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The interface

The MPACT window, with its main areas numbered
The MPACT window. Numbers match the list below.
  1. Sidebar. The Setup tabs (File Selection, Filtering Settings, Analysis Settings, Run) are the workflow, top to bottom. The Results tabs are disabled until an analysis completes.
  2. Run chip and Runs. The chip shows the analysis you are looking at and its state. Runs opens the list of your previous analyses. See Running and managing runs.
  3. Plot controls. Options for the current plot, such as thresholds, views and colour maps. Changes redraw the plot immediately.
  4. Plot toolbar. Navigation, selection tools and image export. See below.
  5. Details panel. Information about the selected feature: m/z, retention time, statistics, abundance by group, MS2 spectrum and database matches.
  6. Status bar. The selected feature (or, on plots of samples, the selected injection) stays here while you move between tabs.

The same layout is used on every result tab, so a feature selected on the volcano plot is still selected when you open the heatmap or Feature Info.

Plot toolbar

Button Action
Reset view Return to the full extent of the plot
Back, Forward Step through previous zoom and pan states
Pan Drag to move the plot
Zoom Drag a rectangle to zoom in (the default)
Box select Drag a rectangle to select the features inside it
Lasso select Draw around features to select them
Cancel selection Leave the box or lasso tool
Format, Save Save the plot as SVG, PNG, JPEG or WebP

Hold Shift with the box or lasso tool to add to the current selection. SVG export is the best choice for figures, since it stays sharp at any size and can be edited in a vector program.

The details panel

The panel has four collapsible sections. Close the ones you are not reading to make room for the others.

  • Details: m/z, retention time, mass defect, maximum abundance, fold change, p and q values, median CV, database hit count and the groups the feature was detected in.
  • Abundance: average abundance per biological group with its propagated uncertainty (left), and the individual sample values (right).
  • MS2 spectrum: the feature's fragment spectrum, if you supplied a fragment database. After an MS/MS library search it is drawn as a mirror plot against the best library match.
  • Database matches: Natural Products Atlas and MS-DIAL library hits, with structures. Step through them with the arrows.

Drag the boundary between the panel and the plot to resize it, or double-click the boundary to reset its width. The › button in the panel header hides it for a full-width plot; ‹ Details at the right edge brings it back. Its size and open sections are remembered.

The dashed circle next to the feature name flags the feature. See Flags.

The details panel showing an MS2 mirror plot and an MS-DIAL library match
The details panel. The feature's MS2 spectrum (top) is mirrored against the matching MS-DIAL library spectrum (bottom), and the match is listed below.

The address bar always names the current tab and analysis, for example app.mpactms.org/#volcano/r_fa0bc6e750adf5ce. Bookmark it or reload the page and you return to the same view. Analyses belong to your workspace, so a link opens only for you, not for someone you send it to.