Peaks and Peak lists

Local extrema

An NMR spectrum contains a number of local extrema (maxima and minima), that are generally referred to as peaks. These local extrema can be characterized by parameters such as frequency or chemical shift, intensity, line width and volume. This characterization is typically done in the process of peak picking.

Peak picking

To analyse and work with local extrema in NMR spectra, typically one performs so-called peak picking, which is the process of identifying the extrema in the NMR spectrum and storing this information on disk as ‘picked peaks’. The picked peaks are descriptors of the local extrema, that can be used in NMR analyses.

Note that it is important to distinguish a real peak or local extremum from the ‘picked peak’: Novice users sometimes think that an NMR analysis program should automatically work with the real peaks, understand what is displayed as a spectrum, and use that information directly without having done the peak picking. However, an NMR analysis program typically needs the picked peaks in order to work with (see Figure 1).

Figure 1. A  2D spectrum window in Analysis. ‘Picked peaks’ are indicated with crossed boxes.

Peak picking can be done automatically or manually, depending on the complexity of the spectrum or noise levels, and usually is a combination of both.

Peaks

In this documentation, if we are speaking about peaks in the context of CcpNmr Analysis, we refer to ‘picked peaks’ unless specifically indicated otherwise.

Peaks are characterized by a number of parameters, with the most important being:

• • Positions in all dimensions

  • Assignments in all dimensions

  • Height

  • Volume

This information is used to display peaks in spectra, and is used to perform specific NMR analyses, such as automated assignments, frequency matching, and generation of geometrical restraints. Notably, peak positions and assignments are used to populate chemical shift lists. Display parameters for peaks are controlled on the level of peak lists.

For many types of analyses, peaks need to be assigned to atoms in a molecule, which is often one of the most important goals in itself. Peak assignments to atoms are always done via resonances. To read more about assignments see here.

Peak lists

A peak list is a collection of ‘picked’ peaks that have been obtained for a spectrum. As described under Spectra, multiple peak lists can be associated with one spectrum, thus allowing the user to group peaks with different origin or status into different peak lists.

If a spectrum has more than one peak list associated with it, only a single peak list can be active at any one time, which is controlled by the user (see Figure 2). It is important to note that it is only possible to manipulate peaks in the active peak list.

Display parameters for peaks, such as color and display symbol, are controlled on the level of peak lists.

Figure 2. One spectrum can have multiple peak lists but only a single peak list can be active at any one time (indicated in red).

Synthetic peak lists

Normally a peak list is created by picking peaks, either automatically or by manual peak picking. However, in some cases it is desirable and useful to create a peak list based on chemical shifts and/or a structure of a molecule. For example, one can generate a ‘theoretical’ peak list based on known chemical shifts and coordinate file. Such peak lists are called synthetic peak lists in CcpNmr Analysis, and can be used alongside normal peak lists in a spectrum.