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  1-D Automatic Phase Correction

iNMR gives the user the choice between three auto-phasing algorithms, for higher flexibility. These methods are quite reliable in 1D spectroscopy. It's also true that they work perfectly in 2D, yet the user should be aware that there is no substitute for experience and knowledge, in that field. In mono-dimensional spectroscopy all new spectra are already phase corrected by iNMR, by with the global method described below, so the user should just concentrate on manual phase correction or try the other methods.

Whatever method you choose, remember that sometimes you get better results if you perform the correction twice.

Global Method

The aim of this method is to rotate the whole spectrum upwards. (More technically speaking: the method keeps changing the phase while monitoring the single lowest point and reading its ordinate value; iteration stops when this value cannot grow anymore). You will easily realize it is not appropriate for experiments like DEPT, APT, NOEdiff, where peaks are expected to be both positive and negative. In the remaining cases it is exceptionally stable, being not affected at all by crowding of peaks, noise or field inhomogeneity. It is affected, however, by baseline distortions. This method is run when the user first creates one or more horizontal marks (alt-click) and then selects the command ‘Process/Autophase’. If you don't like menus, you can find an equivalent icon in the tools palette (dashboard).

Selective Method

If, instead, any number of vertical marks exist, the selective method is used. In this case, the aim of the program is to make symmetric the selected peaks (pointed to by the marks). Needless to say, for the method to work, the marks should fall on isolated, well-shaped peaks. To create a mark, just Cmd-click on the spectrum. Then, you can drag it on any peak. The selective method is more appropriate for spectra containing negative peaks or in the presence of a distorted baseline. It is insufficient in crowded spectra or when the sample has not been properly shimmed. It is also inferior when the digital resolution is low. In other words, it is not the method of choice.

Metabolomic Method

The perfect choice when the the baseline is flat and the signals are concentrated towards the center of the spectral width. If there is a peak at the center, it is ignored (useful if it can't be phased). This is the only method that performs better than manual correction. (Default from version 2.1.4 onward) If you want to use it, check that no marks are visible before issuing the command “Process/Automatic Phase” (or clicking the corresponding icon, or using the keyboard shortcut Cmd-Shift-K).


  2-D Automatic Phase Correction

Global Method

It's the default method. If the spectrum has been processed with the option “hyper-phase”, then the phase is correct along both axes, otherwise the correction is possible along a single axis only. This method is slow and sometimes stops before complete convergence. You can, however, give the command again. The dispersion component is reduced as much as possible, yet the method does not discriminate between positive and negative absorption. If the latter is selected, it's enough to issue the “alt”-command “Process/Phase Inversion” (Cmd + Alt + K) that changes the sign of the spectrum. This method can't be as accurate as a proper manual correction, yet can save a lot of time for non expert users. When there is no phase correction at all, the 2D plot is almost unrecognazible and a beginner just doesn't know where to start from. The automatic correction can do most of the job and bring the spectrum into near-normality, a state in which only minimal phase agjustments are required. These minimal adjustments are easy to perform manually.

Selective Method

When ALL the conditions below are met a selective method is applied:

  1. It's hyper-phased.
  2. A region has been selected by the user (by click-and-drag).

Otherwise the global method is applied. The selective method tries to make all the selected points positive. If you have selected a negative peak, for example, you'll get the spectrum with the sign changed. You can select more than one peak and also portions of peaks. As expected, if you select together positive and negative peaks, the result will be a mess. In the case of homo-nuclear spectra, it's better to select a diagonal peak. Beware that NOESY spectra of small molecules contain positive cross-peaks near to a negative diagonal. If the diagonal is much more intense, however, the method will still work. In general, it's better to select strong peaks. This method is faster, but more difficult to use than the global method. There is no sure rule to predict which peaks will be correctly phased.

Selective Method with Marks

You have the option to apply the selective method just seen and, at the same time, to preserve the phase of another peak. The peak to preserve must be distant from the selection. You mark it with the combination Cmd + Alt + click, which creates a red cross. It's possible to set the vertical mark only or the horizontal mark only. An example of application, with a homo-nuclear spectrum, would be:

See also

An Introduction to Phase Correction

Manual Phase Correction

Phase Correction in Multi-Dimensional Spectroscopy