Many proteomic studies rely on the steady-state analysis of tissues or cell lines to identify markers of diseases or predict drug treatment outcome. In many instances, however, proteome changes upon drug exposure may be better suited to clarify in-cell drug action, identify off-targets or reveal mechanisms involved in drug resistance. Complete drug dose-response curves are however rarely carried out on a proteome-wide scale due to the prohibitively long acquisition times usually required by bottom-up proteomic approaches using liquid chromatography coupled to mass spectrometry.
In this study, microflow liquid chromatography coupled to SWATH acquisition was used for rapid and robust proteome-wide dose-response drug profiling. The 45 min gradient setup enables exactly a one-hour run time injection-to-injection. The microflow-LC SWATH analysis of the LNCaP prostate cancer cell lines resulted in the identification of approximately 5’000 proteins consistently across all the time series and drug treatment conditions. The time-dimension of the dataset allows assessment of the cellular accessibility of the drug and the kinetics of drug action on the proteome scale. The drug concentration dimension allows the assessment of the level of sensitivity/reactivity of the proteins to the various drug concentrations. The dose-response curves of several proteins showed significant IC50 difference between the sensitive LNCaP and the resistant LNCaP-abl cell lines, pinpointing potential cellular pathways involved in the drug resistance mechanisms of LNCaP-abl.