ProtoPure: Literature Mining and Analysis of Protein Purification Protocols at Proteome Scale

ProtoPure, an LLM-based literature-mining workflow, extracts standardized protein purification conditions and finds convergence in recombinant expression practices, with BL21(DE3) systems dominating across thousands of proteins.

• Why it matters: Protein purification choices are still largely empirical, and there is no systematic framework to compare protocols across entire protein families at proteome scale.
• What they did: ProtoPure uses a user-defined UniProt table to select proteins, retrieves and classifies related publications, and extracts 12 standardized purification parameters such as buffer composition and elution conditions.
• The result: The dataset shows BL21(DE3)-based expression systems and recurrent host–inducer–medium–plasmid combinations occur substantially more frequently than expected by chance, while downstream purification parameters remain more diverse.

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