Kai Cheng

Dissecting functional dynamics of fecal-derived in vitro stable microbial communities with metaproteomics

This study uses metaproteomics to analyze how culture medium and donor-specific factors influence the establishment of in vitro fecal microbial communities over time.

MetaUmbra: Statistically Controlled Genome-Level Presence Inference from Metaproteomic Peptides

MetaUmbra infers genome-level presence from metaproteomic peptides using statistical methods, accurately recovering expected genomes in benchmark tests.

MetaPilot enables adaptive genome-aware DDA and DIA metaproteomics using microbial genome catalogues

MetaPilot improves metaproteomics analysis by using genome-aware search-space refinement, enhancing peptide identification in DDA and DIA datasets.

Systematic Metaproteomics Mapping Reveals Functional and Ecological Landscapes of Ex Vivo Human Gut Microbiota Responses to Therapeutic Drugs

This study maps metaproteomic responses of human gut microbiota to 312 drugs, identifying 47 compounds that significantly alter microbial protein profiles and reveal functional state shifts.

Metaproteomics reveals age-specific alterations of gut microbiome in hamsters with SARS-CoV-2 infection

This study uses metaproteomics to identify age-specific changes in the gut microbiome of SARS-CoV-2-infected hamsters, revealing functional alterations and host-microbiome interactions.

MetaLab Platform Enables Comprehensive DDA and DIA Metaproteomics Analysis

MetaLab enables comprehensive DDA and DIA metaproteomics analysis by supporting both modes without requiring DDA results, improving peptide identification in human gut microbiome studies.

Assessing fecal metaproteomics workflow and small protein recovery using DDA and DIA PASEF mass spectrometry

This study evaluates how different experimental workflows affect fecal metaproteomic results, showing that DIA-PASEF improves protein identification and small protein recovery compared to DDA.

Elevated colonic microbiota-associated paucimannosidic and truncated N-glycans in pediatric ulcerative colitis

This study identifies elevated paucimannosidic and truncated N-glycans in the microbiota of pediatric ulcerative colitis patients compared to controls, suggesting a potential role for glycan metabolism in disease pathogenesis.

MetaLab 2.0 enables accurate post-translational modifications profiling in metaproteomics

MetaLab 2.0 improves PTM identification and quantification in metaproteomics by providing an open search workflow with higher accuracy and sensitivity than traditional methods.

A Chemoenzymatic Method for Glycoproteomic N-glycan Type Quantitation

The paper introduces a chemoenzymatic method to quantitatively analyze N-glycan types on glycoproteins, demonstrating its application in characterizing glycan heterogeneity in IgG1 and MCF7 cells.