Chengpin Shen

Beta-DIA: Integrating learning-based and function-based feature scores to optimize the proteome profiling of single-shot diaPASEF mass spectrometry data

Beta-DIA improves proteome profiling by combining deep learning and function-based scores for diaPASEF data, doubling protein group detection in low datasets.

Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics

The paper introduces ConDiGA, a pipeline for constructing accurate protein sequence databases from metagenomic data to improve metaproteomics analysis, achieving deep coverage in synthetic and real microbiota samples.