MassFinder Subtraction

From MassFinder

Jump to: navigation, search
MassFinder 4: Tutorial

This is the fifth lesson of the MassFinder 4 tutorial. You will learn how to calculate average spectra, how to perform on-the-fly background subtractions, to use ion traces and to cut off the beginning or end of chromatograms.


Step 1: Average spectra

You can create average spectra by zooming with the right mouse button the desired part of the chromatogram profile. A reddish box will be drawn to mark the scans that are averaged. If you start in the upper half, you may click anywhere to start; if you start in the lower half, please click in the baseline area of the profile (to distinguish the average operation from the profile stretching).

MassFinder will show the average spectrum as highlighted spectrum. The name of the spectrum gives the averaged range. The hidden top and bottom spectra are meant to emphasise the average mode. The current library matches are hits for the average spectrum.

To end the average mode, just continue to navigate as usual. MassFinder will memorise the average spectrum in the background so that it can be used for average subtraction.

Step 2: On-the-fly subtraction

Image:Tutorial-ButtonSubtraction.png Please click on the delta button to activate the difference mode. Alternatively, you may press the key 'd' to enter the difference mode. MassFinder will subtract the stored average spectrum from all visible GC/MS scans on-the-fly. The mass spectra will have the red label difference to clearly indicate the difference mode.

You may navigate as usual while being in difference mode.

Click again on the delta button to leave the difference mode. Alternatively, you may press the key 'd' to leave the difference mode.

Step 3: Ion traces

With MassFinder you can easily add ion traces to the chromatogram panel. Just hold down the shift key, then click on a m/z label in the highlighted mass spectrum. MassFinder will add the indicated ion trace.

You may add as many ion traces as you require. MassFinder will automatically choose different colors.

Please move to the peak at RI 1490 which we suppose to be a co-elution of at least two constituents and which gives no library hit. In lesson 2 we marked this peak with a red arrow as unknown. Now add the ion traces m/z 119, 147 and 161: Now it is proven that at this position at least two constituents co-elute, since the ion traces maximise at different retention times.

Image:Tutorial-IonTraces-GreyCross.pngClick again on the respective m/z labels to remove the ion trace. Alternatively, you may remove all ion traces by clicking on the gray cross right of delta button.

Step 4: Configuring ion traces

Image:Tutorial-IonTraces-Tools.pngPlease click on the special tools button to open the tools dialog.


You may remove a certain ion trace by selecting it in the list box and clicking on the cross button. With the recolor button you assign a different color to the selected ion trace. You may use the edit box on the left side to add an additional ion trace by just typing the m/z value and pressing ENTER. Typing an existing m/z value will delete the trace.

Step 5: Add basepeak chromatogram

Please click the add BPC button of the tools dialog. This adds a basepeak chromatogram, i.e. a special sort of ion trace that for every scan uses the basepeak of this scan to create the BPC profile. Basepeak chromatograms are particularly suited to detect co-elutions, shoulders and contaminants easily and without need to decide for a bunch of suitable ion traces. In this case, the basepeak chromatogram exhibits two maxima, too, and so proves that at least two constituents are co-eluting at this position.

Try to use basepeak chromatograms whenever you are unsure whether a peak is pure.

Continue with the next lesson of this tutorial: Comparing two runs

Personal tools