The following table describes the parameters for the Xtract deconvolution algorithm on the Component Detection page.
Parameter | Description |
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Deconvolution Algorithm | Select the Xtract (Isotopically Resolved) option. |
Parameters (Xtract) | |
Output Mass Range | Specifies the range for the displayed masses on the x axis of the plots in the Deconvoluted Spectra panes on the Process and Review page. |
Output Mass | Determines whether the Xtract algorithm returns a single peak at either the monoisotopic mass or the monoisotopic MH+ mass for each of the detected components.
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S/N Threshold | Specifies a signal-to-noise (S/N) threshold, x, above which the Xtract algorithm considers a measured peak to be a real (accepted) peak. The Xtract algorithm ignores peaks below this threshold. Any spectral peak must be x times the intensity of the calculated noise for that spectrum before the Xtract algorithm considers the peak. |
Rel. Abundance Threshold (%) | Specifies a relative abundance threshold below which the application filters out data for analysis. This option sets a threshold as a percentage of the most abundant component in the spectrum. The most abundant peak in the deconvoluted spectrum has a relative abundance of 100 percent, and all other peaks are calculated relative to that one. In the Results table on the Process and Review page, the application shows only those components that are greater than or equal to this relative abundance threshold in the deconvoluted spectrum. For example, if the highest peak has an absolute abundance of 1000 and the relative abundance threshold is 1 percent, the application filters out all peaks below an absolute abundance of 10. For this value, 0% displays all results and 100% displays only the most abundant component. |
Charge Range | Specifies the charge state range to be deconvolved, from the lowest charge state to the highest. For example, if you set this parameter range from 2 through 5, the Xtract algorithm considers only charge states 2 through 5 for deconvolution. It ignores charge states 1 and higher than 6. |
Min. Num Detected Charge | Specifies the minimum number of charge states required to produce a component. No components with less than this minimum number appear in the deconvoluted spectrum. This parameter must be an integer greater than or equal to 1. |
Isotope Table | Specifies the type of isotope table to use in the deconvolution. Isotope tables simulate the distribution of isotopic peaks, in m/z, for different monoisotopic mass candidates. The Xtract algorithm chooses the monoisotopic mass with the best fit between the theoretical and the observed isotope distribution. To generate an isotope table, the application uses a chemical formula to describe the type of molecule. You can select one of the following formulas:
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Advanced Parameters (Xtract) Visible only when you select the Show Advanced Parameters checkbox; these parameters typically do not need to be modified. | |
Calculate XIC (checkbox) | When selected, the application calculates the extracted ion chromatogram (XIC) for each detected component. Enabling this parameter can result in a much longer analysis time, so you might avoid using it with complex data or with data where XIC data is unnecessary. The Calculate XIC checkbox is inactive (gray) on the Intact Fragmentation page for processing MS2 spectra. |
Fit Factor (%) | Measures the quality of the match between a measured isotope pattern and an averagine distribution of the same mass. Enter a value between 0 and 100%:
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Remainder Threshold (%) | This parameter is used when the Xtract algorithm attempts to resolve overlapping isotopic clusters; specifies the peak height threshold for smaller overlapping isotopic clusters as a percentage of the height of the most abundant isotopic cluster in the overlap region. For example, if an isotopic cluster in a spectrum has an abundance of 100 and you set the Remainder Threshold parameter to 30%, the Xtract algorithm ignores any overlapping clusters with an abundance less than 30. |
Consider Overlaps | When selected (default), the Xtract algorithm is more tolerant of unexpectedly high peak intensity for a theoretical isotopic cluster, due to the possible presence of overlapping isotopic clusters contributing to the peak intensity. Because this option can lead to increased false positives, select it only in cases where you expect overlapping isotopic clusters in a data set. |
Resolution at 400 m/z | Defines the resolution of the source spectrum at an m/z value of 400. Select one of these options:
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Negative Charge | When cleared, indicates the data was acquired in positive charge mode during the electrospray ionization (ESI) process. When selected (default), indicates the data was acquired in negative charge mode. MS spectra of samples containing nucleotides (such as DNA or RNA) are often collected in negative charge mode. Do not select the Negative Charge checkbox if your data was acquired in positive mode. Results will not be usable. |
Charge Carrier | Specifies the adduct ions introduced during the electrospray ionization (ESI) process. Adduct ions convert neutral molecules into ions.
In negative mode, these ions correspond to losses rather than adducts. |
Minimum Intensity | Specifies a minimum intensity threshold to filter out possible background noise, even when you set the S/N Threshold parameter to zero. |
Expected Intensity Error | Specifies the permissible percentage of error allowed in calculating the ratio of the most abundant isotope to the next isotope higher in mass in the isotope series. |