In LC–MS analysis, every step of sample preparation is critical, especially the choice and use of vial caps and septa. This article systematically covers key preparation techniques, including filtration, protein precipitation, solid phase extraction, liquid–liquid extraction, supported liquid extraction, and derivatization. It also explains how to select Aijiren’s pre-slit PTFE/silicone septa, standard septa, and bonded aluminum caps for different workflows to ensure a secure seal and prevent volatilization and contamination. With a comparative product table, readers can clearly understand the advantages and application scenarios of each cap/septa type, enabling greater reproducibility and data accuracy in pharmaceutical development, proteomics, and environmental testing.