When you select the Enable Automatic Parameter Values checkbox the application automatically determines the following parameters:
Parameter | Description |
|---|---|
Component Detection parameters | |
Entries denoted with an asterisk (*) are determined for Intact Mass Analysis experiments with sliding windows deconvolution only. | |
Absolute MS signal threshold (103 counts, default S/N = 20) | Read only. Specifies the minimum MS signal required for component detection. Absolute MS Signal Threshold = MS Noise Level × S/N Threshold To adjust the value of this parameter, change the MS Noise Level parameter and/or the S/N Threshold parameter. The application provides a visual aid for this signal threshold by displaying a thin red horizontal line on the base peak chromatogram (BPC) displayed on the right side of the Component Detection page in the Absolute MS Signal Threshold in Base Peak Chromatogram area. In general, processing takes much more time if this threshold is below the background noise level in the base peak chromatogram (BPC) or total ion chromatogram (TIC). |
Typical chromatographic peak width (min) | Specifies the typical chromatographic peak width (in minutes) in the LC/MS run. The application automatically determines the typical chromatographic peak width in the raw data file and sets the value to the width of the highest peak in the chromatogram. |
Maximum MS peak width (Da) | Specifies the maximum chromatographic peak width (in minutes) in the LC/MS run. The application automatically determines the maximum chromatographic peak width in the raw data file and sets the initial value as the geometric mean of the width of the highest peak and the range of peak widths the chromatogram. The application considers any peak wider than this mean value to be part of the background and does not include it in the results. |
Restricted retention time range (start and stop times) | Specifies the retention time range; used to truncate the chromatogram and reduce the results to an appropriate chromatographic area. |
Mass tolerance (ppm or Da, depending on resolution) | Specifies the maximum mass difference of the same ion in different scans. The application measures this value in ppm for high-resolution data and Da for low-resolution data. |
Maximum retention time shift (min) | Specifies the maximum retention time shift (in minutes) when the application compares two or more 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: Scan Offset and % 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:
|
*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:
|
*Merge Scheme (Legacy Merge Scheme or Improved Merge Scheme) | |
*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. |
Identification parameters | |
Mass accuracy (ppm) | Specifies the maximum deviation (ppm) between the mass of a theoretical component and the calculated mass of a particular ion used to identify a component.
For non-targeted analyses, the application does not strictly enforce this parameter so that it identifies more components. For targeted analyses, the application strictly enforces this parameter so that it does not identify components outside of the mass tolerance. |