Computational Tools for the Identification and Interpretation of Sequence Motifs in Immunopeptidomes

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

(2017) Jennifer G. Abelin et al.   IMMUNITY

Machine learning reveals a non-canonical mode of peptide binding to MHC class II molecules

(2017) Massimo Andreatta et al.   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

Dominant protection from HLA-linked autoimmunity by antigen-specific regulatory T cells

(2017) Joshua D. Ooi et al.   NATURE

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

Human Leukocyte Antigen (HLA)-DRB1*15:01 and HLA-DRB5*01:01 Present Complementary Peptide Repertoires

(2017) Erika Margaret Scholz et al.   Frontiers in Immunology

Mass spectrometry-based antigen discovery for cancer immunotherapy

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

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

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

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

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

NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets

(2016) Morten Nielsen et al.   Genome Medicine

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

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

High-resolution analysis of the murine MHC class II immunopeptidome

(2015) Adriana Sofron 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

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

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

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

(2014) C Berlin et al.   LEUKEMIA

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

MHC-NP: Predicting peptides naturally processed by the MHC

(2013) Sébastien Giguère et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Cleaning up the masses: Exclusion lists to reduce contamination with HPLC-MS/MS

(2013) Kelly Hodge et al.   Journal of Proteomics

The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

(2013) Dattatreya Mellacheruvu et al.   NATURE METHODS

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

(2012) Massimo Andreatta et al.   BIOINFORMATICS

Peptide-MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity

(2012) Mikkel Harndahl et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Proteomic Study and Marker Protein Identification ofCaenorhabditis elegansLipid Droplets

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

NNAlign: A Web-Based Prediction Method Allowing Non-Expert End-User Discovery of Sequence Motifs in Quantitative Peptide Data

(2011) Massimo Andreatta et al.   PLoS One

MHC Class II epitope predictive algorithms

(2010) Morten Nielsen et al.   IMMUNOLOGY

Accurate and Sensitive Peptide Identification with Mascot Percolator

(2009) Markus Brosch et al.   JOURNAL OF PROTEOME RESEARCH

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