MassFinder Export GC dialog

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MassFinder 4: Manual

The Export chromatogram dialog controls several important functions of MassFinder:

  • checking and re-integrating of marked peaks
  • exporting annotated chromatograms to the clipboard
  • opening the print dialog for chromatograms
  • using the butterfly mode to compare two runs



The Export chromatogram dialog shows the current GC/MS runs of both slots together with all special traces like baselines, smoothed TIC, ion traces or base peak chromatograms.

Identical to the main window the first profile is drawn in black, the second is drawn in blue. All special traces are drawn in the same color as in the main window and these colors can be configured using the Tools dialog.

You may navigate the chromatographic profile with methods analogous to the main window:

  • zoom with the left mouse button by drawing a bounding box
  • shift the range by dragging the time axis with the left mouse button
  • stretch the range by dragging the time axis with the right mouse button
  • double-click the time axis to reset to complete view (default)
  • turn the mouse wheel to change the intensity
  • turn the mouse wheel while holding the shift key down to change the intensity of the active trace separately
  • click the right mouse button anywhere on the chromatogram to toggle back and forth between the previous and current view.

You may exit the dialog by double-clicking anywhere on the chromatogram. MassFinder will then adjust the current scan of the main view to the selected, double-clicked position. Use this method to easily investigate the mass spectra of a certain positon, e.g. after studying chromatograms in butterfly mode or by comparing their ion traces.

The vertical position of labels can be adjusted by dragging the label (left mouse button). Please click above the peak on the first letters of the label.

You may resize the whole window to adjust the size and aspect ratio to your requirements. Please note that the exported graphic has exactly the size of the white profile area.


Visibility of traces

Please note that all traces are listed in the upper right corner of the white profile area. Each label contains the sample name, the type of trace and the slot number ('#1' or '#2'), followed by a small black square indicating the current visibility of that trace.

Click on the square to toggle the visibility on/off. The square is displayed solid black if the corresponding trace is visible; the square is hollow if the trace is invisible.

Activity of traces

Please note that exactly one trace of the list is underlined. This is the active trace which relative zoom can be controlled separately and which is integrated when the integration is mode called.

Please click with the right mouse button on any trace label to activate that trace. The active trace is always underlined.

You may hold the shift key down while turning the mouse wheel to selectively change the intensity zoom factor of the active trace.

Select yellow or red labels

Image:Tutorial-FirstSteps-YellowRed.png The buttons with the yellow and red arrow icon allow to restrict labelling of peaks to only the yellow (including blue), only the red (including hollow) or, if both buttons are activated, all labelled peaks.

Adjust label vertical position

The vertical position of labels can be adjusted by dragging the label (left mouse button). Please click above the peak anywhere on the first letters of the label.

This feature is useful if an area is crowded by labels. You can manually avoid overlapping or colliding labels.

Select label information

Image:Tutorial-FirstSteps-Labels.png The set of label buttons allows to configure what kind of data are displayed as labels. You may select any combination of chemical name, retention time, personal field, internal key number or numbered by visibility.

The numbered by visibility counts the visible peaks. As you drag the time axis and shift peaks in and out of the visible area, the numbers are updated on the fly. This mode is useful for creating numbered chromatogram peaks as they are typically used in scientific publications.

The key number option labels the peaks with the internal library key number. While this option is rarely useful with larger libraries including the Terpenoids Library, this option is valuable if you create a small library of publication-relevant peaks and then want to produce a bunch of labelled profiles with peaks carrying consistent numbers throughout all graphics. To facilitate the work-flow you may easily create a new library based on the currently marked peaks of a GC/MS run (see Options and configuration: Create library from marked peaks).

Print hardcopy of current view

Image:Tutorial-FirstSteps-Hardcopy.png The printer button with red exclamation mark will immediately print an exact hardcopy of the current view, always enlarged to fit the paper. If you want to enjoy good printing resolution you should maximise the window before printing a hardcopy.

Hint: This feature is meant to rapidly get a print-out for immediate usage. In order to receive perfect print quality please use the normal print symbol and the corresponding print dialog.

Copy graphic to clipboard

Image:Tutorial-FirstSteps-CopyClipboard.png You may export exactly the current view to the clipboard by clicking on the copy graphic to clipboard button. You may resize the export chromatogram window to adjust the size and aspect ratio to your requirements. The exported graphic is in vector-based enhanced windows meta file format (*.emf) and can be directly pasted into Microsoft Word or Microsoft Powerpoint. If necessary, you can ungroup the graphic in Powerpoint and recolor and rearrange all elements as desired.

Print dialog

Image:Tutorial-Buttons-Print.png The print button opens the print dialog which offers high-quality printing and advanced printing options like distributing the chromatographic profile over several pages. The print-outs optionally include sample name, file name and method information.

Set range manually


In order to be able to obtain reproducible ranges and intensities MassFinder offers a dialog to set the time range and intensity manually.

Show all integrals

Image:Tutorial-Buttons-ShowAllIntegrals.png By default, MassFinder does not display the integral areas of marked peaks. Only when being in integration mode, MassFinder visualises the integral area of the active peak in red color.

Activating the show all integrals mode, MassFinder will visualise all integral areas of all marked peaks in grey color.



This button activates the integration mode. MassFinder will select the first labelled peak, automatically zoom the profile to an appropriate range and visualise the integral area. The integral and the label of the active peak are shown in red color. In the upper right corner the chemical name and the integral value is displayed. To improve the readability of the integral area, large numbers are grouped in thousands.

Please use the keys '<' and '>' to jump to the next or previous labelled peak. You may re-integrate the active peak anytime. Just use the right mouse button to select start point and end point of the desired integral range.

  • If you keep the mouse pointer above the profile, MassFinder will automatically place the integration anchor on the profile (see picture).
  • If you move the mouse pointer below the actual profile, MassFinder will place the integration anchor exactly as you instruct. This latter method allows to easily create step-wise integrals.

The integral value in the upper left corner is updated on-the-fly while integrating. The result table always reflects the actual integrals and your changes are taken into account immediately.

You can leave the integration mode by clicking a second time on the integral button.

Butterfly mode

Image:Tutorial-ButtonButterfly.png In the butterfly mode MassFinder draws all traces that belong to slot #1 in normal orientation and all traces that belng to slot #2 in upside-down orientation, so that a head-to-tail figure is generated. Such butterfly comparisons facilitate spotting of differences between two fairly similar profiles. Have a look at the peaks around retention time 28 min and 33 min.

Please note that you can not re-integrate while being in butterfly mode. Leave the butterfly mode if you want to re-integrate peaks. You can leave the butterfly mode by clicking the butterfly button a second time.


Instant traces

This feature is available in MassFinder 4.10 and later.

Image:ExportGC-InstantTracesButton.png The Export chromatogram dialog allows the instant display of one additional ion trace that is independent from the main window's ion traces. The instant trace will always be added automatically to both GC/MS runs and can be changed swiftly by scrolling the mouse wheel (Ctrl-wheel).

Activate and deactivate instant traces:

  • Double-click the mouse pointer into the edit box and do not move the mouse pointer outside the button bar. Enter a new ion trace m/z value and press ENTER.
  • Alternatively, you may simply hold down the Ctrl-key and turn the mouse wheel. MassFinder will change the ion trace value with each turn and update the ion trace automatically.
  • You may delete the instant trace by clicking the grey cross button on the right side of the ion trace edit box.

The instant traces are particularly useful in butterfly mode, because they enable to easily spot differences between two runs. They are also valuable in single GC/MS mode if you add one ion trace in the main window and use the instant trace, e.g. in order to detect co-eluting peaks.


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