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)

C - Spectral tree deconvolution from a data dependent MSⁿ chromatogram in Chromatogram Processor window

D - Manual creation using tree editing utilities.

The tree reconstruction automatically assigns node spectra to specific nodes utilities in addition to creating levels, nodes and node connections.

A. The spectral tree reconstruction feature reads Xcalibur raw files stored in a directory and automatically creates a tree according to the precursor m/z and isolation width values. All files (spectra) in a directory should be from an identical chemical entity (compound or chromatographic component) - one directory per tree per compound. This feature works on Xcalibur raw files acquired using direct injection and a single MSⁿ stage. Each file  in a directory can be acquired separately at a specific collision energy, or it can be a wide band activation spectrum, zoom or source CID spectrum, or the sample preparation (pH, concentration, buffer, etc.) can be diverse. Example files of this kind are automatically installed into the \Mass Frontier 50\Chromatograms\Cloramphenicol directory.

To import trees using the tree reconstruction feature, follow these steps:

1. Click on the Import button in the Tree pane in Database Manager
2. Choose Import Tree from the pop-up menu
3. Select the directories you wish to import
4. Click the Add button and then click OK

This procedure allows you to efficiently create an MSⁿ library.

B. Another way to create a spectral tree of a reference compound is given in the following procedure, which allows the reading of various MSⁿ spectra acquired in one run using direct infusion and stored in a single raw file. To use this procedure you must use the Direct Infusion algorithm in the Chromatogram Processor module.

To create a spectral tree from a single run using the tree reconstruction feature, follow these steps:

1. Click on the Chromatogram Processor button in the main Mass Frontier menu bar
2. Select the direct infusion file you wish to process and click the Open button. The file will open in the Chromatogram Processor window.
3. Click on the Component Detection & Spectra Deconvolution button and select the Direct Infusion item from the pop-up menu
4. If required, change the preset parameters and click the Calculate button
5. Click the component triangle on the left side of the TIC pane and the reconstructed spectral tree will be displayed below

This procedure allows you to efficiently create an MSⁿ library.

C. Spectral trees can also be generated from chromatographic components. Chromatographic data must be processed using a different feature. To create a tree from a chromatogram, use the Component Detection & Spectra Deconvolution feature in the Chromatogram Processor module.

Spectral Tree™ is a trademark of HighChem, Ltd., Slovak Republic
Xcalibur® is a registered trademark of Thermo Electron Corporation.