Targeted Proteomics coming of age - SRM, PRM and DIA performance evaluated from a core facility perspective

摘要

The daily operational business of a core facility is normally not allowing for optimization of each method parameter, prior to recording a data set. This is reflected in this study by running the experiments with methods used on a routine basis in our core facility. Our study shows that targeted data acquisition (SRM, PRM) outperforms targeted data extraction strategies (DIA) with respect to quantitative accuracy and precision (especially when the analyte concentration is shifted in to low concentration regimes). Targeted acquisition methods are only suited for monitoring a limited number of targets, but for screening experiments targeted data extraction work-flows clearly outperform targeted data acquisition. The question, whether greater throughput justifies lower sensitivity/specificity has to be answered in the context of the individual research project. Particularly the amount of resources for follow-up experiments will therefore determine the overall success of a study (e.g. the number of identified biomarkers). In addition, large-scale DIA is very resource demanding e.g. on the computational side and more prone to human error. Not all research environments are equally prepared for such challenges and should consider these aspects during experimental design setup.