Systematic Mining of Bioactive Compounds for Wound Healing From Cayratia Japonica Exosome-Like Nanovesicles: A Workflow Combining LC-MS and DeepSeek Models

Abstract Background Plant-derived exosome-like nanovesicles (P-ELNs) effectively deliver bioactive compounds due to their high biocompatibility and low immunogenicity. While liquid chromatography-mass spectrometry (LC-MS) profiles compounds in complex samples, its analysis of large datasets remains limited by traditional methods. Recent advances in large language models (LLMs) and domain-specific systems have enhanced Chinese biomedical data processing and cross-modal pharmaceutical research. Objective This study aimed to create a multimodal framework of LC-MS combined with DeepSeek models for data mining of compounds with wound-healing properties from exosome-like nanovesicles derived from Cayratia japonica (CJ-ELNs). Methods LC-MS identified compounds enriched in CJ (n=3) and CJ-ELNs (n=3), and then compounds specifically enriched in CJ-ELNs were filtered via a four-step filtering workflow. The CJ-ELNs-specific compounds were processed by DeepSeek models for screening naturally active compounds with targeted functions of antioxidation, anti-inflammation, anticellular damage, antiapoptosis, wound healing and tissue regeneration, and cell proliferation. Results A multimodal framework of LC-MS combined with the DeepSeek-DF model was created. With the assistance of artificial intelligence (AI), a total of 46 naturally active compounds derived from CJ-ELNs with targeted functions were identified. Conclusions A self-designed multimodal framework of LC-MS, combined with DeepSeek models, rapidly and accurately identifies naturally active compounds from CJ-ELNs. This AI-powered system innovatively integrates the traditional analytical technique with modern LLMs, thus greatly favoring data mining of active ingredients in traditional Chinese medicine herbs.