The peak-picking routines of NMRViewJ do not determine the volumes of the peaks. Instead, so that the peak picking itself can be as fast as possible, a subsequent analysis routine is used. The peak volume routine is initiated by choosing either Get Volumes or Get eVolumes from the Int menu of the Peak Analysis interface panel. Both these methods will calculate the sum of intensities in the dataset of a footprint region calculated from the peak attributes. By default, the intensities are obtained with the dataset from which the peak list was originally picked, and the dataset must be open within NMRViewJ prior to using the command. The footprint used by the first method is a rectangular region corresponding to the peak bounds identified when the peak was picked (Section 5.2), while the latter (and preferred) method uses an elliptical region whose width is a certain "optimal" multiple of the peak width. The elliptical region minimizes the contribution of noise and neighboring peaks to the calculated peak intensity.
A second advantage of this two-step process is that it makes it possible to measure volumes (or intensities) from a different dataset than the original list was determined from. You can do this by changing the dataset that is associated with the peak list. Bring up a dialog for doing this by selecting the menu item.
You can see the elliptical area that is used by setting the peak display mode (in the Peaks tab of the Spectrum Attributes window) to Ellipse. The ellipse bounds are calculated from the full-width at half -height of each peak, and thus is, unlike the peak bounds, are relatively independent of the threshold used during peak picking.
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A second advantage of this two-step process is that it makes it possible to measure volumes (or intensities) from a different dataset than the original list was determined from. You can do this by changing the dataset that is associated with the peak list. Bring up a dialog for doing this by selecting the menu item.
As with all NMRViewJ operations, peak volumes can be obtained using custom scripts. For example, the script shown in Figure 11 could be used to obtain volumes (or intensities) from a whole series of datasets with regions corresponding to the peaks in a single peak list, such as in the analysis of relaxation data.
The basic process then, is:
Open the Peak Inspector or the Peak Table
Select a peak list to measure.
If desired, change the dataset associated with the peak list with the menu item
Select the , or menu items from the menu.
Plotting peak volumes and intensities can be a useful way to get an overal sense of the distribution of intensities or volumes. You can do these sorts of plots right withing NMRViewJ. Choose or menu items from the menu to generate a plot as shown below. From this plot one might conclude that the threshold used in peak picking was set to low.
Plotting volumes vs. intensities can be useful to get a sense of the relationship between these two factors, and to look for outliers as measured by either method.
