Kevin Yang

Integrating Alternative Fragmentation Techniques into Standard LC-MS Workflows Using a Single Deep Learning Model Enhances Proteome Coverage

The paper develops a deep learning model that integrates multiple fragmentation techniques into standard LC-MS workflows, improving proteome coverage and identification rates.

diaTracer enables spectrum-centric analysis of diaPASEF proteomics data

diaTracer enables spectrum-centric analysis of diaPASEF proteomics data by generating pseudo-MS/MS spectra for direct peptide identification and quantification.

Koina: Democratizing machine learning for proteomics research

Koina provides an open-source, accessible ML/DL prediction service for proteomics, improving integration with existing tools like FragPipe.

MSBooster: Improving Peptide Identification Rates using Deep Learning-Based Features

MSBooster improves peptide identification rates by integrating deep learning-based features into existing workflows with MSFragger and Percolator.