MSstatsQC 2.0: R/Bioconductor package for statistical quality control of mass spectrometry-based proteomic experiments.

MSstatsQC is an R/Bioconductor package for statistical monitoring of longitudinal system suitability and quality control in mass spectrometry-based proteomics. MSstatsQC was initially designed for targeted Selected Reaction Monitoring experiments. This manuscript presents an extension, MSstatsQC 2.0, that supports experiments with global Data-Dependent and Data-Independent acquisition. The extension implements data processing and analyses that are specific to these acquisition types. It relies on the state-of-the-art methods of statistical process control to detect deviations from optimal performance of various metrics (such as intensity and retention time of chromatographic peaks), and to summarize the results across multiple metrics and analytes. Additionally, the web-based graphical user interface MSstatsQCgui, implemented as a separate R/Bioconductor package, provides a user-friendly way to visualize and report the results from MSstatsQC 2.0.