MSstatsQC

MSstatsQC is an R-based software package with a web-based graphical user interface that provides improved statistical methods for system suitability tests (SST) and quality control (QC) in Selected Reaction Monitoring (SRM) experiments. The software adapts modern longitudinal statistical process control methods, such as simultaneous and time-weighted control charts and change point analysis, to address the limitations of currently used statistical methods in proteomics. These methods enhance real-time monitoring, early detection, and prevention of chromatographic and instrumental problems in SRM experiments.

MSstatsQC can be used as a standalone tool or integrated with automated pipelines. While the examples focus on targeted proteomics, the statistical methods implemented in the software can be applied more generally to quantitative proteomics.