*   Fragment Ion Search (FISh)
Fragment Ion Search (FISh) is a data processing method used for intelligent extraction of useful information from chromatograms. The FISh feature removes spectral peaks that are not present in the predefined template. A list of fragments or m/z values serves as the input template (Fragment Source). When you apply the FISh algorithm, all spectral peaks except for the template peaks are removed from the chromatogram. You can use this feature to extract structurally related spectral peaks, for example, peaks related to the parent drug in metabolite ID, or to eliminate the noise or impurity peaks.
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To apply fragment ion search to your data
1.
Click the Apply Fragmentation Ion Search button, , in the Chromatogram Processor toolbar.
The FISh Filter dialog box opens. See Model page in the FISh Filter dialog box.
2.
3.
Click Calculate.
The application displays the status of the FISh processing.
4.
The Chromatogram Processor window displays the detected components.
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To drag actions from one Chromatogram Processor window to another
1.
2.
The application adds these calculated filters and methods to the Actions pane Chromatogram Processor window.
3.
4.
5.
The application copies each action and its associated parameters from the source Chromatogram Processor window to the target Chromatogram Processor window.
The Actions pane reports that the actions are not synchronized.
The detection method must always be the final action, but you can change the order of other filters in the Action pane.
6.
The application moves the selected action.
7.
a.
b.
Click the Apply Actions to Chromatogram button, , in the Action pane toolbar.
The Mass Frontier application processes each of the selected actions for the current raw data file.
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To view an explanation of FISh results
1.
The application adds a FISh page and displays the results.
Saving FISh Parameters to a File
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To save all FISh processing parameters to a file
1.
When all processing is complete, click the Save Actions to a File button, , in the Actions pane of the Chromatogram Processor window.
The Save Chromatogram Actions dialog box opens.
2.
The applications saves the model and options parameters to the specified file.
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To edit FISh parameters before saving them to a file
1.
Click the Change Actions Parameters button, , in the lower left pane of the Chromatogram Processor window.
The Fish Filter dialog box opens. This dialog box does not have a Calculate button. You can edit the FISh parameters on this dialog box, but you cannot begin FISh processing.
The Fish Filter dialog box includes the following pages:
2.
A message in the Actions pane reports that, because of your edits, the FISh parameters are no longer synchronized with the previous filters. This is acceptable only for saving the edited parameters to a file.
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To save FISh model parameters to a file
1.
The Save FISh Flat File dialog box opens.
2.
When you calculate the FISh filter, the application writes the model parameters to a .fish file.
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To save FISh options parameters to a file
1.
The Save FISh Parameters File dialog box opens.
2.
When you calculate the FISh filter, the application writes the options parameters to a .fish.par file.
Loading FISh Parameters from a File
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To load all FISh processing parameters from a file
1.
Click the Load Actions from a File button, , in the Actions pane of the Chromatogram Processor window.
The Load Chromatogram Actions dialog box opens.
2.
When you calculate the FISh filter, the application uses the model and options parameters from the specified .hcca file.
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To load FISh model parameters from a file
1.
2.
The Open FISh Flat File dialog box opens.
3.
When you calculate the FISh filter, the application uses the model parameters in the specified .fish file.
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To load FISh options parameters from a file
1.
The Open FISh Parameters File dialog box opens. Select a FISh Parameters (.fish.par) file and click Open.
When you calculate the FISh filter, the application uses the options parameters in the specified .fish.par file.
Model page in the FISh Filter dialog box
Defines the template list of fragments or m/z values that are not removed from a chromatogram.
Defines the m/z values to use as a reference spectrum.
Opens the Input m/z List dialog box where you can create a list of m/z values. These values do not have implicit tolerance values, so enter these m/z values with the proper number of decimal digits.
Only Peaks that Match Subset of Formula
Opens the Modifications dialog box where you can create new modifications or select predefined modifications.
Use parameters from a saved FISh model (.fish.par) file. When you choose to use a saved file, all other parameter options are unavailable.
Resets the chromatogram to its original (before fragment ion search) state. Uses the determined Mass Merge Power value in Baseline Correction and Noise Elimination, Smoothing, and the JCD Component Detection Algorithm as the starting value.
Options page in the FISh Filter dialog box
Marks the threshold peaks in red when they are large enough to be above threshold value (the point where Mass Frontier preserves peaks). Specifies that the predefined peaks are marked in pink and corresponding TIC are drawn in green. No peaks are removed.
Detect Components
Specifies that only peaks are removed from scans, in contrast to the Filter Precursors option where entire scans are removed. The Mass Frontier application displays these options when you have a data-dependent chromatogram.
Apply to Top Stage Only: When selected, the filter is applied only to top stage scan (usually MS1 scans). Data-dependent scans are not affected in this case.
Remove Data Dependent Scans: This option is active only if Apply to Top Stage Only is selected. When selected, the algorithm removes whole data-dependent scans for which the precursor peak was removed. When cleared, the filter is applied to a data-dependent scan in the same manner as a top stage scan (individually to each peak).
Specifies that all spectra with a precursor ion not found in the predefined list are removed from the chromatogram and precursor ions are removed from parent spectra. This option is enabled for data-dependent chromatograms only.
Mark Isotopic Pattern when Available
If a monoisotopic peak is recognized, the application includes other existing isotopes in the result. Missed isotopes do not influence the recognition of the peaks. This option produces the highest signal and can produce false positive results.
Use Full Isotopic Pattern Only
The peaks are included in the results only if a significant part of the isotopic profile is found in the analyzed spectrum. This option produces the most accurate result but can omit some peaks of low intensity and consumes the most time. The Mass Frontier application changes the option to Mark Isotopic Pattern when Available for data-dependent scans.
Maximum Eliminated Abundance
Use only m/z Range
Opens the Save FISh Parameters File dialog box where you can save your current parameters to a FISh parameters file (.fish.par).
Opens the Open FISh Parameters File dialog box where you can choose a FISh parameters file (.fish.par) to load.


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Related Topics:
  Force Mass Tolerance
  Matrix Conversion
  Thresholding
  Baseline Correction and Noise Elimination
  Smoothing
  Base Peak Chromatogram
  Background Subtraction
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