MS-PROT 2025 is an engaging, hands-on course designed for students interested in the science of proteomics analysis and data interpretation. The course blends essential theory with practical applications, covering core principles of mass spectrometry (MS), protein and peptide identification and quantification, and advanced R-based data analysis. Students will gain real-world insights through interactive sessions, lab tours at the university’s proteomics core facilities, and direct exposure to cutting-edge MS platforms such as Orbitrap and MALDI-TOF. Led by Mohieddin Jafari and Markku Varjosalo, with contributions from leading international and internal experts, the course fosters critical thinking through pre-assignments, quizzes, and a collaborative capstone project based on real proteomics datasets.