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

Automated benchmarking of peptide-MHC class I binding predictions

(2015) Thomas Trolle et al.   BIOINFORMATICS

Biomarkers in Cancer Immunotherapy

(2015) Ton N. Schumacher et al.   CANCER CELL

Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis

(2015) Olga T. Schubert et al.   Cell Host & Microbe

The nature of self for T cells—a systems-level perspective

(2015) Diana P Granados et al.   CURRENT OPINION IN IMMUNOLOGY

Reproducible and Consistent Quantification of theSaccharomyces cerevisiaeProteome by SWATH-mass spectrometry

(2015) Nathalie Selevsek et al.   MOLECULAR & CELLULAR PROTEOMICS

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

Quantitative variability of 342 plasma proteins in a human twin population

(2015) Y. Liu et al.   Molecular Systems Biology

Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps

(2015) Tiannan Guo et al.   NATURE MEDICINE

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

Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions

(2014) Yohan Kim et al.   BMC BIOINFORMATICS

iPortal: the swiss grid proteomics portal: Requirements and new features based on experience and usability considerations

(2014) Peter Kunszt et al.   CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE

Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires

(2014) Elin Bergseng et al.   IMMUNOGENETICS

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

(2014) C Berlin et al.   LEUKEMIA

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

Toward a Human Vaccines Project

(2014) Wayne C Koff et al.   NATURE IMMUNOLOGY

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

(2014) Alexandra Snyder et al.   NEW ENGLAND JOURNAL OF MEDICINE

HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL)

(2014) Daniel J. Kowalewski 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

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

(2014) Diana Paola Granados et al.   Nature Communications

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

A repository of assays to quantify 10,000 human proteins by SWATH-MS

(2014) George Rosenberger et al.   Scientific Data

HLA Class I Alleles Are Associated with Peptide-Binding Repertoires of Different Size, Affinity, and Immunogenicity

(2013) S. Paul et al.   JOURNAL OF IMMUNOLOGY

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

Combining Results of Multiple Search Engines in Proteomics

(2013) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system

(2013) Ben C Collins et al.   NATURE METHODS

Accelerating Next-Generation Vaccine Development for Global Disease Prevention

(2013) W. C. Koff et al.   SCIENCE

Memory T Cells in Latent Mycobacterium tuberculosis Infection Are Directed against Three Antigenic Islands and Largely Contained in a CXCR3+CCR6+ Th1 Subset

(2013) Cecilia S. Lindestam Arlehamn et al.   PLoS Pathogens

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

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

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

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

Using iRT, a normalized retention time for more targeted measurement of peptides

(2012) Claudia Escher et al.   PROTEOMICS

More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS

(2011) Annette Michalski et al.   JOURNAL OF PROTEOME RESEARCH

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

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

iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates

(2011) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

The MHC class I peptide repertoire is molded by the transcriptome

(2008) Marie-Hélène Fortier et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Building consensus spectral libraries for peptide identification in proteomics

(2008) Henry Lam et al.   NATURE METHODS

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