Process data | Import | Peak Table | Metadata | Filter | Convert retention time to "rt in minutes" or "rt in seconds" | Preprocess MS2 data | Annotating data | Molecular formula prediction | Annotations | Operational Metabolomic Units (OMUs) | Calculating distances | Clustering into OMUs | Annotation of OMUs | OMU-based Ecological Analyses | Alpha Diversity | Beta Diversity | Visualizations | Principal Coordinate Analysis (PCoA) | Hierarchical Clustering | Network Plot | Using Group Averages | Combined data frames | Heat map | Box Plot

Process data | Import | Peak Table | Metadata | Filter | Convert retention time to "rt in minutes" or "rt in seconds" | Preprocess MS2 data | Annotating data | Molecular formula prediction | Annotations | Operational Metabolomic Units (OMUs) | Calculating distances | Clustering into OMUs | Annotation of OMUs | OMU-based Ecological Analyses | Alpha Diversity | Beta Diversity | Visualizations | Principal Coordinate Analysis (PCoA) | Hierarchical Clustering | Network Plot | Using Group Averages | Combined data frames | Heat map | Box Plot

Load required libraries | Filter MS1 feature table with mpactr | Interactive scatter plot of all input ions and their fate during filtering | Correlation between samples at different levels | Correlation between each individual sample | Correlation between technical replicates | Correlation between biological replicates | Dendrogram | Fold change analysis | Calculate fold change | Visualize fold change for compounds in a 3D scatter plot | Test for compounds with significant fold changes | Volcano plot

Load data into R | Accessing data in mpactr object | Extract peak table | Extract metadata | Reference semantics | Filtering | Mispicked ions filter | Remove ions that are above a threshold in one biological group | Remove non-reproducible ions | Remove insource fragment ions | Chaining filters together | Summary | View passing and failed ions for a single filter | View passing and failed ions for all input ions | Visualize filtering QC with tree map plot

Reference semantics | Deep copy: specifics of the R6 class