Pick peaks

Instructions

Basic peak picking

To pick a peak in a nD spectrum window, hold down 'CTRL' and click the left mouse button. To pick peaks with this procedure, no parameters related to peak finding need to be set and a peak can be picked anywhere where desired.

To automatically pick one or more peaks in a region, draw a box in the region of interest with the left mouse button while simultaneously holding down 'SHIFT' and 'CTRL'. The result of this peak picking depends on a variety of parameters that can be set in Peak: Peak Finding (see below). 

Setting the parameters for peak finding

The peak finding parameters can be set in the Peak: Peak Finding popup, which is accessible through M: Peaks: Peak Finding. Normally the default values are a good starting point, however, it is recommended to check and modify the peak finding parameters if needed to obtain better results.

Tips: In general it is good practice not to rely on automated peak picking routines too much: use these peak pickers in a conservative way for an initial picking, and add/modify the peaks later on. In particular, the peak picking depends on the contour levels that are set for the spectrum. To avoid picking a lot of noise peaks start at a high contour base level. In case the automated peak picking missed some low intensity peaks, these can be added later by lowering the contour level and picking them separately. When picking peaks in windows with more than 2 dimensions it can be helpful sometimes to increase the "Extra thickness in orthogonal dims". The peak picking in multidimensional windows can also be influenced by setting the "+-1 allowed in any dim" instead of "+-1 in at most one dim". 

Region peak finding

To pick peaks in a specific region of interest in a nD window, Analysis is equipped with a procedure that lets the user specify a peak picking region for each dimension. This is done separately for each spectrum in the tab {Region Peak Find}, in Peak: Peak Finding (see below).

To initiate the region peak finding, first choose a peak list to add picked peaks to by selecting a peak list in the upper left pulldown menu named "Peak List:". By default, the table contains one region row that is that spans the complete spectrum for inclusion in the peak picking. You can now:

• • Select a region row and click [Whole region] to set the region row to cover the whole spectrum.

  • Click [Add Region] to add a new region row, which may then be set for exclusion or inclusion when peak picking large areas. Set interval and condition for a region row by double clicking in the table cells. 

  • Click [Adjust Params] to go to the panel for setting the parameters that control how local extrema are picked ({Find parameters}). 

  • End by clicking [Find Peaks!] to perform wide range peak picking based on the defined regions and parameters. 

The Region peak finding procedure can take quite a long time, especially for multidimensional spectra due to the large amount of data to process.