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*   Spectral Tree Window
Spectral Tree Arrangement
The Mass Frontier application uses spectral tree representation for MSn spectra. A spectral tree consists of the following components.
Symbolize MSn stages starting at n=1.
Graphical symbols of precursor m/z values, or precursor m/z ranges if the isolation width is included.
Stand for the product or calculated spectra of identical precursor m/z values or m/z ranges or for chromatograms.
Node product spectra, called parallel spectra, represent spectra acquired at various collision energies and isolation widths or that use wideband activation. They can also be zoom spectra, 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 (see Spectral Tree Chromatograms).
Parallel spectra
Note  Chemical structures are associated with nodes and not with entire trees. This means you can assign fragments for product spectra. The top-level node MS1 should hold the structure of the neutral compound.
You can store complete trees in a library and update them at any time. For additional information, see Library Utilities. Any complementary information associated with a single stage spectrum or a chromatogram can be associated with a node spectrum or node chromatogram (see Using the Info Page).
Spectral Tree Layout
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, Source CID spectrum, and Chromatogram.
Because display and editing actions affect the selected node item, its color helps distinguish item selection. For additional information, see Manually Create and Edit a Spectral Tree.
To change color settings
Choose Options > Settings from the Mass Frontier main menu.
The Options dialog box opens.
Click Spectrum in the Layouts section.
The Spectrum page of the Options: Spectrum & Tree Layout dialog box opens.
Click the MS Tree tab.
The MS Tree page opens.

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Related Topics:
  Generating a Spectral Tree
  Copying and Pasting a Spectral Tree
  Spectral Tree Node Items
  Searching Spectral Trees
  Spectral Tree Chromatograms
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