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*   Spectral Tree Search
The Mass Frontier application processes MSn spectra in hierarchically consistent spectral trees that you can search in spectral or chromatographic libraries. The Advanced page in the Spectral Tree Search dialog box contains options for spectral tree searching. See Advanced page of the Spectral 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 to search.
Use the Source CID Spectra option when dealing with source CID spectra. When you have a library that consists exclusively of source CID spectra and your unknown spectrum is also a source CID, you should exclude other spectra types from the search. If no such library is available, you can search source CID spectra in product CID spectra, but pay careful attention to 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.
Two combinations relate to the tree search:
See Spectrum Search.
When you search a single spectrum in library trees, the Mass Frontier application compares the spectrum to every spectrum in the tree hierarchy and individually calculates the match factor. You can search a single spectrum in the top level only (full scan, source CID), everywhere except for the top level (first stage) or everywhere in the tree.
When you search a tree (unknown) against spectral trees in a library, the application compares the spectrum according to a special logic. See Searching an unknown against a library. 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.
Searching an unknown against a library
You can search a spectral tree using two options. You can include or exclude the top tree level (full scan, source CID) from a search, and the MSn stage of the tree spectra can be identical (identity search) or not identical (subtree search):
The Spectral Tree Search dialog box includes the following pages:
Tree page of the Spectral Tree Search dialog box
The On option applies the search constraints defined in the Search Constraints dialog box. See Search Constraints.
The Off option ignores the search constraints defined in the Search Constraints dialog box.
When selected, the application displays the search results in the current Database Manager window and adds the search results to the Work spreadsheet.
Available when you have a copied spectral tree on the Clipboard. Lets you search for a spectral tree other than the currently selected spectral tree in the Database Manager window.
Advanced page of the Spectral Tree Search dialog box
Locates a library spectrum that closely matches an unknown. Provides an exact match of query and library structure.
Retrieves spectra library entries of similar compounds when the unknown is not in the library or its spectrum is distorted so badly that a reliable match is not possible.
Search Selected Spectrum in MS^n Trees
Top Level Only
(SCID, Single Stage MS)
Ignore Top Level
(Full Scan with Unspecific Ions)
Uses an identity search with the MSn stage of the tree spectra.
Ignore Top Level
(Full Scan with Unspecific Ions)
Available when you have a copied spectral tree on the Clipboard. Lets you search for a spectral tree other than the currently selected spectral tree in the Database Manager window.


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Related Topics:
  Spectrum Search
  (Sub)Structure Search
  Name Search
  Formula Search
  Molecular Mass Search
  ID Number Search
  CAS Number Search
  Fragmentation Data Search
  Retention Time Search
  Search Constraints
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