The following table describes the parameters in the Source Spectra Method area on the Component Detection page.
Parameter | Description |
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Source Spectra Method | |
Displays the three deconvolution methods for generating the source spectra:
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Parameters visible for the Sliding Windows option | |
Sliding Windows Definition area | |
RT Range | Displays the retention time (RT) range (in minutes) to which the sliding windows deconvolution is applied. By default, these values automatically correspond to the values in the Time Limits boxes (in the Chromatogram Parameters area). You can change these values to limit the RT range for sliding windows deconvolution. Afterwards, if you change the Time Limits values, the RT Range values reset automatically to match the Time Limits values. When you load multiple raw data files for the experiment, if the RT Range changes for any raw data file, the change applies to all of the loaded raw data files. |
Target Avg Spectrum Width | Specifies the width, as a retention time (RT) (in minutes) of the sliding window. Reducing the Target Avg Spectrum Width value improves time resolution, but reduces processing speed. Increasing this value increases processing speed but reduces time resolution. You can achieve the best results when the window width is between 0.25 and 2.0 times the width of the characteristic peaks in the spectrum. For most cases, the optimum value might be half the width of the characteristic peaks. If you select the Enable Automatic Sliding Window Parameters Values checkbox above the Processing Method table before editing the processing method, the Target Avg Spectrum Width value is optimized based on the scan data from the first (or only) loaded raw data file. You can edit the value as needed. However, each time you change the RT Range parameter or select the Target Avg Spectrum Offset > Scan Offset option, the application automatically resets this parameter to the optimized value. |
Target Avg Spectrum Offset | Specifies the offset between successive sliding windows as a number of scans or as a percentage value. You can select from these two options:
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Merging Parameters area | |
Merge Tolerance | Determines how close two components in successive sliding windows must be in mass for the application to identify them as a single component. A value that is too high might result in merging components that should remain separate. A value that is too low might result in false-positive component detection when two or more components remain separate that should have merged. Select the unit for this parameter: ppm or Da The best value for this parameter is conditional, but tests suggest the following:
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Max RT Gap | Specifies the maximum allowed retention time (RT) separation (in minutes) between two successive individual members of a merged component identified by the sliding windows algorithm. If the separation between members exceeds this value, the application divides the candidate component into two components separated by a gap in RT. As with the Merge Tolerance parameter, a value that is too high might result in merging components that should remain separate. A value that is too low might result in false-positive component detection when two or more components remain separate that should have merged. This parameter should be comparable to (or slightly less than) the expected separation in RT between distinct components with the same mass. |
Min. Number of Detected Intervals | Specifies the minimum number of sliding window intervals that a component must appear in for the application to consider the component valid. A value that is too low might allow noise peaks to appear as false positives. A value that is too high might result in legitimate components being discarded. Set this parameter to a value large enough to exclude results that are implausibly narrow in retention time but small enough to include results of realistic duration. Values in the range of 3 through 8 generally give good results. A good approach is to use whichever is larger: 3 or the minimum number of windows that can fit onto a peak. If you select the Enable Automatic Sliding Window Parameters Values checkbox above the Processing Method table before editing the processing method, the application automatically sets the Min. Number of Detected Intervals to an optimized value by reading the scan data from the first (or only) loaded raw file. You can edit the value as needed. However, each time you reselect the Target Avg Spectrum Offset > Scan Offset option, the application resets this parameter to the optimized value. |
Parameters visible for the Auto Peak Detection option The Sensitivity and Rel. Intensity Threshold (%) parameters in the Chromatogram Parameters area control the same values displayed for this option. See Chromatogram Parameters area parameters. | |
Parameter visible for the Average Over Selected Retention Time option | |
RT Range | Displays the retention time (RT) range (in minutes) to which the average over selected retention time deconvolution is applied. By default, these values are from 0.000 to 0.000. To select the source spectrum, you can enter the appropriate RT values or change the values by averaging an area in the chromatogram. Afterwards, if you change the values in the Time Limits boxes (in the Chromatogram Parameters area), the RT Range values do not change, unless any portion of the RT range is outside of the current Time Limits range. In this case, the RT Range values reset automatically to fit inside the Time Limits range. When you load multiple raw data files for the experiment, if the RT Range changes for any raw data file, the change applies to all of the loaded raw data files. |