Lecture
This lecture discusses the challenges and limitations in the field of proteomics, particularly focusing on the complexity and dynamic range of protein analysis. The instructor outlines the difficulties faced when analyzing proteomes, which generate a highly complex mixture of peptides after digestion. The limitations of classical data-dependent acquisition (DDA) methods are highlighted, including issues with reproducibility and missing values. The lecture introduces the concept of data-independent acquisition (DIA) as a solution to these challenges, allowing for more comprehensive coverage of samples and reduced missing values. The instructor provides statistical insights into proteome coverage, illustrating the trade-offs between analysis time and the number of proteins identified. Additionally, the lecture touches on the complexities of quantitation and the study of post-translational modifications (PTMs), emphasizing the dynamic nature of these modifications and the ongoing challenges in fully understanding their functional relevance. Overall, the lecture provides a thorough overview of the current state and future directions in proteomics research.