Wenrong Chen

XL-Ranker: A Computational Workflow for Prioritizing Protein-Protein Interactions from Cross-Linking Mass Spectrometry Data

XL-Ranker resolves peptide-mapping ambiguity in XL-MS data to infer high-confidence PPIs, improving the reliability of interaction networks.

Characterization of proteoform post-translational modifications by top-down and bottom-up mass spectrometry in conjunction with UniProt annotations

The paper introduces PTM-TBA, a software pipeline that identifies and localizes post-translational modifications in proteoforms using top-down and bottom-up mass spectrometry combined with UniProt annotations.

Evaluation of machine learning models for proteoform retention and migration time prediction in top-down mass spectrometry

The paper evaluates machine learning models for predicting proteoform retention and migration times in top-down mass spectrometry, finding high accuracy with Prosit and a neural network model.

Proteoform Identification by Combining RNA-Seq and Top-down Mass Spectrometry

This paper introduces TopPG, a tool for identifying proteoforms with genetic alterations and alternative splicing using top-down mass spectrometry data from colorectal cancer cells.