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Peak Picking

Peak Picking


PP — Peak Picking

Commands and parameters that affect peak picking (details below):

MH – Minimum Height, the threshold for selecting peaks
RM – RMS noise parameter, to distinguish between a peak and noise
ZL – Zero List, clears the list of peaks
Ctrl-P — Toggle on/off display of peak labels
PN – Peak labels on, to display peak labels
PF – Peak labels off
CB or Ctrl-B — Toggle on/off display of clipboard text on the screen (see also:  Notes subroutine)

The Define Peaks subroutine provides more options for peak picking and labeling.

This operation selects all peaks in the displayed region, indicating which peaks have been selected with vertical lines on the display. Peaks are selected if they meet 2 criteria: peak height must exceed the minimum height (MH) value and the peak must decrease by RM multiples of RMS noise after reaching a maximum. (This latter is to avoid picking multiple "peaks" for a broad peak in a noisy spectrum.)

When PP is executed, a peak list is placed into the Clipboard. For example,

Interpolated Peak Listing PEAK    POINT   HEIGHT    REL.HT    HZ       PPM  1 	1574    113459    43.49    776.17   2.586  2 	1578    120172    46.07    768.21   2.559  3 	1746    217882    83.52    439.81   1.465  4 	1789    136120    52.18    356.09   1.186  5 	1793    266988   102.35    348.20   1.160  6 	1797    127982    49.06    340.29   1.134

Height is peak height in absolute units, Rel. Ht is peak height relative to the tallest peak in the spectrum set to 100.  Peak frequency is reported in Hz and ppm.

The peak list can be created using either spaces or tabs to separate the columns.  With space-separated columns, when a fixed size font is used, the columns line up. (Best for pasting into Notepad).  Tab-separated columns are best for pasting into a spreadsheet program.

The choice is determined by a setting in the nuts.ini file, and can be toggled between the 2 options with the TB command.

When the file is saved, the peak list is saved in the file "tailer", so it can be recalled later.

This information can be pasted into and edited or printed from any text editor or word processor, such as the Notepad. The peak list (or any other text in the Clipboard) can be placed on the screen (in the upper left corner, by default) using the Ctrl-B command, which displays the contents of the clipboard on the screen. The font for the clipboard display is set with FC, from the Edit menu or within the NUTS.INI file. The list will be easiest to read if the font is a fixed-width font, such as Courier, so that the columns line up.

The PP command also displays peak labels on peaks. By default, the labels are placed at the top of the screen, but this can be changed in the nuts.ini file. The display of peaks is toggled off (an on again) using Ctrl-P. The peak labels can be edited and other parameters selected using the DP subroutine. The list can be removed with the Zero List (ZL) command.

By default, NUTS uses interpolation to find the peak maximum, which gives a more accurate value for the peak frequency. The interpolation can be turned off from the dialog box which allows setting of the chemical shift reference. From the NUTS base level, press and hold the left mouse button and type O to bring up this dialog box.

Peak frequencies or other text labels can be displayed above each peak. To do this, the peaks must be selected within the DP subroutine, rather than with the PP command.

Setting the threshold (minimum height, MH) — The Minimum Height value is expressed as a percentage of the tallest peak in the spectrum. The simplest way to determine the optimum value for MH is by using the cursor from the base level of NUTS (not in Zoom). Press and hold the left mouse button and place the horizontal cursor line at the height you want for the threshold and type M. Note that if Fixed Scaling (FS) of the display has been turned on, setting Minimum Height with the cursor will not work properly. Minimum height may also be entered by typing MH, which brings up a dialog box and allows a value to be entered. If the peak selection misses peaks which have small splittings, try a smaller value of RM.

Because setting MH and executing peak picking are commonly performed together, NUTS has an optional shortcut, which can be set in the nuts.ini file.  If this option is turned on, setting MH with the cursor also performs a peak pick.

As of  April, 2000, the MH command has been modified to allow use in the non-two letter command mode.  The command can be MH or MinHt.  If it has no arguments, then the standard dialog box comes up and allows the user to enter an MH value.  If it has one argument, that argument is converted to a number between zero and 100.0 and the MH value is set to that number.  If it has two arguments, and the second argument is "rms", then the MH value is set to the first argument times the current rms noise of the spectrum.  

For example, 

mh 5        sets the Minimum Height to 5

mh 5 rms    sets Minimum Height to (5 * rms value)


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Last updated: 6/1/03.