Pouya Faridi

This paper evaluates CID and IRMPD fragmentation methods for HLA class I immunopeptidomics, finding they identify unique peptides missed by HCD, especially for non-basic anchor alleles and peptides lacking lysine, arginine, or histidine.

The paper identifies 25% of 7,264 non-canonical open reading frames (ncORFs) as producing translated gene products, supported by over 3,000 peptides from 3.8 billion mass spectra.

The paper benchmarks plasma proteomic workflows across species and methods, showing workflow choice significantly impacts detected proteins and depth.

The paper compiles HLA typing and expression data for 287 pediatric cancer cell lines to support immunotherapy research and personalized treatment development.

The paper expands and refines a reference catalog of human non-canonical open reading frames (ncORFs) by incorporating more datasets and introducing a translation signature score framework to prioritize high-quality ncORFs.

This study identifies six immunogenic peptides in diffuse midline glioma (DMG) linked to the H3K27M mutation, offering potential targets for T cell-based immunotherapy.

This study reanalyzes single-cell RNA sequencing data to show that myeloid-derived suppressor cells in severe COVID-19 patients exhibit upregulated transposable elements, potentially enhancing their suppressive function.

This study shows that impaired proinsulin handling in β-cells increases MHC-I bound peptides and activates inflammasomes, potentially contributing to autoimmune diabetes.

The paper provides detailed experimental protocols and an open-source tool, MhcVizPipe, for analyzing MHC I and II ligand datasets in immunopeptidomics.