The Component Detection page includes five sections: Select Task to Be Performed, Peak Detection, Ion Alignment, and Mass Measurement on the left side, and Base Peak Chromatogram Display on the right side.
Select the Show Advanced Parameters checkbox to edit advanced options that are hidden by default. Normally, these advanced parameters do not need to be edited.
Parameter | Description |
|---|---|
Parameters marked with an asterisk (*) are only displayed when the Show Advanced Parameters checkbox is selected at the bottom left side of the Component Detection page. | |
Select Task to Be Performed (drop-down menu) | |
Find All Ions in the Run | Detects individual ions found in the analysis. Displays information about each ion in the Charge State Results table. |
Find All Masses in the Run (default) | Detects individual masses found in the analysis. Displays information about each mass found in the analysis in the Consolidated Results and Charge State Results tables.
|
Find Peaks in the Total Ion Chromatogram | Detects peaks in the total ion chromatogram (TIC), deconvolves the spectra, and identifies MS2 spectra associated with the major ions constituting these peaks. |
Find Peaks in the Base Peak Chromatogram | Detects peaks in the base peak chromatogram (BPC), deconvolves the spectra, and identifies MS2 spectra associated with the major ions constituting these peaks. |
Find Peaks in the Analog Chromatogram | Detects peaks in the analog chromatogram. |
Find All Ions with MS/MS | Detects ions that have an associated MS/MS spectrum. |
Peak Detection | |
Absolute MS Signal Threshold | 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). |
MS Noise Level | Specifies the noise level in the raw data files. |
S/N Threshold | Specifies the signal-to-noise threshold in the raw data files. |
Beginning Peak Width (min) | Specifies the peak width (in minutes) at the beginning of an LC/MS run. |
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 experimental LC/MS data file and sets the value to the width of the highest peak in the chromatogram. |
Ending Peak Width (min) | Specifies the peak width (in minutes) at the end of an LC/MS run. |
Maximum Chromatographic Peak Width (min) | Specifies the maximum chromatographic peak width (in minutes) in the LC/MS run. The application automatically determines the maximum chromatographic peak width in the experimental LC/MS run 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. |
Use Restricted Time | Activates the Time Limits boxes so that you can enter a restricted time range. |
Time Limits | Specifies the retention time range; used to truncate the chromatogram and reduce the results to an appropriate chromatographic area. |
*Relative MS Signal Threshold (% of highest peak) | Specifies the MS signal threshold value as a percentage of the highest peak. This parameter defines the relative threshold abundance, as a percentage of the base peak, for the detection of a component that co-elutes with a larger component in the same experiment. |
*Relative Analog Threshold (% of highest peak) | Specifies the analog threshold value as a percentage of the highest peak. |
*Width of Gaussian Filter (represented as 1/n of chromatographic peak width) | Specifies the width of the Gaussian filter as a percentage of the typical chromatographic peak width. Using a Gaussian filter to read the LC/MS file, the application averages nearby full MS scans by applying a moving Gaussian function to improve the signal-to-noise ratio (S/N) of each scan. Setting the width of the Gaussian filter is an important step when optimizing the S/N of each scan. Width of the Gaussian filter = 1/n, where n is an integer between 1 and 10. For example, a value of n = 4 means the filter width is 25% of the chromatographic peak width. A value of n = 1 represents maximum sensitivity (filter width = 100% of the typical chromatographic peak width) and n = 10 represents maximum resolution (filter width = 10% of the typical chromatographic peak width) for a Gaussian filter. Lower this number to optimize sensitivity and increase this number to optimize chromatographic resolution. |
*Minimum Valley to Be Considered as Two Chromatographic Peaks (%) | Specifies the size, as a percentage value, for the minimum valley that the application considers as two separate chromatographic peaks. |
*Minimum MS Peak Width (Da) | Specifies the minimum MS peak width (in Daltons). The application uses the Minimum MS Peak Width and the Maximum MS Peak Width parameters to generate a range for the isotopic envelope of the ion. |
*Maximum MS Peak Width | Specifies the maximum MS peak width (in Daltons). The application uses the Maximum MS Peak Width and the Minimum MS Peak Width parameters to generate a range for the isotopic envelope of the ion. |
*Mass Tolerance (ppm or Da) | 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. |
Ion Alignment | |
Maximum Retention Time Shift (min) | Specifies the maximum retention time shift (in minutes) when the application compares two or more LC/MS runs. |
Mass Measurement | |
*Maximum Mass (Da) | Specifies the maximum mass (in Daltons) for a component in the LC/MS run. |
*Mass Centroiding Cutoff (% from base) | Specifies the cutoff (as a percentage from the base peak chromatogram (BPC)) for the change in the calculation of the average mass of a component when the application uses centroiding to smooth signal density to a single maximum point. |
Show Advanced Parameters (checkbox) | Select this checkbox to display advanced options that are hidden by default. |