaktuni et al.   NATURE BIOTECHNOLOGY

CancerMine: a literature-mined resource for drivers, oncogenes and tumor suppressors in cancer

(2019) Jake Lever et al.   NATURE METHODS

Response to Comment on “A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands”

(2019) Pouya Faridi et al.   Science Immunology

Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands

(2019) Marthe Solleder et al.   MOLECULAR & CELLULAR PROTEOMICS

A large peptidome dataset improves HLA class I epitope prediction across most of the human population

(2019) Siranush Sarkizova et al.   NATURE BIOTECHNOLOGY

Low HLA binding of diabetes-associated CD8+ T-cell epitopes is increased by post translational modifications

(2018) John Sidney et al.   BMC IMMUNOLOGY

Present status and future perspective of peptide-based vaccine therapy for urological cancer

(2018) Wataru Obara et al.   CANCER SCIENCE

Enhanced Global Post-translational Modification Discovery with MetaMorpheus

(2018) Stefan K. Solntsev et al.   JOURNAL OF PROTEOME RESEARCH

ProteomeTools: Systematic characterization of 21 post-translational protein modifications by LC-MS/MS using synthetic peptides

(2018) Daniel Paul Zolg et al.   MOLECULAR & CELLULAR PROTEOMICS

Immunopeptidomic Profiling of HLA-A2-Positive Triple Negative Breast Cancer Identifies Potential Immunotherapy Target Antigens

(2018) Nicola Ternette et al.   PROTEOMICS

PDV: an integrative proteomics data viewer

(2018) Kai Li et al.   BIOINFORMATICS

Employing proteomics in the study of antigen presentation: an update

(2018) Sri H. Ramarathinam et al.   Expert Review of Proteomics

A tissue-based draft map of the murine MHC class I immunopeptidome

(2018) Heiko Schuster et al.   Scientific Data

The Length Distribution and Multiple Specificity of Naturally Presented HLA-I Ligands

(2018) David Gfeller et al.   JOURNAL OF IMMUNOLOGY

Revealing the cellular degradome by mass spectrometry analysis of proteasome-cleaved peptides

(2018) Hila Wolf-Levy et al.   NATURE BIOTECHNOLOGY

Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification

(2018) Brendan Bulik-Sullivan et al.   NATURE BIOTECHNOLOGY

The Immune Epitope Database (IEDB): 2018 update

(2018) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Mapping the MHC Class I–Spliced Immunopeptidome of Cancer Cells

(2018) Juliane Liepe et al.   Cancer Immunology Research

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

(2017) Jennifer G. Abelin et al.   IMMUNITY

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

(2017) Rebecca F. Alford et al.   Journal of Chemical Theory and Computation

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

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

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

(2017) Andy T Kong et al.   NATURE METHODS

Is It Possible to Develop Cancer Vaccines to Neoantigens, What Are the Major Challenges, and How Can These Be Overcome?

(2017) Olivera J. Finn et al.   Cold Spring Harbor Perspectives in Biology

Chimeric-antigen receptor T (CAR-T) cell therapy for solid tumors: challenges and opportunities

(2017) An-Liang Xia et al.   Oncotarget

The antigenic identity of human class I MHC phosphopeptides is critically dependent upon phosphorylation status

(2017) Fiyaz Mohammed et al.   Oncotarget

High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock

(2017) Nawsad Alam et al.   PLoS Computational 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

Identification of Glycopeptides as Posttranslationally Modified Neoantigens in Leukemia

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

Nowhere to hide: unconventional translation yields cryptic peptides for immune surveillance

(2016) Shelley R. Starck et al.   IMMUNOLOGICAL REVIEWS

Arginine (Di)methylated Human Leukocyte Antigen Class I Peptides Are Favorably Presented by HLA-B*07

(2016) Fabio Marino et al.   JOURNAL OF PROTEOME RESEARCH

Synthetic Uncleavable Ubiquitinated Proteins Dissect Proteasome Deubiquitination and Degradation, and Highlight Distinctive Fate of Tetraubiquitin

(2016) Sumeet K. Singh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Proteogenomics connects somatic mutations to signalling in breast cancer

(2016) Philipp Mertins et al.   NATURE

Cystine addiction of triple-negative breast cancer associated with EMT augmented death signaling

(2016) X Tang et al.   ONCOGENE

Common errors in mass spectrometry-based analysis of post-translational modifications

(2016) Min-Sik Kim et al.   PROTEOMICS

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

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

(2016) Curtis McMurtrey et al.   eLife

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

Illuminating the dark matter of shotgun proteomics

(2015) Owen S Skinner et al.   NATURE BIOTECHNOLOGY

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

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

Software eyes for protein post-translational modifications

(2014) Seungjin Na et al.   MASS SPECTROMETRY REVIEWS

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-B*51 the primary risk in Behcet disease

(2014) G. R. Wallace   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Glutamine Sensitivity Analysis Identifies the xCT Antiporter as a Common Triple-Negative Breast Tumor Therapeutic Target

(2013) Luika A. Timmerman et al.   CANCER CELL

The Human Leukocyte Antigen–presented Ligandome of B Lymphocytes

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

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

The Effect of Proteasome Inhibition on the Generation of the Human Leukocyte Antigen (HLA) Peptidome

(2013) Elena Milner et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

Determination of Deamidation Artifacts Introduced by Sample Preparation Using 18O-Labeling and Tandem Mass Spectrometry Analysis

(2012) Yi Du et al.   ANALYTICAL CHEMISTRY

A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet

(2012) Kelvin Ma et al.   BMC BIOINFORMATICS

Cross-Allele Cytotoxic T Lymphocyte Responses against 2009 Pandemic H1N1 Influenza A Virus among HLA-A24 and HLA-A3 Supertype-Positive Individuals

(2012) J. Liu et al.   JOURNAL OF VIROLOGY

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

Software Lock Mass by Two-Dimensional Minimization of Peptide Mass Errors

(2011) Jürgen Cox et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

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

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

Identification of a Novel Class of Farnesylation Targets by Structure-Based Modeling of Binding Specificity

(2011) Nir London et al.   PLoS Computational Biology

The impact of human leukocyte antigen (HLA) micropolymorphism on ligand specificity within the HLA-B*41 allotypic family

(2010) C. Bade-Doding et al.   HAEMATOLOGICA

HLA-A alleles and infectious mononucleosis suggest a critical role for cytotoxic T-cell response in EBV-related Hodgkin lymphoma

(2010) H. Hjalgrim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sub-angstrom modeling of complexes between flexible peptides and globular proteins

(2010) Barak Raveh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Long, Naturally Presented Immunodominant Epitope from NY-ESO-1 Tumor Antigen: Implications for Cancer Vaccine Design

(2009) L. M. Ebert et al.   CANCER RESEARCH

Post-translationally modified T cell epitopes: immune recognition and immunotherapy

(2009) Jan Petersen et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Impact of clonal competition for peptide-MHC complexes on the CD8+ T-cell repertoire selection in a persistent viral infection

(2008) K. K. Wynn et al.   BLOOD

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

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

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