MassFinder Tools dialog

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MassFinder 4: Manual

The tools dialog offers routines related to chromatographic profile, e.g.

  • to create and configure ion traces
  • to cut-off the beginning or end of runs
  • for calculating background corrections
  • for baseline correction of GC data
  • for reducing the scan rate of runs
  • for calculating relative retention factors


Open the Tools dialog

Please click on the tools button as indicated in the screen shot. The button is only active if a GC/MS or GC run is open.

Administrate traces

The administrate traces group box lets you add, remove and configure chromatographic traces.

By default, MassFinder displays the total ion chromatogram (TIC) as black profile (GC #1) or blue profile (GC #2) in the main window.

Smooth TIC

The smooth TIC button adds a smoothed profile calculated by Gaussian smoothing based on the total ion chromatogram. Use this routine if the native profile is noisy and peak picking difficult or impossible. Peak detection and finding reasonable integration anchors is much easier in smooth profiles. Do not use this routine if your native profile is already smooth.

You may configure the degree of smooting by setting the Gaussian smooth factor in the option dialog. Try the smallest value possible to obtain a suitable profile. Do not exaggerate smoothing.

While peak-picking and determination of integration anchors is performed on the smoothed profile (if selected as active trace), calculation of the integral itself is performed on the native data. Thus, the integral value is not influenced or adulterated by using Gaussian smoothing, but reflects your true data. Gaussian smoothing is just a method to ease the process of detecting and analysing peaks. Its does not destroy or modify native data, it is just a different visualisation of the same data.

In the main window you may select the active trace used for peak-picking by right-clicking on the trace label in the upper right corner of the profile panel. The active trace is underlined. This is the same principle as used in the export chromatogram dialog.


The Add BPC' button adds a base peak chromatogram trace.

The base peak is the signal of a mass spectrum with 100% abundance, i.e. the most-intense peak of a mass spectrum. The base peak chromatogram is defined as the profile resulting from extracting the base peak ion at each point of the profile. Obviously, the base peak can vary from scan to scan. Base peak chromatograms are very useful to detect co-eluting peaks, because in many cases they emphasise spectra-to-spectra variations. Naturally, BPC are not as good for detecting co-eluting compounds with mass spectra having the same base peak.

The example shows the total ion chromatogram (TIC) in black and the base peak chromatogram (BPC) in pink. Please note that the labelled peaks, particularly the one on the right flank, would probably have been overlooked without using the BPC trace.

Add baseline

The add baseline button calculates and approximates the baseline of the total ion chromatogram. This is particularly useful for correcting GC data (without mass spectral information). Visualising the baseline before executing the permanent baseline correction enables you to predict the result.

The upper example shows the total ion chromatogram in black and the baseline in orange. The lower example shows the same GC after permanent baseline correction.

Image:ToolsDialog-Baseline.png Image:ToolsDialog-BaselineCorrected.png

Add ion traces

The edit box allows you to create extracted ion chromatograms (EIC), usually called ion traces. An ion trace is defined as the profile resulting from extracting the intensity of a specified ion at each point of the profile. Ion traces are useful for many purposes, e.g. to search for certain constituents with rare or typical mass signals or for detecting co-eluting peaks.

Just type any mass signal (number) in the edit box and press ENTER. MassFinder adds the new ion trace and assigns a different color to the new ion trace. You may delete an ion trace by entering its value again (if the same number is still displayed in the edit box, you can just press ENTER again to toggle the ion trace on and off). Alternatively, you can select it and then click the blue cross button to delete a certain trace.

You may re-color each ion trace by selecting it and clicking the recolor button. You may reset all colors to the automatically assigned colors by clicking the reset colors button.

Series traces

This method was suggested to be implemented into MassFinder by Hugues Brevard of Robertet S.A., Grasse, France.

MassFinder supports special "series traces", which are sums of ion traces separated by m/z 14 units, i.e. methylene CH2 units. Example: The series 14 represents the sums of m/z 14, 28, 42, 56, ... 308, while the series 15 represents the sums of m/z 15, 29, 43, 57, ... 309. Thus, there exist exactly 14 different series traces with 14 to 27 as first member. The series may start with a higher member, e.g. m/z 29, 43, 57, ... 309 (without 15) if desired.

