MassFinder Library administration

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MassFinder 4: Tutorial

This is the seventh lesson of the MassFinder 4 tutorial. You will learn how to view and modify library entries, how to add new entries and how to create your own libraries.


Step 1: Preparations

Please restart MassFinder and open the oil2122.mfg demo file. Perform an auto-report and locate the unknown peak (hollow blue arrow) at retention time 10.19 min. Select this peak as current spectrum. MassFinder does not find a proper match for this peak.

Step 2: Adding a new library entry

Please press the '+' key on the numerical key pad of your keyboard. MassFinder will display the add library entry dialog.

Please note that MassFinder will fill in as many fields as possible. Particularly the retention index, retention time, original file and user field is set. You may just click OK to add the new library entry, since there is no need to enter any additional data. Naturally, if you add new library entries, in most cases you want at least give a proper name and molecular formula.

Please just click OK and observe that MassFinder immediately uses the new entry and displays it as library hit. Since it is the identical spectrum with an identical retention index, the hit quality is 100%.

We hope that you agree that adding a library entry to a MassFinder library is extremely fast and easy.

Hint: You will later learn how to use more than one library at the same time. MassFinder will always add the new entry to the currently selected library. The title bar of the add library entry dialog shows to which library the new entry will be added.


Step 3: Viewing and modifying a library entry

Please press the '*' key (asterisk, multiply sign) on the numerical key pad of your keyboard. MassFinder will display the modify library entry dialog, which looks identical to the add library entry dialog.

You may modify and add data to any library entry at any time. You may use this dialog both to view or to modify library entry data.

Please enter the molecular formular C15H24 (use capital letters for C and H). Please observe how MassFinder automatically calculates for molecular weight and the double bond equivalents.

Double bond equivalents (DBE) are defined as the sum of rings and unsaturations in the molecule. Examples: A saturated acyclic hydrocarbon has DBE 0, an epoxide or cyclohexane has DBE 1, an alkene or ester has DBE 1, an alkyne has DBE 2. The concept of double bond equivalents is very useful for easily checking whether a molecular structure fits to a molecular formula. Further, certain mass spectral fragmentation series are connected to the DBE value and will give similar m/z signals.

Step 4: Viewing and modifying mass spectral data

Please switch to the mass spectrum tab sheet of the modify library entry dialog. You may view the mass spectrum in detail and check the m/z list of all stored signals. You may navigate in the mass spectrum as usual.

Please click on the lock button in the lower left corner to allow editing the mass spectrum. Now you may freely edit the m/z list and delete, modify or add signals. You may paste text from the clipboard, e.g. in order to enter mass spectral data from Word or pdf documents. MassFinder will automatically recognise pairs of numbers representing mass-abundance pairs and ignore all other characters like commas, brackets and so on. You may click on the recalculate button next to the lock button to clean-up the m/z list after importing text. Editing the mass spectrum can also be reasonable in order to delete signals you know are contaminations, e.g. m/z 207 polysiloxane background.

Hint: An alternative way to convert text to a mass spectrum is using the open dialog: Select text single mass spectrum import as data file format and open any text file. The MassFinder installation contains the file /demo/example.txt which can be a start point to enter any mass spectrum manually.

Step 5: Creating a new library

Please select the close library button to close the current library.

Select any mass spectrum in the GC/MS, e.g. the unknown compound discussed before, and press the '+' key on your numerical key pad. MassFinder will automatically create a new library and show the normal add library entry dialog. Click OK.

MassFinder immediately uses the new library and display the new library entry as hit.

You can now save the new library using the save library button and assign a new name, e.g. MyTest.mfl.

Step 6: Manually opening a library

Please click the open library button and select the default library EssentialOils4.mfl. Please note that MassFinder can keep several libraries open at the same time. All open libraries are listed in the library selection box.

By default, MassFinder searches only the selected library and ignores the other open libraries. If the unknown compound is still the current mass spectrum, MassFinder will now display no hit, because EssentialOils4.mfl is selected and MyTest.mfl is in the background.

Please press down the All button next to the library selection list. Now MassFinder will search all open libraries after each other and display all library hits (no matter to which library they belong) sorted by match quality. In this mode, the library hits are indepedent of the currently selected library. The currently selected library is only relevant as target library when adding new entries.

Step 7: Library abbreviation

Please note the abbreviation {EO} for EssentialOils4.mfl or {MT} for MyTest.mfl after the chemical name of the library hits, so you know to which library each hit belongs. The library selection list shows both the name and the abbreviation of the library, so that you can easily lookup which abbreviation denotes which library.

MassFinder automatically assigns the abbreviation to each library: If possible, MassFinder uses the first two capital letters, otherwise the first two letters. When deciding for a name of a new library, try to use capital letters in the appropriate and sensible positions, so that the generated abbreviation makes sense to you. You can rename the library whenever you want and MassFinder will derive and use a new abbreviation.

Step 8: Closing the new library

Please select the new library MyTest.mfl in the library selection list. Then click the close library button to close the selected library. Now MassFinder automatically selects the default library EssentialOils4.mfl as curent library.

Step 9: Practical considerations for your own libraries

Naturally, you are encouraged to try and create test libraries for training purposes without any limitation.

However, please first read the next lesson Analysing your own data and be sure to understand the concept of retention indices before starting to create your own libraries with MassFinder. Secondly, please read the section Library Tools of the MassFinder Manual to learn about options and caveats of library creation.

This options and caveats include

  • the employment of the two separate retention index fields RI1 and RI2
  • the management of molecular structure graphics
  • the creation of libraries based on the currently marked peaks of a GC/MS run
  • possible uses of fields like comment, user or additional data
  • the intended use of the personal field (currently called ID)

MassFinder also offers several administration tools to check the library integrity or to clear certain fields to reduce the library size.

Step 10: Additional comments

  1. Please note that you can configure MassFinder to automatically open several libraries at start-up. For example, this is reasonable to do if you want to use your proprietary institute's library and our Terpenoids Library at the same time or at least want to switch between both libraries quite often. Please read the section MassFinder Options of the MassFinder Manual for further details.
  2. Please note that we offer a step-by-step guide for the conversion of Agilent ChemStation MS libraries to MassFinder format. So if you happen to have proprietary libraries in ChemStation MSD format, you will be able to continue to use your libraries with MassFinder.
  3. Many other library formats can be converted to MassFinder format by commercial third-party software like Palisade MassTransit or by exporting JCAMP-DX or MSP files from your spectrometer's acquisition and library software. We will be glad to assist you in converting your libraries, so please do not hesitate to contact us!

Please continue with the next lesson of this tutorial: Analysing your own data

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