A comprehensive CHO SWATH-MS spectral library for accurate quantitative profiling of 10k proteins

A comprehensive Chinese hamster ovary (CHO)-cell specific spectral library, containing extensive information of high-quality spectral ions covering more than 10k CHO cell proteins, was constructed to provide confident and reproducible protein identification and quantification in data-independent SWATH-MS analysis. The applicability of CHO spectral library was tested in the analyses of different CHO samples including whole cell lysate, harvested cell culture fluids, and downstream processing samples. The portability of CHO spectral library was also demonstrated in the processing and analyses of SWATH-MS data sets collected from multiple LC-MS instrumental setups and various CHO cell lines.