Most current proteomics workflows, while highly developed and sophisticated, are usually not compatible with routine proteome analysis due to due heaviness of technical procedures and lack of reproducibility. Therefore, the development of reliable high-throughput proteomic platforms represents a crucial step for the advancement of proteomics research. In this thesis three examples of such platforms have been investigated. Every step of these pipelines was studied and subjected to further improvement, in order to enhance their efficiency and practicability. Many developments presented in this thesis can be helpful in different fields of proteomics. Engineering high-throughput proteomics pipelines will increase the role of proteomics in life science research and open new avenues for biomarkers discovery.