Peak-picking means extracting the frequencies of the peaks, either from the whole spectrum or from selected regions. These frequencies are usually reported on the plot. Not all the peaks are considered. When they are so tall that they go out of the plot, they are filtered out. There is also a minimal threshold value: the weakest signals are ignored. It is fundamental to understand how this threshold is set.
To extract the frequencies you use a specialized tool (command: Tools > Peak-Picker), which is the same both in 1-D and n-D spectroscopy. The difference of 2-D peak-picking is explained into the closing paragraph. When you use the tool for the second time on the same region, the old labels are replaced.
The frequencies are stored with the spectrum and indexed by Spotlight. You can use the J Manager to convert them into coupling constants and chemical shifts.
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to perform this task |
this is how to proceed |
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defining/removing a visible threshold |
Option-click to create/delete an horizontal mark that can be moved with the mouse. The visible threshold overrides the temporary threshold. When there are many horizontal lines, the lowest one is considered. |
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defining a temporary threshold |
When you click with the cross-shaped picker tool, and no threshold exists yet, the imaginary horizontal line passing through the cross defines the threshold. |
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defining a fall-back threshold |
It corresponds to the user preference called Short Distance (found at the bottom-left of the second panel). If the value of this option (expressed in screen points) is less than 4, a built-in value of 4 is used. The fallback threshold takes the lowest precedence. It is employed when you first select a region, then choose the picker tool. |
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picking some peaks |
Select a region with the picker tool. |
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picking all the peaks |
Triple-click with the picker tool. |
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picking a single peak |
Click INTO the peak with the picker tool. |
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picking a secondary maximum |
When two peaks are too close, the picker tool only sees the highest one. To pick the smaller peak, Control-click and select Pick Peak. |
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picking a shoulder |
Control-click the shoulder and select Pick Mouse. iNMR will not search the nearest maximum, as it usually does, but will register the exact frequency where you have clicked. |
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removing a single label |
Click the corresponding peak with the picker tool. |
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removing some labels |
Set the threshold so high that all the peaks are lower and select the region with the picker tool. You can set the threshold and select a region with a single operation (click and move the mouse). |
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removing all the labels |
Hold down the option key and choose View > Remove Frequencies. The alternative is a triple click with a very high threshold. |
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hiding the labels |
Choose View > Peak Frequencies. The same command shows them again. |
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reporting the frequencies in Hz |
The frequencies are normally reported with the same unit used for the scale. If you prefer the labels in Hz, even when the scale is in ppm, press the apostrophe key. Press it again to revert the option. |
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reporting the line widths |
Press the double quotes key. Press it again to revert the option. |
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hiding the small ticks over the selected peaks |
Open the User Preferences and set Short Distance = 0. |
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changing the color, the font, the size or the number of digits of the labels |
You can change all these things inside your User Preferences. |
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printing or saving the list of frequencies |
Choose Edit > Copy > List of Peaks and paste it where you need. |
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retrieving another spectrum with the same peak |
⌘-click on the peak to mark it. Choose Edit > Search. The field “peak at” will be already filled. Set the desired ppm range and other options, then click Search. Your old spectra can be searched if they have been saved and you have already performed peak-picking on them. |
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2-D Peak Picking keeps many similarity with the 1-D operations described o far. It also includes a dialog,
that offers additional choices. To open the dialog choose the picker tool and double click the spectrum.
The dialog also appears when you select a region that already contains a frequency label.
The controls inside the dialog are easy to understand, if you have already mastered 1-D peak-picking.
The threshold normally corresponds to the lowest contour of the plot.
The merging concept is not completely new. In 1D, when 2 peaks are separated by a single intermediate point,
they are considered a unique peak. In 2-D, peaks are also merged, but you are allowed to specify
the minimum distance (in Hz) for two peaks to be considered different entities.
When you specify a value larger than the coupling constants, a multiplet is treated like a single peak.