Open experiment: quantitative proteomics analysis of thyroid-cancer tissue slices using ultra-high performance liquid chromatography-tandem mass spectrometry

Open experiments play crucial roles in developing undergraduate students' practical abilities, innovative thinking, and teamwork. This open experiment is designed to use ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) in proteomics, a frontier field, by quantitatively analyzing thyroid-cancer-tissue-slice samples. Various reagents are first screened for further study by evaluating their abilities to extract proteins. This approach aims to foster students' hands-on abilities and their scientific-research thinking. The liquid-chromatography method is subsequently optimized to enable deep-coverage of the proteome, thereby enhancing students' understanding of liquid chromatography and mass spectrometry. Paraffin-embedded thyroid-cancer-tissue slices are finally subjected to quantitative proteomic analysis, resulting in the identification of 33 differentially expressed proteins, thereby demonstrating their potential use in disease-typing applications. This open experiment integrates theoretical and experimental knowledge gained through instrumental analysis, analytical chemistry, and biochemistry, thereby imparting scientific research thinking and innovative spirit to undergraduates. It also provides students with opportunities to expand and solidify theoretical knowledge through hands-on instrumental operation and experiments, which helps to build a systematic knowledge framework and develop a comprehensive understanding of relevant fields. Moreover, it stimulates undergraduate interest in scientific research, cultivates innovative thinking, and fosters team cooperation.