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*   Generating Formulas from Peaks
Use the Formula Generator module to calculate the possible elemental composition for any spectral peak by selecting the peak in a Database Manager or Chromatogram Processor window.
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To open a Formula Generator window
1.
Click the Formula Generator button, , in the Mass Frontier main toolbar.
–or–
Choose Tools > Formula Generator from the Mass Frontier main menu.
The Formula Generator window opens.
Formula Generator window
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To specify molecular formula options
1.
The Molecular Formula Settings dialog box opens to the Peaks page.
2.
See Peaks page.
3.
Click the Limits tab to see the Limits page. Verify that the Charge setting matches the polarity of the MS mode you used for spectral acquisition.
See Limits page.
4.
Click the Elements tab to see the Elements in Use page. Verify the maximum number of elements used for calculation.
See Elements in Use page.
5.
Use the options in the Molecular Formula Settings dialog box to speed up calculations, restrict the number of possible formulas, or set the charge state and polarity.
Peaks page
Removes all columns from the formula list except the Formula column. This option is meaningful only in the Auto Annotation > Generate Formulas feature in the Database Manager window.
Displays the Theoretical m/z column in the formula list.
Show m/z Delta
Delta Units
Displays the Delta (units) column in the formula list.
Limits page
Specifies whether to use the nitrogen rule in the elemental composition calculation. The choices include:
Specifies whether to use an algorithm for the exclusion of implausible formulas with improbably high numbers of hydrogens.
Specifies whether to exclude formulas if the atoms cannot be connected in any way using valences common in organic chemistry.
Ring plus Double Bond Equivalent (RDBE)
Displays only formulas for which RDBE is within the From–To range. RDBE limits the calculated formulas to those that make sense from a chemical perspective.
Elements in Use page
Specifies whether Mass Frontier will consider isotopes of particular elements with a maximum number when calculating formulas. For information about isotope patterns, see Displaying Isotope Patterns.
Opens the Select Element dialog box where you can specify a new element. The application uses the new element when calculating formulas.
Opens the Enter Molecular Formula dialog box where you can specify a new formula. The software uses the new formula to derive upper limits for individual elements (see Elements in Use page). These limits are considered when the software calculates formulas.
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To automatically calculate the m/z tolerance value
Select the Acquired from Source check box.
When you generate possible formulas for a peak, the application automatically calculates the m/z tolerance value from the source spectra.
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To generate possible formulas for a peak
1.
The Formula Generator window minimizes to a bar.
2.
The Formula Generator window lists all possible formulas. All the decimal places are accurately transferred to the Formula Generator. To choose which columns of information are displayed in this list, see Peaks page.


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Related Topics:
  Specifying Mass/Abundance Options
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