Mass spectrometry–based identification of MHC-bound peptides for immunopeptidomics

In Immunopeptidomics We Need a Sniper Instead of a Shotgun

(2018) Pouya Faridi et al.   PROTEOMICS

Discrimination Between Human Leukocyte Antigen Class I-Bound and Co-Purified HIV-Derived Peptides in Immunopeptidomics Workflows

(2018) Thomas Partridge et al.   Frontiers in Immunology

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

(2017) Jennifer G. Abelin et al.   IMMUNITY

Neoepitopes as cancer immunotherapy targets: key challenges and opportunities

(2017) Cory A Brennick et al.   Immunotherapy

Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens

(2017) Michael S. Khodadoust et al.   NATURE

The SysteMHC Atlas project

(2017) Wenguang Shao et al.   NUCLEIC ACIDS RESEARCH

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

The Potential and Challenges of Exploiting the Vast But Dynamic Neoepitope Landscape for Immunotherapy

(2017) Els M. E. Verdegaal et al.   Frontiers in Immunology

Towards the knowledge-based design of universal influenza epitope ensemble vaccines

(2016) Qamar M. Sheikh et al.   BIOINFORMATICS

Characterization of the Antigen Processing Machinery and Endogenous Peptide Presentation of a Bat MHC Class I Molecule

(2016) James W. Wynne et al.   JOURNAL OF IMMUNOLOGY

Immunodominant West Nile Virus T Cell Epitopes Are Fewer in Number and Fashionably Late

(2016) Saghar Kaabinejadian 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

Human Leukocyte Antigen (HLA) B27 Allotype-Specific Binding and Candidate Arthritogenic Peptides Revealed through Heuristic Clustering of Data-independent Acquisition Mass Spectrometry (DIA-MS) Data

(2016) Ralf B. Schittenhelm 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

Six alternative proteases for mass spectrometry–based proteomics beyond trypsin

(2016) Piero Giansanti et al.   Nature Protocols

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

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

(2016) Juliane Liepe et al.   SCIENCE

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

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

Gapped sequence alignment using artificial neural networks: application to the MHC class I system

(2015) Massimo Andreatta et al.   BIOINFORMATICS

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

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

Towards identification of immune and genetic correlates of severe influenza disease in Indigenous Australians

(2015) E Bridie Clemens et al.   IMMUNOLOGY AND CELL BIOLOGY

Early Kinetics of the HLA Class I-Associated Peptidome of MVA.HIVconsv-Infected Cells

(2015) Nicola Ternette et al.   JOURNAL OF VIROLOGY

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

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

(2015) Jennifer G Abelin et al.   Nature Protocols

A comprehensive analysis of peptides presented by HLA-A1

(2015) K. Giam et al.   TISSUE ANTIGENS

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

(2015) Etienne Caron et al.   eLife

Revisiting the Arthritogenic Peptide Theory: Quantitative Not Qualitative Changes in the Peptide Repertoire of HLA-B27 Allotypes

(2015) Ralf B. Schittenhelm et al.   Arthritis & Rheumatology

Peptide–MHC multimer-based monitoring of CD8 T-cells in HIV-1 infection and AIDS vaccine development

(2014) Alena Y Reguzova et al.   Expert Review of Vaccines

The Cellular Redox Environment Alters Antigen Presentation

(2014) Jonathan A. Trujillo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Direct Interrogation of Viral Peptides Presented by the Class I HLA of HIV-Infected T Cells

(2014) J. C. Yaciuk et al.   JOURNAL OF VIROLOGY

Expanding Proteome Coverage with Orthogonal-specificity α-Lytic Proteases

(2014) Jesse G. Meyer et al.   MOLECULAR & CELLULAR PROTEOMICS

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

A comprehensive analysis of constitutive naturally processed and presentedHLA-C*04:01(Cw4) - specific peptides

(2014) R. B. Schittenhelm et al.   TISSUE ANTIGENS

Flow-cytometric analysis of rare antigen-specific T cells

(2013) Petra Bacher et al.   CYTOMETRY PART A

Discovering naturally processed antigenic determinants that confer protective T cell immunity

(2013) Pavlo Gilchuk et al.   JOURNAL OF CLINICAL INVESTIGATION

A molecular basis for the association of the HLA-DRB1 locus, citrullination, and rheumatoid arthritis

(2013) Stephen W. Scally et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Abacavir induces loading of novel self-peptides into HLA-B*57

(2012) Michael A. Norcross et al.   AIDS

Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach

(2012) Massimo Andreatta et al.   BIOINFORMATICS

MHC Class II Tetramers

(2012) G. T. Nepom   JOURNAL OF IMMUNOLOGY

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

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

Immune self-reactivity triggered by drug-modified HLA-peptide repertoire

(2012) Patricia T. Illing et al.   NATURE

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

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

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

Specificity and detection of insulin-reactive CD4+ T cells in type 1 diabetes in the nonobese diabetic (NOD) mouse

(2011) F. Crawford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C

(2009) Rasmi Thomas et al.   NATURE GENETICS

HLA class I molecules consistently present internal influenza epitopes

(2009) A. Wahl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Immunomic Analysis of the Repertoire of T-Cell Specificities for Influenza A Virus in Humans

(2008) E. Assarsson et al.   JOURNAL OF VIROLOGY

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