Magno Junqueira

Asking the Data: Conversational Interrogation of LC-MS/MS Proteomics Data Sets with an LLM Agent

The paper introduces a conversational framework using an LLM agent to interrogate proteomics data sets, identifying issues in four LC-MS/MS datasets and demonstrating its feasibility in reanalyzing data.

Sample Preparation and Homology-Driven Search Shape the First Holobiont Proteome of the Marine Sponge Viles ophiraphidites (formerly Topsentia ophiraphidites)

The paper compares sample preparation workflows and homology-driven search strategies to characterize the proteome of a marine sponge, finding S-Trap with homology layers provides the most comprehensive and consistent results.

A fast TMT-based proteomic workflow reveals neural enrichment in neurospheres of hiPSC-derived neural stem cells

The paper compares proteomic profiles of hiPSC-derived neural stem cells in 2D monolayers and 3D neurospheres, finding neurospheres show neural pathway enrichment and increased neuronal identity.

The effect of aging on post-translational modifications of wild-type human SOD1 and the A5V ALS mutant

This study examines how aging affects post-translational modifications (PTMs) of wild-type and A5V ALS mutant human SOD1, revealing age-related changes in oxidation, formylation, and carboxylation.

Proteome Complexity Scales with Architecture in Human Neural Models

The paper compares proteomic complexity across human neural models, finding increased molecular complexity in tissue-like models that better reflect in vivo brain biology.

Quantitative profiling of axonal guidance proteins during the differentiation of human neurospheres

This study quantifies proteomic changes during human neurosphere differentiation, identifying upregulated axon guidance pathways and a functional assay for neurite outgrowth.