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*   Spectrum Search
The Mass Frontier application uses search algorithms developed by HighChem and the National Institute of Standards and Technology (NIST). The HighChem Low Res and NIST algorithms are based on the optimized dot-product function, and an additional term that is based on ratios of peak intensities. The HighChem Low + High Res algorithm is based on weight distance between spectra. The application includes peak accuracies when it calculates the match factor.
The query spectrum can originate from the Database Manager, Components Editor, or Chromatogram Processor modules by selecting a spectral scan in a chromatogram. In addition, you can paste the query spectrum from the Clipboard into the search dialog box. In this case, you can copy the spectrum into the Mass Frontier application only.
With the spectrum search option you can choose between Identity or Similarity searches. Identity searching is designed to locate a library spectrum that closely matches an unknown. You use similarity searching to retrieve 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.
After doing a spectrum search, the application stores the search results in the Work library in the Spreadsheet view. After the search is complete, the application adds a match factor column (Match) to the Spreadsheet view. See Spectrum search results. The match factor is a number from 1 to 999 that specifies the measure of similarity between the query spectrum and the library reference spectrum. A match factor of 999 means a perfect match. To draw your attention to a match greater than 930, a “lightning” icon, , is displayed in the Match column of the Spreadsheet view.
The Spectrum Search dialog box includes the following pages:
Spectrum search results
If the Identity search does not provide an acceptable match—that is, the unknown has not been positively identified—you might use a Similarity search. In this case, the algorithm does not use the high mass peak index, but uses wider abundance ranges instead. The search results from a Similarity search can be of value in deducing structure, especially in establishing a structural proposal for an unknown spectrum.
To establish a structural proposal for an unknown, you can switch to the Structures view. From the search results of similar compounds you might recognize some common structural features, which are displayed in the structures grid. You can copy the structures to the Structure Editor and put the pieces of the structural “puzzle” together to create an initial structure. You can then paste this structure back into a Database Manager window to the record that holds the unknown spectrum. After this, comparing the peaks in the spectrum with generated fragments can provide valuable information about the consistency of the proposed structure and unknown spectrum. If the m/z values of the fragments do not match the spectrum, you can modify the structure and repeat this procedure. However, if the structures in the search results are highly diverse and dissimilar, you must combine this approach with other methods.
Spectrum page in the Spectrum 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 in the Spectrum 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 spectrum on the Clipboard. Lets you search for a spectrum other than the currently selected spectrum in the Database Manager window.


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Related Topics:
  Spectral Tree 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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