Introduction | Alternative software for data quality assessment | Installation | Questions and bugs | Create Spectra, MsExperiment, and Chromatograms objects | Create Spectra and MsExperiment objects from mzML files | Chromatograms example | Create Spectra and MsExperiment objects from (feature-extracted) intensity tables | Calculating the quality metrics on Spectra, MsExperiment, and Chromatograms objects | List of included metrics | Metrics shared between Spectra and Chromatograms | Chromatograms-specific metrics | Obtain the metrics in data.frame-format | Obtain the metrics in mzQC-format | Remove empty spectra prior to the calculation | Visualizing the results | Appendix | Session information | References

Introduction | Questions and bugs | Prepare the environment | Appearance of user interface depends on the data input | QC analysis of TCGA RNA-seq data | Sidebar | Tab: Samples | Histogram | Mosaic plot | Tab: Values | Boxplot/Violin plot | Trend/drift | Coefficient of variation | Mean-sd plot | MA plot | ECDF | Distance matrix | Features | Tab: Dimension Reduction | PCA | PCoA | NMDS | tSNE | UMAP | Tab: DE | Sample meta-data | Model matrix | Contrast matrix | Top DE | Volcano plot | QC analysis of proteomics data | Tab: Measured Values and Missing Values | Barplot for samples | Histogram Features | Measured Variables | Missing Variables | Histogram Features along variable | UpSet | Measured Values | Missing Values | Sets | Appendix | Session information | References