You may add series traces by entering the negative number of the base member. Example: Enter -15 to create the series with m/z 15, 29, 43, 57, ... 309. Enter -29 to create the same series starting with 29 instead.

In summary, series traces allow to easily spot certain substance classes, depending on their oxygen or nitrogen content (e.g. amines by series m/z 30, ...; alcohols by series m/z 31...) or their degree of unsaturation (e.g. saturated hydrocarbons by series m/z 43, ...). You are invited to experiment with these series traces.

Reasonable application of these series traces require knowledge about your analytes and experience with similar types of analytes. This method is particularly useful when applied to the comparisons of two GC/MS runs, e.g. to detect adulterations or contaminants. You may use the butterfly mode of the export chromatogram dialog to compare ion traces of different runs.

If you like this special feature, please do not hesitate to inform us about your application. We will continue to update this section on a regular basis.

Handling of ion traces in the main window

Hiding ion trace

You may hide ion traces by clicking with the left mouse button on the little square on the right side of trace label in the upper right corner of the profile panel. This method is identical to the export chromatogram dialog. The black square will turn into a hollow square. Click again to make the trace visible again.

Adding ion traces in the main window

Please note that you can add and remove ion traces in the main window by shift-clicking any mass signal of the highlighted mass spectrum (hold the shift key down, then click with the left mouse button anywhere on the desired mass). Repeat the procedure to toggle the trace on and off. You can add as many ion traces as you like.

Deleting all traces in the main window

Please note that you can remove all special traces (smooth, BPC, baseline, ion traces) by clicking on the black cross button on the left side of tools dialog button in the main window. You cannot remove the total ion chromatograms (black profile in GC #1 and blue profile in GC #2), but you can make them invisible by left-clicking on the little black square on the right side of the trace label. A TIC cannot be hidden if no other trace is left of the same run.

Cut-off run-time

The cut-off run time group box allows to remove leading or tailing parts of a run. This is particularly useful to cut-off the solvent peak of GC-FID data or to remove the heating-off period at the end of runs.

MassFinder will cut-off all scans from the beginning up to the current scan (highlighted scan), or from the current scan up to the end, respectively.

Please note that MassFinder will automatically select beginning or end depending on whether the current position is in the first or last half of the run. You may change the automatic selection, though.

MassFinder can also reduce the scan-rate of the run by deleting every n-th scan. For example, setting the value to 2 will remove every second scan and thus result in a run with half the amount of scans. This is useful if a high scan rate has led to a vast amount of unnecessary data and makes processing tedious.

Please note that MassFinder's feature of displaying three consecutive scans after each other in the main window, is valuable only together with a suitable scan rate, so that a sequence of scans shows slight variations from scan to scan. Very high scan rates produce consecutive scans that are almost identical. High scan rates are not recommendable anyway, because the signal-to-noise ratio and sensitifivity of your instrument decreases. The scan rate should be adjusted to your chromatographic resolution and typical peak widths of approximately 5-10 scans per peak.

Subtracting routines

Permanent subtraction

The background correction button carries out the current subtraction in the entire visible range. The result of each subtraction is exactly identical to the on-the-fly subtraction in the main window. Thus, we recommend to check the result of important regions with the on-the-fly mode (delta button in the main window) before carrying out the permanent background subtraction.

Please note that MassFinder applies the subtraction only on the visible area. Please adjust the visible area in the main window so that it represents exactly the area you want the background correction to work on. You may use multiple background corrections in different regions after each other.

Please note that MassFinder does modify the GC/MS data irrevocably when using the permanent subtraction. There is no way to undo this subtraction. Naturally, MassFinder never modifies the native data file of your instruments acquisition, so you can always start over from scratch by re-opening the native data file. MassFinder only writes to his own data file format, i.e. *.mfg files.

Baseline correction

As discussed above in the section add baseline you can perform a permanent baseline correction. This feature curently works only for GC data without mass spectral information.

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