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*   Searching Spectral Trees
You can use the Mass Frontier application for processing MSn spectra in hierarchically consistent spectral trees that can be searched in spectral or chromatographic libraries. Select from various options on the Advanced page in the Spectra or Tree Search dialog box. 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 is searched. For additional information, see Processing Data-Reduced Chromatograms or Spectral Tree Arrangement.
To perform a spectral tree search
Click the Search button, , in the Database Manager window and choose Tree from the menu.
Choose Search > Tree from the Mass Frontier main menu.
The Tree page of the Spectral Tree Search dialog box opens.
Select either the Selected Spectrum Search option or the Tree Search option.
In the Libraries area, select the Active check box for the libraries you want to search.
Click the Advanced tab.
The Advanced page of the Spectral Tree Search dialog box opens.
If you have a library that consists exclusively of source CID spectra and your unknown spectrum is also a source CID, select only the Source CID Spectra check box. If no such library is available, you can search source CID spectra in product CID spectra, but use care regarding the search results. Source CID spectra might contain fragmentation products from all the ions present in the source, including adduct or cluster ions, while product CID spectra are preferably generated from protonated or deprotonated ions.
If you selected the Selected Spectrum Search option on the Tree page, select one of the following search options.
The application compares the spectrum to every spectrum in the tree hierarchy and individually calculates the math factor.
If you selected the Tree Search option on the Tree page, select one of the following search options.
When you search a tree (unknown) against spectral trees in a library, the application compares the spectrum according to a special logic. It compares the corresponding spectra on an identical level (MSn stage) with a common precursor m/z by using an algorithm based on the optimized dot-product. The application ignores a spectrum that appears on one side only, which does not adversely affect the search result. If there are several corresponding spectra (single node with average, composite, parallel, or other spectra), the Mass Frontier application accepts the best match (optimistic approach). The total match factor is calculated from all the non-zero match factors.

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