Christine Carapito

This study optimizes a DDA-PASEF-based immunopeptidomics workflow to enhance HLA class I peptide coverage in low-input samples.

The paper investigates how Achromatium sp. expresses protein variants in response to temperature changes using proteomics and a newly assembled protein atlas.

This study shows that 2'-O-Me modifications on rRNA are dynamically regulated during seed-to-seedling transition in Arabidopsis and affect ribosome translation.

This paper introduces a normalization framework to decouple protocol and instrument effects in multicenter proteomics studies, demonstrating its application to the PME13 dataset.

This study establishes quality control standards for single-cell proteomics through inter-laboratory benchmarking, identifying software and technical factors affecting data reliability.

This study investigates the effects of manganese dioxide on macrophages under repeated exposure, finding mitochondrial dysfunction, oxidative stress, and inflammation.

This study shows that therapeutic poxviruses induce the secretion of immunostimulating and anti-tumoral extracellular vesicles, which can reduce tumor growth in mice.

The paper optimizes label-free single-cell proteomics workflows to achieve robust quantification of up to 5,000 proteins per Hela cell at 55 samples-per-day throughput.

The paper generates a benchmark dataset to evaluate proteomics instruments and workflows using high-throughput LC gradients across multiple platforms and organisms.

The paper presents the E. coli PeptideAtlas build, a comprehensive pan-proteome resource covering 4,755 proteins and over 10,000 PTM sites from 40 datasets.

The paper develops a tool to track exosomal cargoes by labeling Rab7 partners using proximity labeling and mass spectrometry.

This study evaluates the effects of nanomaterials on human immune cells, finding that PLGA NPs enhance NK cell function while Si-Gd NPs impair T cell activation.

The paper investigates the effects of red and black iron oxide pigments on macrophages, finding that red iron oxide causes mitochondrial dysfunction, oxidative stress, and pro-inflammatory cytokine secretion.

DeepLC uses transfer learning to improve LC retention time prediction across different experimental setups and peptide modifications.

The paper introduces a high-throughput mass-spectrometry-based assay to measure protein-ligand affinity constants, demonstrating its application to 14-3-3 isoforms and phosphopeptides.

This study identifies astrogliosis and neuroinflammation as pathogenic mechanisms underlying scoliosis in zebrafish caused by cilia dysfunction.

TIMS2Rescore is a data-driven rescoring pipeline optimized for DDA-PASEF data that improves protein identification in proteomics analyses.

The paper introduces msqrob2PTM, a workflow for differential abundance and usage analysis of PTMs and peptidoforms in proteomics data, showing it performs on par or better than existing methods.

The paper performs a multiomic analysis of ALS patients and mouse models to identify sex differences, molecular subclusters, and the MAPK pathway as a therapeutic target.

MS2Rescore improves immunopeptide identification rates by integrating retrained MS2PIP, DeepLC, and Percolator, achieving higher spectrum identification rates and unique peptide counts.

This study shows Ral GTPases regulate exosome biogenesis and organ colonization, promoting metastasis through MCAM/CD146 modulation in breast cancer.