J. Alfredo Blakeley‐Ruiz

The paper compares AUC and SpC quantification methods in metaproteomics, finding AUC outperforms SpC in accuracy and dynamic range, but MBR harms AUC results.

This study shows that dietary protein source affects gastrointestinal health, with animal-based protein causing more GI symptoms and intestinal permeability than plant-based protein.

The paper evaluates statistical methods for differential metaproteomics, finding that several approaches effectively identify differentially abundant proteins despite data challenges.

The paper investigates how co-inoculation with AMF and PSB affects tomato rhizosphere dynamics across growth stages using metagenome-informed metaproteomics.

The paper proposes a roadmap for fair reuse of public microbiome data by introducing a Data Reuse Information tag (DRI) to facilitate communication between data creators and consumers.

This study compares DIA-MS and DDA-MS for metaproteomics, finding DIA-MS provides more reproducible and accurate protein and peptide identifications across laboratories.

This study shows dietary protein source affects host physiology through both direct and microbiota-mediated mechanisms in mice and humans.

This study shows that different dietary protein sources alter gut microbiota composition and function in mice, affecting amino acid and mucus degradation processes.

The paper quantifies dietary protein digestion and microbial processing in mice, showing some proteins escape host digestion and are modified by gut microbiota, with health-relevant proteins differentially enriched.

This paper uses stable isotope fingerprinting to link gut microbiota to their carbon sources and shows diet-induced substrate switching in vivo.