Peak picking and manipulation

Focusing on the HSQC spectrum ("window1") the next task is to define some contour extrema as peaks. There are two common ways to pick peaks. One is to search for all extrema in a boxed region. Try this in the HSQC window by holding down 'Shift' and 'Ctrl' whilst clicking with the left mouse button and dragging the box to define a rectangular pick region.

Note that when the peaks are picked the contours will carry diagonal crosses to denote the peak position. Each peak will also have some annotation to the top right of the cross, which we discuss below.

Locate the contours near the point at 8.7 ppm on the 1H axis and 118.4 on the 15N axis:

These contours represent two overlapping peaks where the extrema search will only pick one of the peaks. To define the second peak position hold down 'Ctrl' and click on the location to pick the new peak:

Now we will select some of the peaks, e.g. artifacts or noise, for deletion. To delete peaks, click with the left mouse button and drag a box over a region containing peak crosses (without holding down any keys). When the mouse button is released you will see that the peaks in the defined region are highlighted with a border around the cross. To select just a single peak click near its centre with the left mouse button. To delete the selected peaks press 'del' or select R: Peak: Delete selected.

If you have peaks selected and then select a different set of peaks you will see that the selection is completely substituted for a new one. You can add picked peaks to an existing peak selection by holding 'Shift' while you choose. Note that you can select peaks in several different spectra, and from different windows, in this manner.

Next try moving a peak. For this select a single peak, move the mouse cursor to the desired position and press the 'p' key. Alternatively you can hold the 'p' while you move the mouse. If the selected peak is near, but not exactly at, an extremum you can shift it to the extremum with 'P' (e.g. 'Shift' + 'p'), as long as there is no existing peak already at that position (in the same peak list).

To open a table containing a list of peaks, select M: Peaks: Peak Lists. In the {Peak Table} tab select a spectrum for which you have picked peaks with the top left pulldown menu. Click on one of the peak rows so that it is highlighted, then click on [Find Peak] - remember to select the correct window with the pulldown to the left of the command button. This will locate the peak and centre it within its window.

With the table and the spectrum window both visible, select the peak in the contour window and move it to a different position. - Watch in the peak list table as the peaks ppm values are continuously updated. This is a general feature of tables in Analysis. The tables are updated when things change, to reflect the immediate state of the underlying data.

It is also possible to move a peak by editing its position value in the table. Do this by double clicking on a "Shift" column (e.g. |Position F1|) in the table for one of the peaks that you can see in the spectrum window. Edit the peak position for that dimension, but not so much that the peak would not be visible on screen, and press 'Return' to see the peak move relative to the contours.  

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