MassFinder Autoreport

From MassFinder

Jump to: navigation, search
MassFinder 4: Tutorial

This page is the third lesson of the MassFinder 4 tutorial. You will learn how to use the auto-report feature to rapidly let MassFinder automatically identify major peaks, how to view and export labelled chromatograms, how to view the result table of your GC/MS run and how to check the integration and re-integrate peaks if necessary.

Contents

Step 1: Open the data file

Please open the data file oil2122.mfg once again to start over from scratch.

MassFinder will warn you that you modified the data file, in this case that you added yellow and red labels in the previous lesson of this tutorial. Just click OK to this message and continue opening the same data file you opened before.

Step 2: Auto-report: Peak-picking and identification

Please click on the Auto-report button, i.e. the yellow flash icon in the upper left corner as indicated in the screen shot.

MassFinder will perform a peak-picking and identification procedure and assign labels to all recognised peaks. Solid blue arrows indicate identified peaks (which would manually be yellow) and hollow blue arrows indicate unknown peaks (which would manually be red). Hollow arrows appear if MassFinder detects a peak but does not find a library match.

MassFinder uses an integral rejection threshold, i.e. the peak-picking finds only peaks whose integral exceeds a certain minimum area. You will learn later how to modify the peak-picking parameters yourself and how to adapt the peak-picking mechanism to your own data file requirements (see Analysing your own data and Options and configuration).

All marked peaks, i.e. yellow, red and blue arrows, are integrated automatically and you will learn later on in this lesson how to view and re-integrate the peaks.

Step 3: Auto-report: Result table

Please click on the Result Table button as indicated in the screen shot to show a table with all marked peaks, their retention indices, hit quality values and integration results.

You can copy the data to the clipboard by using the button with the Excel icon. The clipboard data is formatted so that it can be directly pasted into Microsoft Excel or Microsoft Word for further processing.

Please press the escape key or close the window to exit the result table dialog and return to MassFinder's main window.

Image:Tutorial-FirstSteps-ReportTable.png

Step 4: Export chromatogram

Please click on the export chromatogramm button as indicated in the screen shot to show the export chromatogram dialog window.

Step 5: Navigating in the export chromatogram dialog

Again, you can navigate in the export chromatogram dialog with the same methods you learned for the main window profile and the mass spectra:

  • zoom with the left mouse button
  • 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

In addition you can also

  • click the right mouse button anywhere on the chromatogram to toggle back and forth between the previous and current view.

You may resize the window to adjust the size and aspect ratio to your requirements.

Image:Tutorial-FirstSteps-ExportGC.png

Step 6:Copy graphic to clipboard

Image:Tutorial-FirstSteps-CopyClipboard.png You may export the current view to the clipboard by clicking on the copy graphic to clipboard button. The exported graphic is in a scalable vector-based format (Windows enhanced 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 separately as desired.

This tutorial will not explain all options and features of the export chromatogram dialog. The MassFinder Manual gives a detailled description of everything in the section Export GC dialog.

Step 7: Integration

Image:Tutorial-FirstSteps-Integral.png Please click on the integral button in order to check how MassFinder automatically integrated the labelled peaks. Please use the keys '<' and '>' to jump to the next or previous labelled peak. The integral area and the label of the active peak is always shown in red color. In the upper right corner the chemical name and the integral is repeated. To improve the readability of the integral area, large numbers are grouped in thousands. You can leave the integration mode by clicking a second time on the integral button.

Step 8: Re-integrating peaks

You may re-integrate the active peak (that with the red integral) 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 pointed. This latter method allows to easily create step-wise integrals.

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

Step 9: Return to the main view

You can exit the export chromatogram dialog by pressing the escape key or by closing the window.

The next time you will return to export chromatogram dialog, the window size will be exactly as you left it. This makes it possible to easily create several graphics with the same size and aspect ratio.


Continue with the next lesson of this tutorial: Parametric retrieval

Personal tools