Mass Frontier uses spectral tree representation for MSⁿ spectra. A spectral tree consists of levels, nodes, node connectors, and node items. The levels symbolize MSⁿ stages starting at n=1. The node connector is a graphical symbol of the precursor m/z value, or the precursor m/z range if the isolation width is included. The node is a holder of node items. The node item stands for the product or calculated spectra of identical precursor m/z value or m/z range or for a chromatogram. Node product spectra, called here parallel spectra, represent spectra acquired at various collision energies and isolation widths, or using wide band activation or they can be zoom spectra, or source CID spectra, or any other spectra that enhance reproducibility in compound identification. If a node contains more than two parallel spectra, the average and composite spectra are automatically calculated. In addition to spectra, each node can contain a chromatogram.

A spectral tree consists of levels, nodes, node connectors, and node items. Node items are divided into five groups that are differentiated by the displayed color: Single, Average, Composite, and Source CID spectrum, and Chromatogram. Color settings can be changed in the Options | Spectrum Layout dialog window in the MS Tree page. Since display and editing actions affect the selected node item, the item selection is also distinguished by color.

A spectral tree can be created in four ways as follows:

A - Reconstruction from raw files where each file contains a single MSⁿ experiment (direct infusion)

B - Reconstruction from a single raw file that contains various MSⁿ experiments in one run (direct infusion)

Spectral trees can be manually created and edited in Database Manager in the Spectral Tree pane. All editing actions are accessible from the pane buttons and from the pop-up menu that is displayed by right clicking the mouse button.

Note: All actions described below are only applied to the selected node or spectrum.

Some mass spectrometric techniques may generate spectra whose appearance is very dependent on the experimental conditions and sample preparation. To allow the management and search of diverse product spectra with an identical precursor ion for a single chemical entity, Mass Frontier uses spectral trees that can contain nodes with several node items. The node item stands for any product or calculated spectrum of an identical precursor m/z value or m/z range (node spectra) or for a chromatogram.

Mass Frontier allows the exchange of trees between windows, records, chromatographic components or programs (e.g. Excel). This can be done using standard copy and paste commands. When using the paste command, you must distinguish between a single spectrum and a tree. So be sure to use the correct paste option when exchanging trees.

Mass Frontier allows the processing of MSⁿ spectra in hierarchically consistent spectral trees that can be searched in spectral or chromatographic libraries using various options that can be found in the Advance page in the Spectra or Tree Search dialog window. Each node in spectral trees can consist of four types of spectra (average, composite, parallel and source CID) and you can specify the type of spectra that will be searched in.

Mass Frontier supports spectral trees that can contain nodes with data reduced chromatograms. Chromatograms can be assigned to every node. This allows you to store product ion chromatograms for a particular precursor m/z value. In contrast to spectra, only one chromatogram per node is allowed. Tree chromatograms with components or selected scans are fully searchable. A node chromatogram can be reviewed or reloaded from the original data file in Chromatogram Database Viewer, which can be launched from the button  of the same name in Database Manager. Node chromatogram components or selected scans can be edited in the Components Editor window.

At HighChem, we have been collating spectral trees (MSⁿ spectra) for a number of years and these are available in Mass Frontier. This unique collection contains high quality ion trap spectra of human and veterinary pharmaceuticals, endogenous metabolites, drugs of abuse and doping agents. The library contains spectral trees acquired by electrospray ionization (ESI) in both the positive and negative ion mode. Each spectral tree contain name, structure and CAS number. HighChem Spectral Tree Libarry™ currently contains more than 7.000 individual spectra of 1041 positive and 524 negative ESI spectral trees.