MassFinder Tutorial

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MassFinder 4: Tutorial

Welcome to the world of MassFinder!

We believe that MassFinder is one of the most convenient software systems to do GC/MS with and we hope you will become an enthusiastic user as well. We are confident that with these step-by-step tutorials you will become an expert MassFinder user in a very short time.

We offer all customers intensive support by email or phone. If you have got any problems, inquiries or even suggestions on how to further improve MassFinder, please do not hesitate to contact us. We will do our best to solve all issues reported and to implement new features we consider to be of interest for the majority of users. It is our policy to provide all updates of MassFinder 4.x free of charge to all registered users, so every user will benefit from all modifications and enhancements.

If you have very special requirements of additional MassFinder features, we will gladly give you a free quotation for a customised, individual MassFinder version that solves your institute's or company's challenges.

About the MassFinder 4 tutorial!

This tutorial uses a step-by-step approach to teach the fundamental aspects of MassFinder. If you follow each step, you will swiftly and easily learn how to use all important MassFinder features. Please refrain from using your own data files at this moment; the tutorial data files are selected to offer the best and most rapid access to all important features. Later on in this tutorial you will learn how to analyse your own data files.

Please note that the tutorial does not cover all features and options of MassFinder. A complete explanation of all details of each dialog can be found in the MassFinder Reference Manual.

This first lesson will teach you step-by-step to open, visualize and navigate GC/MS data files.


Step 1: Starting MassFinder 4

Please ensure the dongle is connected to your computer. Start MassFinder 4 by double-clicking on MassFinder4.exe. Alternatively, you might have added a shortcut on your desktop, in the quick launch bar or in your start menu. If you have any problems with starting MassFinder, please read the installation instructions carefully.

Step 2: Opening a data file


Please click on the button "open GC/MS" as indicated in the picture above. If you hover with the mouse pointer over a button, a short help message will appear describing what the button does. This hover help will work almost for all buttons, dialogs and input boxes in MassFinder.

MassFinder will now display the open dialog box. For this tutorial, please select the file oil2122.mfg and click the OK button. Alternatively, you can double-click the file in order to open it.

Step 3: The first look on the user interface

The main MassFinder window is divided in three vertical panels:

  • left: chromatogram profile displayed vertically from top to bottom
  • center: three consecutive mass spectra of the GC/MS data file
  • right: up to three mass spectra of the library (search hits)

The name of the data file, oil2122.mfg, is displayed in the title bar of the window.

Step 4: Navigation

Please note first, that you always see three consecutive scans of your GC/MS run on top of each other. The center scan is highlighted (light yellow background), the upper and lower scans have grey background. The center, highlighted scan should usually have your attention, because MassFinder applies all commands you will learn later (e.g. library search, add to library, export as graphic) to that highlighted scan.

The blue line in the center of the chromatogram indicates which point of the chromatogram represents the highlighted scan. The scan on top is exactly one scan before that, the scan on bottom is exactly one scan after the blue line (and after the highlighted one in the center).

There are several methods to navigate the GC/MS and to select exactly the scans you are interested in. You will learn all methods in this part of the tutorial.


Please use the mouse pointer to click on the chromatogram peak as shown in the picture on the right. MassFinder will instantly select exactly that scan you pointed to as the new highlighted scan displayed in the center.

Without knowing, you also just performed your first library search with MassFinder. In the moment you selected the new scan in the chromatogram, MassFinder executed a library search and now displays the best library hit on the right side, also highlighted with yellow background. Please feel free to click to other GC/MS positions and see how fast MassFinder displays the according library matches. If the right panel (where the library hits are shown) remains empty, MassFinder was not able to find a match.

The screen should now look similar to the following screen shot (red text added for this tutorial):



Please select a range of the chromatogram as indicated on the right. Point the mouse to the upper left corner of the desired range, press the left mouse button down (and hold it down), then drag the mouse to the lower right corner of the desired range and release the mouse button. Please note, that the first click needs to be pretty far left in the area of the chromatogram's base line.

Hint: If you want to cancel a zoom you already started, drag the mouse to a position higher than the starting point and release the button.

Again, MassFinder not only zooms into the desired range, but also performs a library search of the new highlighted scan.

Moving scan-by-scan

Please note, how convenient it is to always see three consecutive scan after each other. This makes detecting co-eluting peaks, overloading effects, and all other kinds of slightly varying mass spectra very easy. In many cases, you would like to exactly move one scan up or down or to move scan-by-scan through a range of the chromatogram: Position the mouse pointer anywhere on one of the three GC/MS spectra and turn the mouse wheel up or down to move scan-by-scan. You may turn the wheel fast to scroll smoothly.

Adjusting to the peak

You can press the space key to adjust your active scan to the top of the closest peak.

Shifting the displayed range

Press down the left mouse button anywhere on top of the chromatogram (and hold it down), then drag the mouse to shift the displayed range of the chromatogram. Release the mouse button when you reached the desired position. Please note, that the first click must not be near the base line, since that would indicate mouse-zoom operation.

Stretching the displayed range

Press down the right mouse button on the lower half of the chromatogram (and hold it down), drag the mouse to stretch or compress the chromatogram, release the button when ready. Note, that MassFinder does not change the highlighted, active scan!

Hint: Do not start with this mouse operation in the baseline area of the profile. Just click anywhere on the main profile area. The baseline area and the upper half are reserved for creating average spectra, which you will learn in a later section.

Display the complete chromatogram

Double-click anywhere near the base line of the chromatogram to show the complete chromatogram. Directly after opening a GC/MS, MassFinder always automatically displays the complete chromatogram.

Modifying the intensity

You may easily change the intensity axis of the chromatogram by positioning the mouse pointer anywhere on top of the chromatogram profile and turning the mouse wheel up or down.

Later you will learn that there is an option to decide whether MassFinder will auto-adjust the intensity when zooming into the chromatogram with the mouse or maintain the intensity scale.

Please play around with all these navigation methods before proceding. You should feel comfortable with these mouse operations since they are basic for successfully employing MassFinder.

Continue with the second lesson of this tutorial: Lesson 2: Identifying peaks

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