MassFinder Comparing two runs

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MassFinder 4: Tutorial

This is the sixth lesson of the MassFinder 4 tutorial. You will learn how to open two GC/MS runs at the same time, how to compare them with each other and how to tranfer annotations from one to the other.


Step 1: Opening the first data file

Please open the file /demo/Geranium1-MSD.mfg which you will find in the folder demo of your MassFinder installation.

If you wish you may navigate and analyse this GC/MS run of a geranium essential oil sample before continuing with step 2.

Step 2: Opening the second data file

Image:Tutorial-Button12.pngPlease click on the 2 button. MassFinder will show the open dialog you already know. Please select the file Geranium2-MSD.mfg which is another geranium essential oil sample.

Please note that the second GC/MS run is always shown in blue color, while the first GC/MS run is shown in black color. Please note that the buttons '1' and '2' have black and blue color as well.

Step 3: Overlayed or separate

Image:Tutorial-ButtonOverlay.pngPlease click the overlay button in order to see both profiles (black and blue) or only the currently selected profile which is at this moment the blue profile.

Image:Tutorial-Button12.pngPlease click the buttons '1' and '2' to switch between the runs. If the overlay mode is deactivated, you will see only the selected run (black or blue). If the overlay mode is activated, you will see both profiles anyway. Please mark some peaks yellow or red to observe the colored arrows turning grey when being the secondary profile in overlay mode.

Please zoom into any part of the GC/MS runs to more clearly see the superimposition of both profiles. Switch the overlay feature on and off a few times.

Step 4: Export GC dialog

Image:Tutorial-ButtonButterfly.png Please enter the export chromatogram dialog. Again you will see both profiles overlayed. Now click on the butterfly button in the upper left corner of the export chromatogram dialog. Please observe how easy it is to spot differences between these two fairly similar profiles. Have a look at the peaks around retention time 28 min and 33 min.

Please note that you cannot re-integrate peaks 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.

Both in normal mode and butterfly mode you can show or hide each profile trace selectively. Please locate the list of traces in the upper right corner of the white profile area and click on the little black square right of the trace names. Traces with a solid black square are visible and traces with a hollow square are hidden.


Step 5: Auto-report results in comparison

Please select the first GC/MS, then click the auto-report flash button. Then switch to the second GC/MS and again click the auto-report flash button. Now both GC/MS runs have been automatically analysed. Please switch back to the first GC/MS run, then open the result table dialog.

As you can see, MassFinder added a second column with percentage values, so that you can compare the content of each constituent easily.

While this example has two runs done under the same chromatographic conditions, MassFinder can also analyse in exactly the same fashion two completely different GC/MS runs. For example, you could measure the same sample on two different stationary phases like DB1 (unpolar) und DB-Wax (polar) which give completely different order of elution for the constituents. Still MassFinder will create a result table with all constituents and side-by-side percentages. If MassFinder finds a certain constituent only in one of both samples, the associated table cell will remain empty.

Typical scenarios include:

  • Compare a reference GC/MS run with another sample, i.e. in quality control.
  • Compare the same sample measured on different stationary phases
  • Open the GC/MS and GC-FID of the same sample at the same time: Identify by MS, quantify by FID.

Step 6: Transferring annotations

Please open the sample Geranium1-MSD.mfl in slot #1 and then the corresponding Geranium1-FID.mfl in slot #2. You will now compare simultaneously measured GC/MS and GC-FID runs with each other, identify the constituents in the GC/MS, copy the labels to the GC-FID peaks and quantify by both GC/MS and GC-FID.

After opening the GC-FID sample the extremely high solvent peak of the GC dominates the whole profile view. Please select any scan just after the solvent peak as shown in the screen shot.

Image:Tutorial-Buttons-Tools.png Then open the special tools dialog and click on cut-off as shown in the next screen shot. This will remove all scans earlier than the selected scan from the GC-FID run. Please note that MassFinder automatically selected cut-off beginning. If you had selected a scan near the and, MassFinder would have automaticall suggested cut-off end of data.

Now both profiles are shown with reasonable intensity zooms and can be compared easily with each other. Please switch to slot #1 and click auto-report. For a real sample you would now start to check all identifications, check and re-integrate the peaks and add some yellow or red labels.

Image:Tutorial-Buttons-CopyAnnotations.png Please now click on the copy annotations button to transfer all labels from slot #1 to slot #2. This is necessary because the GC-FID peaks have no mass spectra and cannot not be identified otherwise. Click OK to the confirmation dialog, then switch over to slot #2, which now has labelled peaks as well.

Please open the result table dialog and note the two percentages columns. You may now export the results to excel or print the result table.

Continue with the next lesson of this tutorial: Library administration

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