Use the LC/MS Spectral Deconvolution method configuration for Spectral Deconvolution. The Spectral Deconvolution method parameters are in the Spectral Analysis > MS Spectral Deconvolution. |
These parameters are used by the deconvolution algorithm to find and group-related ions, to calculate charges, and to calculate molecular weight. Use the default settings to include both high and low molecular weight compounds. For individual samples, you may want to change some of them.
Run automatic deconvolution | Select this check box if you want to run deconvolution automatically during each data processing. |
Use RT Window |
Optional: Select a retention time window. Automatic deconvolution will only run on spectra of TIC peaks within the specified time. |
TIC peak type |
Select what peak type automatic deconvolution should use from a TIC SCAN signal:
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TIC peak threshold | Select how peaks should be filtered from a TIC SCAN signal:
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These combo boxes list common positive and negative adduct ions. The selected ion is used during deconvolution to compensate for the adduct ion used to produce multiply-charged spectra.
To add a positive or a negative adduct, enter its chemical formula into the corresponding input field, and click +. To delete an adduct from the list, right-click it, and select Delete.
Use m/z range | Select this check box if you want to view Spectral Deconvolution results from a specific m/z range. Selecting the check box enables the fields where you set this m/z range. The MS Spectrum window will show the m/z range in light grey after running Deconvolution. |
Low molecular weight | Sets the lowest molecular weight that will be reported by Deconvolution. The default is 500 amu. |
High molecular weight | Sets the highest molecular weight. The default is 50,000 amu. |
Maximum Charge | The maximum charge does not necessarily indicate an absolute cutoff for charge assignments. It just indicates the largest charge that can be applied to a peak being used to search for related peaks. For example, assume that the maximum charge is 30 and, if a charge of 30 is applied to peak A when searching for related peaks, peak A finds related neighbors with charges 27 - 29 and 31 - 33. The peaks with charges 31 - 33 will not be ignored simply because the maximum charge is 30. However, a charge state above 30 would not be applied to peak A when it is searching for related peaks. The default values for Maximum Charge (50) and Minimum peaks in set (3) are set so that both high and low molecular weight compounds will be found. Be careful in using these defaults if you have a spectrum with many peaks and you have set Minimum peaks in set to a value of 3. It is easy for the algorithm to find extra components of 2 or 3 peaks under these conditions. To restrict the algorithm, lower the maximum charge when Minimum peaks in set is 3. Components with only 2 or 3 peaks usually have low molecular weights, so a lower charge range is appropriate. For example, a charge of 30 on a peak with an m/z value of about 1500 gives a molecular weight near 45,000. Therefore, changing the maximum charge to 30 is sufficient for compounds with a molecular weight no greater than 45,000. If a higher maximum charge is required to find high molecular weight compounds, change Minimum peaks in set to 4 or more. High molecular weight compounds usually have components with multiple peaks. An alternative approach is to use Low molecular weight and High molecular weight to constrain the range of masses that Deconvolution will report. When using Low molecular weight and High molecular weight, it is still a good idea to set the maximum charge to an appropriate value as well. |
Minimum peaks in set |
This parameter is the minimum number of related ions required before the ions are considered a set and can be separated from the original spectrum. The default and minimum is 3. Increasing this value can help limit the components found for a spectrum with many ions. When the minimum number of ions is 3, there is special handling of of ions with charge states +1 and +2 or -1 and -2, +2 and +3 or -2 and -3, +3 and +4 or -3 and -4, +1 or -1 only, and +2 or -2 only (only if ion width is <= 0.4) sets. MW agreement, existence of isotopes, isotope spacing, isotope ratios, and peak widths are used for low charge assignment. |
Show unmatched peaks | If you select this check box, data points that do not belong to a group of related ions will be included as an object in the intermediate results. By default, the check box is cleared, that is, only matched peaks are included. Looking at the unmatched peaks can give you a clue about the presence of small, undetected multiply-charged series. |
MW Agreement (0.01%) | Determines how closely the ions shifted by their charge states must match each other in molecular weight. The values are entered as whole numbers but are expressed as 0.01%. Thus, the range is 0 to 100 (that is, 0 to 1%); default is 5 (0.05%). A lower value means the ions must be more closely matched in molecular weight. A higher value means the ions can be further away from the averaged molecular weight. A zero value means that ions must match exactly. A lower non-zero value tightens the restrictions when determining which components are valid for the data. |
Absolute noise threshold | The larger of relative Relative abundance threshold (%) and absolute Absolute noise threshold determines which ions are used to find related ions for a component. Use Absolute noise threshold to examine small signals. Default is 1000. Range is 0 to 1,000,000. |
Relative abundance threshold (%) | The value of this parameter represents a percentage of the abundance of the largest ion in the spectrum. Any ion whose abundance exceeds the abundance cutoff can be used to predict other ions in a set. Default is 10%. The larger of relative Relative abundance threshold (%) and Absolute noise threshold determines which ions are used to find related ions for a component. Absolute noise threshold is particularly useful for examining large signals; you may want to lower it for small signals. This value does not prevent ions in the spectrum from being in a set of related ions; it just prevents smaller ions from being used to predict other ions in a set. |
MW algorithm |
Select the algorithm used to determine molecular weight. The default is Curve Fit, which gives the best results when ion sets are Gaussian in distribution or have isotopic resolution. Centroid gives a weighted average of the data points above the MW algorithm threshold (%). |
MW algorithm threshold (%) | Determines what portion of the resulting reconstructed mass envelope will be used to find the molecular weight. This value represents a percentage of the highest abundance in the envelope. The data points occurring above this abundance threshold are used to determine the molecular weight. Default is 40%. You may want to raise this parameter if the data is noisy or if the "final" peak is highly asymmetrical to prevent the asymmetrical portion of the envelope near the envelope base from being used in the MW calculations. If this value is set too high, only a small number of data points will be used in the curve fit, which could cause the curve fit to fail. If the curve fit fails, try using the MW algorithm parameter Centroid for low charge states or noisy data. Otherwise, try lowering the MW algorithm threshold (%). The algorithm starts at the maximum of the largest ion and heads down the leading side of the ion peak along the data points toward the assigned cutoff. If it encounters resolved or unresolved isotopes that rise more than 10% from the downward slope, the algorithm will draw a cutoff line from the low point before the rise back across the ion peak to a point on the trailing edge that is directly opposite the low point. |
Envelope threshold (%) | Determines how strictly the shape of a group of ions must match a somewhat Gaussian shape before the algorithm accepts the group as a component. Range 0 through 100%. Zero means that envelope shape will not be enforced. The higher the number the stricter the enforcement of shape. The default value is 50, which means that the abundance of an ion on the upward slope of the envelope can be no lower than 50% of the abundance of the ion to its left. It also means that the abundance of an ion on the downward slope of the envelope can be no lower than 50% of the ion to its right. |