Commands:
View > Chromatogram Map
Edit > Label Selected Peaks
Edit > Remove All Labels
File > Export > Chromatogram as mzML…

A chromatogram map view displays a two dimensional intensity map of a chromatographic run. It gives a good overall impression of the chromatographic resolution and the location of fragmented and identified peptides or ions.

A Chromatogram Map view is generated by using the Add View button of a chromatogram data object in the data collection list view or by using the command View > Chromatogram Map. A chromatogram map gives an overview over an entire chromatographic data set.

Activities:
  • Zooming in: holding the Alt key and dragging the mouse over the map to define the region to zoom in to
  • Zooming in with constant axis ratio: holding the keys ⌥ ⇧ and dragging the mouse over the map
  • Restoring the former view: double mouse click into the map region. Up to three views are stored.
  • Generate a selection for peak labelling: click-drag mouse of a map region
  • Add a selection for peak labelling: click-drag mouse of a map region
  • Label the most abundant peak in every selection: command Edit > Label Selected Peaks
  • Remove a label: by deleting its text
  • Remove all labels: command Edit > Remove All Labels
  • Generating a chromatogram: ⌥ ⌘ click-dragging the mouse generates a mass chromatogram of the chosen x-axis interval
  • Generating a single spectrum: ⌥ ⌘ mouse click into the map generates a spectrum at the chosen time coordinate
  • Generating a summed spectrum: ⌥ ⌘ click-dragging the mouse generates a summed spectrum of the chosen y-axis interval
  • Measuring within the map: click-dragging the mouse - care is advisable because a lot of data might be accessed
  • Moving within a zoomed map: the arrow keys ↑, ↓, →, ← move the map in the chosen direction. Keeping the Alt key pressed ⌥↑, ⌥↓, ⌥→, ⌥← rapidly shifts the map in the chosen direction. The map can be scrolled.
  • Changing the staining intensity: Shifting the slider changes the ion intensity for the most intense staining, shifting the slider changes the ion intensity for the lowest staining
  • Displaying all precursors that had been selected for fragmentation: dragging the link icon of the chromatogram’s precursor view onto the map - clicking onto a precursor marker displays the fragment spectrum
  • Displaying all ions of an ion group on the map: dragging the link icon of an ion group onto the map - clicking onto a ion marker displays the ion’s chromatogram
  • Displaying all precursors of identified peptides: dragging the link icon of a Mascot search result view onto the map - clicking the precursor marker displays the fragment spectrum and the peptide sequence
  • Defining a norm-protein to normalise the quantities of all proteins determined from this chromatogram to its quantities: dragging a protein line from a Database Search View onto the map.
  • Dropping a chromatogram from an aligned chromatogram group that contains the chromatogram of the map onto the map overlays the map with the second chromatogram’s map in its aligned form
  • Several chromatograms can be overlaid simultaneously
  • A menu allows to set the top-most chromatogram - with two sliders the transparency and the staining level of the top-most chromatogram can be regulated
  • The command Edit > Cut removes the top-most chromatogram overlay
  • Exporting the entire chromatogram in mzML format: File > Export > Chromatogram as mzML…