Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

Naive Precursor Frequencies and MHC Binding Rather Than the Degree of Epitope Diversity Shape CD8+ T Cell Immunodominance

(2014) M. F. Kotturi et al.   JOURNAL OF IMMUNOLOGY

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

Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells

(2014) Nils A Kulak et al.   NATURE METHODS

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

Re-examining class-I presentation and the DRiP hypothesis

(2014) Kenneth L. Rock et al.   TRENDS IN IMMUNOLOGY

Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides

(2014) Diana Paola Granados et al.   Nature Communications

A catalog of HLA type, HLA expression, and neo-epitope candidates in human cancer cell lines

(2014) Sebastian Boegel et al.   OncoImmunology

Acetylation-Mediated Proteasomal Degradation of Core Histones during DNA Repair and Spermatogenesis

(2013) Min-Xian Qian et al.   CELL

The repertoire of human tumor-associated epitopes — identification and selection of antigens and their application in clinical trials

(2013) Sebastian P Haen et al.   CURRENT OPINION IN IMMUNOLOGY

HLA ligandome tumor antigen discovery for personalized vaccine approach

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

The Human Leukocyte Antigen–presented Ligandome of B Lymphocytes

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

Positional Bias of MHC Class I Restricted T-Cell Epitopes in Viral Antigens Is Likely due to a Bias in Conservation

(2013) Yohan Kim et al.   PLoS Computational Biology

Properties of MHC Class I Presented Peptides That Enhance Immunogenicity

(2013) Jorg J. A. Calis et al.   PLoS Computational Biology

Kinetics of Antigen Expression and Epitope Presentation during Virus Infection

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

Mining the mutanome: developing highly personalized Immunotherapies based on mutational analysis of tumors

(2013) Willem W Overwijk et al.   Journal for ImmunoTherapy of Cancer

Human leukocyte antigens (HLA) associated drug hypersensitivity: consequences of drug binding to HLA

(2012) J. Yun et al.   ALLERGY

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

(2012) Massimo Andreatta et al.   BIOINFORMATICS

MHC I-associated peptides preferentially derive from transcripts bearing miRNA response elements

(2012) D. P. Granados et al.   BLOOD

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

(2012) Valérie Dutoit et al.   BRAIN

Personalized peptide vaccination: a new approach for advanced cancer as therapeutic cancer vaccine

(2012) Masanori Noguchi et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Next-generation peptide vaccines for advanced cancer

(2012) Akira Yamada et al.   CANCER SCIENCE

Optimized Fast and Sensitive Acquisition Methods for Shotgun Proteomics on a Quadrupole Orbitrap Mass Spectrometer

(2012) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

Multipeptide immune response to cancer vaccine IMA901 after single-dose cyclophosphamide associates with longer patient survival

(2012) Steffen Walter et al.   NATURE MEDICINE

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

(2012) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Proteome Sampling by the HLA Class I Antigen Processing Pathway

(2012) Ilka Hoof et al.   PLoS Computational Biology

Origin and plasticity of MHC I-associated self peptides

(2011) Danielle de Verteuil et al.   AUTOIMMUNITY REVIEWS

A Genome-wide Multidimensional RNAi Screen Reveals Pathways Controlling MHC Class II Antigen Presentation

(2011) Petra Paul et al.   CELL

NetMHCcons: a consensus method for the major histocompatibility complex class I predictions

(2011) Edita Karosiene et al.   IMMUNOGENETICS

Machine learning competition in immunology – Prediction of HLA class I binding peptides

(2011) Guang Lan Zhang et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation

(2011) E. Caron et al.   Molecular Systems Biology

Major source of antigenic peptides for the MHC class I pathway is produced during the pioneer round of mRNA translation

(2011) S. Apcher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DRiPs solidify: progress in understanding endogenous MHC class I antigen processing

(2011) Jonathan W. Yewdell   TRENDS IN IMMUNOLOGY

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

Genome-Wide Kinetics of Nucleosome Turnover Determined by Metabolic Labeling of Histones

(2010) R. B. Deal et al.   SCIENCE

The relevance of minor histocompatibility antigens in solid organ transplantation

(2009) Miranda Dierselhuis et al.   Current Opinion in Organ Transplantation

Combination of FASP and StageTip-Based Fractionation Allows In-Depth Analysis of the Hippocampal Membrane Proteome

(2009) Jacek R. Wiśniewski et al.   JOURNAL OF PROTEOME RESEARCH

Histone levels are regulated by phosphorylation and ubiquitylation-dependent proteolysis

(2009) Rakesh Kumar Singh et al.   NATURE CELL BIOLOGY

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Systematic Characterisation of Cellular Localisation and Expression Profiles of Proteins Containing MHC Ligands

(2009) Agnieszka S. Juncker et al.   PLoS One

Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods

(2008) Hao Zhang et al.   BIOINFORMATICS

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

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

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH