Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands

PRMTs and Arginine Methylation: Cancer’s Best-Kept Secret?

(2019) James Jarrold et al.   TRENDS IN MOLECULAR MEDICINE

Post-translational modification of OCT4 in breast cancer tumorigenesis

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T-Cell Immunopeptidomes Reveal Cell Subtype Surface Markers Derived From Intracellular Proteins

(2018) Niclas Olsson et al.   PROTEOMICS

Identification of Native and Posttranslationally Modified HLA-B*57:01-Restricted HIV Envelope Derived Epitopes Using Immunoproteomics

(2018) Sri H. Ramarathinam et al.   PROTEOMICS

MHCflurry: Open-Source Class I MHC Binding Affinity Prediction

(2018) Timothy J. O'Donnell et al.   Cell Systems

Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups

(2018) Tenley C. Archer et al.   CANCER CELL

A curated resource for phosphosite-specific signature analysis

(2018) Karsten Krug et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

MS-Rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments

(2018) Massimo Andreatta et al.   PROTEOMICS

Role of Mechanotransduction and Tension in T Cell Function

(2018) Jérémie Rossy 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

The crucial role of protein phosphorylation in cell signaling and its use as targeted therapy (Review)

(2017) Fatima Ardito et al.   INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE

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

High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome

(2017) Chloe Chong et al.   MOLECULAR & CELLULAR PROTEOMICS

The antigenic identity of human class I MHC phosphopeptides is critically dependent upon phosphorylation status

(2017) Fiyaz Mohammed et al.   Oncotarget

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

Unsupervised HLA Peptidome Deconvolution Improves Ligand Prediction Accuracy and Predicts Cooperative Effects in Peptide–HLA Interactions

(2016) Michal Bassani-Sternberg et al.   JOURNAL OF IMMUNOLOGY

A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens

(2016) Adán Alpízar et al.   MOLECULAR & CELLULAR PROTEOMICS

Arabidopsis PROTEASOME REGULATOR1 is required for auxin-mediated suppression of proteasome activity and regulates auxin signalling

(2016) Bao-Jun Yang et al.   Nature Communications

Ultrastructural Characterization of the Lower Motor System in a Mouse Model of Krabbe Disease

(2016) Valentina Cappello et al.   Scientific Reports

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

(2015) Massimo Andreatta et al.   BIOINFORMATICS

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

A comprehensive analysis of peptides presented by HLA-A1

(2015) K. Giam et al.   TISSUE ANTIGENS

Protein Phosphorylation: A Major Switch Mechanism for Metabolic Regulation

(2015) Sean J. Humphrey et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

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

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

The IPD and IMGT/HLA database: allele variant databases

(2014) James Robinson et al.   NUCLEIC ACIDS RESEARCH

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

Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling

(2014) Kirti Sharma et al.   Cell Reports

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

CD19-Targeted T Cells Rapidly Induce Molecular Remissions in Adults with Chemotherapy-Refractory Acute Lymphoblastic Leukemia

(2013) R. J. Brentjens et al.   Science Translational Medicine

DNA hydrogel-based supercapacitors operating in physiological fluids

(2013) Jaehyun Hur et al.   Scientific Reports

Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire

(2012) D. A. Ostrov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

(2010) M. Valiev et al.   COMPUTER PHYSICS COMMUNICATIONS

Confident Phosphorylation Site Localization Using the Mascot Delta Score

(2010) Mikhail M. Savitski et al.   MOLECULAR & CELLULAR PROTEOMICS

Phospho.ELM: a database of phosphorylation sites--update 2011

(2010) H. Dinkel et al.   NUCLEIC ACIDS RESEARCH

Identification of Natural MHC Class II Presented Phosphopeptides and Tumor-Derived MHC Class I Phospholigands

(2009) Verena S. Meyer et al.   JOURNAL OF PROTEOME RESEARCH

Phosphorylated self-peptides alter human leukocyte antigen class I-restricted antigen presentation and generate tumor-specific epitopes

(2009) Jan Petersen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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