MassFinder Parametric retrieval

From MassFinder

Jump to: navigation, search
MassFinder 4: Tutorial

This is the fourth lesson of the MassFinder 4 tutorial. You will learn how to filter the library for specific entries (parametric retrieval), how to perform the unique reverse search and how to export mass spectra for presentation or documentation purposes.


Step 1: Filtering the library: Parametric retrieval

MassFinder offers powerful parametric retrieval to filter library entries and present the results sorted by several parameters. Please return to MassFinder's main window and click on the filter button as shown in the screen shot.

Please enter limonene in the chemical name search box and select retention index as sort order. as shown in the screen shot. Then click OK. MassFinder will display 6 hits whose chemical name contains the phrase limonene. Please note that this fragment is found no matter whether you use lower case or upper case letters and no matter whether the fragment appears alone or as part of a larger chemical name.


Step 2: Browsing the filter results

Please note that MassFinder prints the warning search filter in red letters in every library mass spectrum. This is to avoid confusion between library hits and filter results.

Please note that MassFinder arranged the search results initially so that the library entry with the closest retention index to the target spectrum was highlighted. You may turn the mouse wheel in order to view all six search results.

You may quit browsing the search results by clicking the filter button a second time. MassFinder immediately returns to its normal library hit mode. Alternatively, you may press the key 's' to enter or quit the filter mode.

Step 3: Reverse search

Introduction to reverse search

MassFinder's unique reverse search feature gives an answer to the question, whether a certain library entry occurs anywhere in the GC/MS run. The 'reverse search' feature allows you to select any library entry and let MassFinder search the GC/MS for the scan with the highest similarity. You may employ this attractive feature e.g. in the following cases:

  1. You would like to know whether the current GC/MS run contains the selected library entry. For instance, the new European guidelines for the declaration of cosmetic ingredients could make you want to search for specific compounds. However, please note that MassFinder's reverse search can only find compounds, if they occur as pure peak. Negative search results do not mean that the compounds can not be a constituent of your sample.
  2. In many cases, MassFinder presents more than one library hit and you might want to know whether one of the hits has a better matching GC/MS scan anywhere else in order to assign several pretty similar compounds correctly. Also, if the best hit MassFinder presents is fairly low rated, you might be interested whether there is a better matching scan for this library entry in order to exclude the possible hit.

Naturally, there are many more sensible cases to employ the reverse search feature and you may use it whenever you like.

Performing the reverse search

  • Please browse the library so that the entry of Limonene is highlighted.
  • To perform the reverse search, click with the right mouse button anywhere on the limonene library spectrum.
  • Note how MassFinder adjusts the highlighted GC/MS scan of the left panel, so that scan 213, retention time 5.38 min, becomes the active scan. This spectrum is most similar to limonene.
  • Press 's' to quit the filter mode.
  • Press space to move to the top of the peak.
  • Compare the normal library match and note that it is indeed limonene. Check the mass spectral similarity as well as the retention index.

Step 4: Filter by partial mass spectra

Please enter the filter dialog box once again, deactivate the chemical name search, then switch over to the second tab Mass spectrum. Click into the lower white memo box and enter the numbers "204 10 161 100 175 10" (you may press ENTER after each pair of numbers).

Please observe how MassFinder on the fly paints the according mass spectrum.

Click OK to return to the main view in filter mode. MassFinder will find 7 spectra which contain the entered partial mass spectrum, sorted by retention index, arranged so that the closest retention index is highlighted.


Step 5: Sorting by retention index

There are situations where you want to search yourself for a particular spectrum with similar retention index, e.g. if you are aware that the scan of interest is a mixture or not representative for other reasons or when you just would like to know which compounds have a pretty similar retention index.

MassFinder enables you to sort the whole library by retention index rather than match quality. Press the RI button to toggle between the two sorting modes: Sorted by overall match quality or sorted by retention indices. In the latter case, MassFinder automatically applies the all entries filter and jumps to the library entry with the closest retention index. Naturally, you can navigate the library as usual.

Click RI again to leave this mode.

Step 6: Export mass spectra

Please click on the export mass spectrum button as indicated in the screen shot.

MassFinder can export any mass spectrum to the clipboard as

  • high-quality, scalable graphic (Windows enhanced meta file format)
  • classical m/z mass list of the labelled peaks
  • Excel table including all ions and abundancies.
  • SVG graphic for display in any internet browser

Image:Tutorial-Buttons-GCLib.pngThese two buttons let you select whether to display and export the current GC/MS scan or the current library scan.

If you are interested in the other options and features of this dialog, please read the section MassFinder Export MS dialog of the MassFinder Manual.


Continue with the next lesson of this tutorial: Average and subtraction

Personal tools