Structure Editor is an easy-to-use, full-featured structure drawing tool. Structure Editor automatically calculates the mass of a selected fragment and the corresponding loss. Many different kinds of chemical structure created in this module can be used throughout the program.

Database Manager provides a number of convenient ways for organizing and processing mass spectra, chemical structures and libraries. A user-friendly spreadsheet format is provided for data handling. Advanced database query and search features give the user instant access to the information needed for rapid compound identification. User libraries containing spectra, MSⁿ spectral trees, chromatograms, chemical structures and extensive compound characteristics can be created at the click of a mouse. This module supports data exchange with Microsoft Excel.

Chromatogram Processor has been designed for the convenient extracting and processing of mass spectral scans by users of hyphenated chromatographic techniques such as GC-MS or LC-MS. Powerful components detection and spectra deconvolution algorithms allow the automated extraction of individual spectra or sepctral trees from complex chromatographic data files. This module also provides visual tools for selecting particular spectra from MSⁿ experiments.

Components Editor allows the user to edit, search and organize chromatographic components stored in a library or generated by the Components Detection and Spectra Deconvolution feature. This module presents users with a complete set of management tools to delete unrelated components, add chemical structures, edit extensive data fields, process spectral trees, annotate spectral peaks and sort search hit lists for every component in a processed chromatogram. Components Editor is a modal window accessible from the Database Manager or Chromatogram Processor window.

Fragments & Mechanisms module is an expert system for the automated generation of fragments and detailed fragmentation and rearrangement mechanisms from a user-supplied chemical structure. This module consists of a system that includes a comprehensive set of known reaction mechanisms and comprehensive collection of library mechanisms, allowing automated prediction at an expert level. This module can be generated either from Structure Editor or Database Manager module.

The Fragmentation Library module allows the creation and management of fragmentation mechanism databases. This module contains an expert system that automatically extracts a decomposition mechanism for each fragmentation reaction in the database and determines the compound class range that the mechanism can be applied to. Mass Frontier uses this expert system to apply database mechanisms to a user provided structure and automatically predicts the fragmentation reactions for a given compound.

Fragments Comparator shows a series of fragments in a table format. Columns are made up of individual compounds and rows show either mass-to-charge ratios or the structures of fragments. This module allows an effective comparison of the product ions of analogous molecules.

Spectra Classifier allows the user to retrieve and organize spectra intended for classification. Because spectra can be classified according to various criteria (structural, physical and other properties), it is useful to organize the spectra into different groups. Such groups of spectra can be visually represented in different ways (using colors, symbols and numbers) highlighting similarities or dissimilarities among the user-chosen spectral groups.

Spectra Projector displays the results of Principal Component Analysis (PCA) and Fuzzy Clustering classification methods. Mass spectral data can be classified using 2D or 3D projections in which each point represents a spectrum. If the class membership of an unknown spectrum needs to be determined, it can be opened or pasted into an existing projection.

Neural Networks is the second classification strategy available in Mass Frontier. Mass spectra are classified using a powerful method called Self-Organizing Maps (SOM), which are a special class of neural network. If two or more spectra activate the same neuron, we can assume that the corresponding compounds will exhibit similar physical or chemical properties, or biological activities.

Isotope Pattern displays the relevant isotopic profile, whenever a structure or fragment is selected in the program. Isotope pattern can also be calculated from a user-supplied molecular formula.

Periodic Table allows you to display the terrestrial isotopic abundance of elements and their multi-atomic isotopic profiles.

Formula Generator allows you to calculate list of theoretical molecular formulas that best fit an m/z value.

Report Creator allows you to create customizable reports from modules displayed on the screen. Reports can be printed or exported as pdf files.