12.7 MassTools - Plug-in for mass spectrometry


12.7.1 Introduction

This plug-in was developed as interface to simplify the use of the VEGA ZZ database engine in mass spectrometry research fields in which it's a common practice to submit the experimental monoisotopic masses as database queries to identify molecules.


12.7.2 Installation

The MassTools plug-in isn't included in the standard VEGA ZZ package and it's provided as separated setup. It  must be installed after VEGA ZZ setup and includes the plug-in and a test database containing  6850 molecules (flavonoids) collected by M. Arita et al.


12.7.3 Usage

To start the plug-in, you must select Tools Mass spectrometry tool in VEGA ZZ main menu:


Main window of Mass Spectrometry Tool

This interface allows to submit queries to a specific database (Database field in the Search options box) including the Monoisotopic mass and the isotopic confidence range (ppm). The query results, obtained clicking Search button,  are retrieved in Molecules found box showing monoisotopic masses, formulas and molecule names. The maximum number of molecules of the report can be limited by Max. results value. When you click a molecule in the list, its 2D structure is automatically shown in 2D structure tab. Double clicking on each item in the report, you can visualize the isotopic distribution.


Isotopic distribution


Moreover, right-clicking each result item, you can show the context menu in which you can choose:


Menu item Description
Show structure

Show the 3D structure in VEGA ZZ main window. It's equivalent to double click on the molecule line.

Isotopic distribution

Show the isotopic distribution in the Isotopic distribution box.

Save as ...

Save the report to a file that can be in CSV (Comma Separated Values) or DIF (Data Interchange Format) format. Both formats can be opened by Microsoft Excel and include the Mass, Formula and Name fields.


Copy the value under the mouse pointer to the clipboard.

Copy row

Copy the whole data (Mass, Formula and Name together) included in the currently selected line to the clipboard. The fields are separated by space characters.

Copy all

Copy the entire report to the clipboard using the CSV format.

Send to Excel

Send the report to Microsoft Excel using the DDE connection.


The Isotopic distribution chart has an own context menu as explained in the following table:


Menu Item Menu subitem Description
Edit Copy chart Copy the chart to the clipboard.
Copy data Copy the data used to build the chart (isotopic masses and relative abundances) to the clipboard. The data is line formatted: each line contains mass and % abundance separated by a single space character.
Send to exp. Send the data to the Experimental data box to compare the isotopic distribution with that of another molecule.
Zoom In Zoom in the chart
Out Zoom out the chart.
Reset Revert the zoom factor to the starting value.
Print - Do a hard copy of the current chart.


The chart zoom factor can be controlled by the mouse, keeping pressed the left button and defining a rectangle over the area to zoom in. To zoom out or to revert to the starting zoom factor, you can use the suitable functions of the context menu.

To compare the isotopic distribution of a molecule in the database with that obtained experimentally, you must paste the experimental data in Experimental data box in mass-abundance format (each number must be separated by space or carriage return character) and click Update button. In the chart are shown both isotopic distribution at the same time (red for the database molecule and blue for the experimental data). The Rms value, shown in the chart, summarizes how the two isotopic distributions are similar: lowest values mean similar distributions and zero means the same distribution.

Clicking Default button, all fields in the form are set to the default values.