New Developments in MSstatsQC: MSstatsQCgui a new R/Bioconductor package, quality control for targeted and discovery proteomics workflows, machine learning based quality monitoring

MSstatsQC and its graphical user interface, MSstatsQCgui, are two R/Bioconductor packages for statistical analyses of longitudinal system suitability and quality control (QC) of mass spectrometry-based proteomics experiments. MSstatsQC supports quality improvement activities for data-dependent, targeted and data-independent spectral acquisition by detecting different types and patterns of deviations from optimal performance. It integrates these patterns across multiple metrics (such as intensity, retention time etc.) of multiple analytes relying on the state-of-the-art statistical process control (SPC) methods. Availability and implementation: The code, the documentation and example datasets are available open-source at www.msstats.org/msstatsqc under the Artistic-2.0 license. The package can be downloaded from www.msstats.org/msstatsqc or from Bioconductor www.bioconductor.org and used in an R command line workflow