Chromatogram Traces view shortcut menu. - Proteome Discoverer Software - Chromatogram Traces view shortcut menu. - Proteome Discoverer Software

Chromatogram Traces view shortcut menu. - Proteome Discoverer Software - Chromatogram Traces view shortcut menu. - Proteome Discoverer Software - Proteome Discoverer Software

Proteome Discoverer 3.1 User Guide

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User Guide

Software version

3.1

The following table lists the commands in the Chromatogram Traces view shortcut menu.

Chromatogram Traces view shortcut menu commands
Command	Description
Undo Last Zoom/Pan	Reverses the last zoom or pan movement.
Undo All Zoom/Pan	Zooms out to the full data acquisition time for the chromatogram on the x axis and the height of the largest chromatogram peak on the y axis.
Keep Zoom	Maintains the same zoom range, as you select components with different peak areas. This command overrides the Zoom to Detected Peaks command as you select different table rows.
X-axis Zoom
Keep Zoom	Freezes the x-axis magnification until you select one of the other x-axis options.
To Detected Peaks (Active Plot)	Autoscales the x axis for all the selected PSMs or peptide groups.
To Detected Peaks (All Plots)	Autoscales the x axis for all the selected PSMs or peptide groups.
Y-axis Zoom
Auto Scale Y Axis	(Default) Scales the y axis to the maximum intensity within the current x-axis (retention time) zoom range. Manual zooming of the y axis is unavailable in this mode.
Manual (Synchronize All Plots)	Scales the y axes of all the plots to the same scale. Manual zooming on both axes is available.
Manual (Each Plot Individual)	Changes only the y-axis scaling of the current plot. Manual zooming on both axes is available.
Copy
Image	Copies an image of the Chromatogram Traces View, including the legend, to the clipboard. You can paste the image into a Microsoft Office document as a raster image or into a vector-drawing program as a vector image.
Points	Copies the data as a two-column list of data points and copies the scan header. The first column lists the retention time, and the second column lists either the relative intensity or the counts.
Export
Image As	Opens the Save As dialog box, where you can specify a file name and save the contents of the Chromatogram Traces View as one of these selectable image formats: EMF, PNG, GIF, JPG, TIFF, or BMP. The EMF format is a vector image.
Points As	Opens the Save As dialog box, where you can specify a file name and save the contents of the Chromatogram Traces View as a text file. Default name: Chart.txt When the trace is a plot of relative intensity versus retention time, the application saves the data points as a two-column list. The first column lists the retention time, and the second column lists the relative intensity (%). When the trace is a plot of area (in counts) versus retention time, the second column lists the area of the peaks.
Plots
Add Plot	Adds an empty active plot to the Chromatogram Traces View. Only the screen size limits the maximum number of displayed plots. When you reach the screen limit, the Chromatogram Traces View shows as empty with this message: Not enough space for drawing chart properly.
Remove Plot	Removes the active plot, which has a gray border. Adding more than one plot activates this command.
Remove Other Plots	Removes all of the plots in the Chromatogram Traces View. Adding more than one plot to the Chromatogram Traces View activates this command.
Freeze Content	Keeps the chromatogram of the currently selected row in the view when you select another row in the current table or another result table. The application uses X marks, rather than a different color, to distinguish the frozen chromatogram trace.
Clear Frozen Content	Clears the frozen chromatogram from the view.
Distribute Selection to All	Updates all of the plots simultaneously as you select different table rows. When the Plots > Distribute Selection to All option is not selected, only the active plot updates.
Display Options
Show tooltips	Displays a popup box with the exact time and intensity value when you place the cursor, +, over a trace peak.
Show Gridlines	Adds grid lines to the view.
Show Detected Peaks	Uses a fill color for the integrated area under the detected trace peaks. Turning off this command removes the fill color.
Show Markers	Determines whether to display the vertical line at the retention time where the MS2 spectrum for the PSM was acquired.
Show Legend	Displays a legend for the sample groups at the top of the view.
Legend Size	Specifies the number of legend lines that you want the application to display. Range: 1–10 rows
Relative Intensity	Displays the y-axis scale as relative intensity (0 to 100%). The legend changes to Intensity [%]. The default y-axis scale is an absolute scale; the y-axis legend is intensity [counts].
Crop to Detected Peaks	Redraws only the trace peaks of the displayed traces. Does not redraw the baseline portions of the traces as you select different table rows.
Show Unaligned	Displays a trace or traces without any alignment.
Show RT-Aligned	Display a trace or traces with chromatographic alignment derived from the Feature Mapper node.
Show RT- and (Group-) Apex Aligned	Displays a trace or traces with chromatographic alignment derived from manual recalculation in the Chromatogram Traces view.