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This is the recording of the third meeting of the third session of IBRE Bioinformatics Club, an open series of online seminars dedicated to the discussion of best practices in modern bioinformatics and computational biology. During this meeting, which took place on September 2, 2025, we have discussed the applications of AI in the analysis of proteomic data and immune repertoires. Together with our speakers, we talked about their experience in applying state-of-the-art deep learning and large language models (LLMs), as well as their perspective on the future of AI-assisted analysis of complex data. Two expert speakers have presented their perspective on the topic: 1. Dr. Yana Safonova, assistant professor at the Penn State University, PA, USA/Department of Computer science and engineering, Huck institutes of Life Sciences, PA, USA; 2. Dr. Pavel Sinitcyn, assistant professor at the Utrecht University, Netherlands.