HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy

The nf-core framework for community-curated bioinformatics pipelines

(2020) Philip A. Ewels et al.   NATURE BIOTECHNOLOGY

Improved Prediction of MHC II Antigen Presentation through Integration and Motif Deconvolution of Mass Spectrometry MHC Eluted Ligand Data

(2020) Birkir Reynisson et al.   JOURNAL OF PROTEOME RESEARCH

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes

(2020) Chloe Chong et al.   Nature Communications

Identification of the Cryptic HLA-I Immunopeptidome

(2020) Florian Erhard et al.   Cancer Immunology Research

A Quantitative Proteome Map of the Human Body

(2020) Lihua Jiang et al.   CELL

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

(2019) Dongxue Wang et al.   Molecular Systems Biology

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

(2019) Markus W. Löffler et al.   Genome Medicine

Defining HLA-II Ligand Processing and Binding Rules with Mass Spectrometry Enhances Cancer Epitope Prediction

(2019) Jennifer G. Abelin et al.   IMMUNITY

MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics

(2019) Leon Bichmann et al.   JOURNAL OF PROTEOME RESEARCH

The Human Immunopeptidome Project: a roadmap to predict and treat immune diseases

(2019) Juan Antonio Vizcaíno et al.   MOLECULAR & CELLULAR PROTEOMICS

Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes

(2019) Julien Racle et al.   NATURE BIOTECHNOLOGY

HLA and proteasome expression body map

(2018) Sebastian Boegel et al.   BMC Medical Genomics

Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry

(2018) Lena Katharina Freudenmann et al.   IMMUNOLOGY

qPortal: A platform for data-driven biomedical research

(2018) Christopher Mohr et al.   PLoS One

In Immunopeptidomics We Need a Sniper Instead of a Shotgun

(2018) Pouya Faridi et al.   PROTEOMICS

Quantification of HLA-DM-Dependent Major Histocompatibility Complex of Class II Immunopeptidomes by the Peptide Landscape Antigenic Epitope Alignment Utility

(2018) Miguel Álvaro-Benito et al.   Frontiers in Immunology

Actively personalized vaccination trial for newly diagnosed glioblastoma

(2018) Norbert Hilf et al.   NATURE

Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry

(2018) Ngoc Hieu Tran et al.   NATURE METHODS

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Noncoding regions are the main source of targetable tumor-specific antigens

(2018) Céline M. Laumont et al.   Science Translational Medicine

A Case for a Human Immuno-Peptidome Project Consortium

(2017) Etienne Caron et al.   IMMUNITY

Unveiling the Peptide Motifs of HLA-C and HLA-G from Naturally Presented Peptides and Generation of Binding Prediction Matrices

(2017) Moreno Di Marco et al.   JOURNAL OF IMMUNOLOGY

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

Targeted Feature Detection for Data-Dependent Shotgun Proteomics

(2017) Hendrik Weisser et al.   JOURNAL OF PROTEOME RESEARCH

Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer

(2017) Ugur Sahin et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

The SysteMHC Atlas project

(2017) Wenguang Shao et al.   NUCLEIC ACIDS RESEARCH

The immunopeptidomic landscape of ovarian carcinomas

(2017) Heiko Schuster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive analysis of normal adjacent to tumor transcriptomes

(2017) Dvir Aran et al.   Nature Communications

‘Hotspots’ of Antigen Presentation Revealed by Human Leukocyte Antigen Ligandomics for Neoantigen Prioritization

(2017) Markus Müller et al.   Frontiers in Immunology

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0

(2016) Matthew The et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

(2016) Hannes L Röst et al.   NATURE METHODS

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

Systematic identification of genes with a cancer-testis expression pattern in 19 cancer types

(2016) Cheng Wang 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

A Deeper Look into Comet—Implementation and Features

(2015) Jimmy K. Eng et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

(2015) Mikhail M. Savitski et al.   MOLECULAR & CELLULAR PROTEOMICS

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

Conserved Peptide Fragmentation as a Benchmarking Tool for Mass Spectrometers and a Discriminating Feature for Targeted Proteomics

(2014) Umut H. Toprak et al.   MOLECULAR & CELLULAR PROTEOMICS

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Cardiovascular toxicity and titin cross-reactivity of affinity-enhanced T cells in myeloma and melanoma

(2013) G. P. Linette et al.   BLOOD

Identification of a Titin-Derived HLA-A1-Presented Peptide as a Cross-Reactive Target for Engineered MAGE A3-Directed T Cells

(2013) B. J. Cameron et al.   Science Translational Medicine

Properties of MHC Class I Presented Peptides That Enhance Immunogenicity

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

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

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

Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry

(2009) Lukas Reiter et al.   MOLECULAR & CELLULAR PROTEOMICS

The MHC class I peptide repertoire is molded by the transcriptome

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

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

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