Predicting antigen presentation—what could we learn from a million peptides?

D Gfeller, M Bassani-Sternberg - Frontiers in immunology, 2018 - frontiersin.org
Antigen presentation lies at the heart of immune recognition of infected or malignant cells.
For this reason, important efforts have been made to predict which peptides are more likely …

[HTML][HTML] Defining HLA-II ligand processing and binding rules with mass spectrometry enhances cancer epitope prediction

JG Abelin, D Harjanto, M Malloy, P Suri, T Colson… - Immunity, 2019 - cell.com
Increasing evidence indicates CD4+ T cells can recognize cancer-specific antigens and
control tumor growth. However, it remains difficult to predict the antigens that will be …

Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity

M Bassani-Sternberg, C Chong… - PLoS computational …, 2017 - journals.plos.org
The precise identification of Human Leukocyte Antigen class I (HLA-I) binding motifs plays a
central role in our ability to understand and predict (neo-) antigen presentation in infectious …

Mass spectrometry based immunopeptidomics leads to robust predictions of phosphorylated HLA class I ligands

M Solleder, P Guillaume, J Racle, J Michaux… - Molecular & Cellular …, 2020 - ASBMB
The presentation of peptides on class I human leukocyte antigen (HLA-I) molecules plays a
central role in immune recognition of infected or malignant cells. In cancer, non-self HLA-I …

A large peptidome dataset improves HLA class I epitope prediction across most of the human population

S Sarkizova, S Klaeger, PM Le, LW Li, G Oliveira… - Nature …, 2020 - nature.com
Prediction of HLA epitopes is important for the development of cancer immunotherapies and
vaccines. However, current prediction algorithms have limited predictive power, in part …

The role of mass spectrometry and proteogenomics in the advancement of HLA epitope prediction

AL Creech, YS Ting, SP Goulding, JFK Sauld… - …, 2018 - Wiley Online Library
A challenge in developing personalized cancer immunotherapies is the prediction of
putative cancer‐specific antigens. Currently, predictive algorithms are used to infer binding …

The pockets guide to HLA class I molecules

AT Nguyen, C Szeto, S Gras - Biochemical Society Transactions, 2021 - portlandpress.com
Human leukocyte antigens (HLA) are cell-surface proteins that present peptides to T cells.
These peptides are bound within the peptide binding cleft of HLA, and together as a …

Mass spectrometry profiling of HLA-associated peptidomes in mono-allelic cells enables more accurate epitope prediction

JG Abelin, DB Keskin, S Sarkizova, CR Hartigan… - Immunity, 2017 - cell.com
Identification of human leukocyte antigen (HLA)-bound peptides by liquid chromatography-
tandem mass spectrometry (LC-MS/MS) is poised to provide a deep understanding of rules …

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

LK Freudenmann, A Marcu, S Stevanović - Immunology, 2018 - Wiley Online Library
The entirety of human leukocyte antigen (HLA)‐presented peptides is referred to as the HLA
ligandome of a cell or tissue, in tumours often termed immunopeptidome. Mapping the …

Unveiling the peptide motifs of HLA-C and HLA-G from naturally presented peptides and generation of binding prediction matrices

M Di Marco, H Schuster, L Backert… - The Journal of …, 2017 - journals.aai.org
The classical HLA-C and the nonclassical HLA-E and HLA-G molecules play important roles
both in the innate and adaptive immune system. Starting already during embryogenesis and …