Immunopeptidome profiling in pulmonary fibrosis provides a platform for identifying therapeutic targets https://pubmed.ncbi.nlm.nih.gov/42010059/

ARMH3 acts as a central scaffold at the Golgi/TGN through interactions with Arl5, GBF1, and PI4KB

www.biorxiv.org/content/10.64898/2026.04...

Mapping intratumor heterogeneity across layers for advancing immunotherapy https://pubmed.ncbi.nlm.nih.gov/41997129/

NetMHCIIphosPan: A Machine Learning Tool for Predicting HLA Class II Antigen Presentation of Phosphorylated Peptides https://pubmed.ncbi.nlm.nih.gov/41994856/

Clinical peptidomics for respiratory diseases: matrices, workflows, and translation towards treatable traits, with a focus on COPD https://pubmed.ncbi.nlm.nih.gov/41987058/

Deterministic Acceptance Limits for Statistical Equivalence Testing in Hydrogen/Deuterium Exchange Mass Spectrometry https://pubmed.ncbi.nlm.nih.gov/41985126/

Dynamic myosin 10 coupling to DCC and β1 integrin is mediated by intrinsically disordered regions during filopodial transport and patterning

www.biorxiv.org/content/10.64898/2026.04...

Use of hydrogen deuterium exchange mass spectrometry in tandem with modern structural biology https://pubmed.ncbi.nlm.nih.gov/41979917/

Integrated kidney and urine proteomics define encrypted antimicrobial peptides as effectors of host defence in human pyelonephritis

www.biorxiv.org/content/10.64898/2026.04...

Long Non-Coding RNA-Derived Peptides as a Novel Source of Tumor Neoantigens: Expanding the Immunopeptidome Beyond Canonical Coding Regions https://pubmed.ncbi.nlm.nih.gov/41972540/

Extending the MARTINI 3 Coarse-Grained Forcefield to Polypeptoids

www.biorxiv.org/content/10.64898/2026.04...

Deep learning enables direct HLA typing from immunopeptidomics data

www.biorxiv.org/content/10.64898/2026.04...

Nonsense-mediated mRNA decay inhibition reshapes the cancer immunopeptidome https://pubmed.ncbi.nlm.nih.gov/41956098/

Machine Learning-Driven Antigen Selection Reveals Conserved T-Cell Targets for Broad Coronavirus Vaccination

www.biorxiv.org/content/10.64898/2026.04...

A targetable dependency on nonsense-mediated decay for proteostasis and immune control in small cell lung cancer

www.biorxiv.org/content/10.64898/2026.03...

From prediction to precision: how immunopeptidomics advances neoantigen discovery https://pubmed.ncbi.nlm.nih.gov/41927395/

Resolution of recursive data corruption to transform T-cell epitope discovery

www.biorxiv.org/content/10.64898/2026.03...

Residue-Level Determination of Small-Molecule-Protein Affinities by Hydrogen-Deuterium Exchange Mass Spectrometry https://pubmed.ncbi.nlm.nih.gov/41915381/

In-source fragmentation in mass spectrometry-based proteomics: prevalence, impact, and strategies for mitigation

www.biorxiv.org/content/10.64898/2026.03...

Dimethyl Sulfoxide Enhances HLA Peptide Identification https://pubmed.ncbi.nlm.nih.gov/41893728/

Autophagy shapes the peptide repertoire of rheumatoid arthritis-associated HLA class II alleles

www.biorxiv.org/content/10.64898/2026.03...

HaDeX2: multi-dimensional analysis of hydrogen-deuterium exchange mass spectrometry data https://pubmed.ncbi.nlm.nih.gov/41838411/

Conformational signatures of native ligand and pharmacochaperone binding in rhodopsin https://pubmed.ncbi.nlm.nih.gov/41867874/

Conformational dynamics of SARS-CoV-2 spike on a membrane reveals the allosteric effects of furin cleavage and the D614G mutation https://pubmed.ncbi.nlm.nih.gov/41861002/

Epithelial MHC II antigen presentation dynamically informs intestinal homeostasis and injury

www.biorxiv.org/content/10.64898/2026.03...

RiboBA: a bias-aware probabilistic framework for robust ORF identification across diverse ribosome profiling protocols

www.biorxiv.org/content/10.64898/2026.03...

The HLA-C 06:02-presented skin immunopeptidome: A valuable resource for unravelling the autoimmune pathogenesis of psoriasis https://pubmed.ncbi.nlm.nih.gov/41848455/

HaDeX2: multi-dimensional analysis of Hydrogen-Deuterium Exchange Mass Spectrometry data https://pubmed.ncbi.nlm.nih.gov/41838411/

Mapping the Modification Landscape of MHC-I Epitopes: A Framework for Immunogenic Peptidomimetic Antigen Design

www.biorxiv.org/content/10.64898/2026.03...

Ligand-specific conformational dynamics of the α_2A-adrenergic receptor revealed by hydrogen-deuterium exchange mass spectrometry https://pubmed.ncbi.nlm.nih.gov/41812653/