Peak-picking

Peak picking is usually performed to measure chemical shifts (in ppm relative to a reference peak in the spectrum) or to measure line separations (in Hz) in multiplets in order to calculate or at least to estimate coupling constants. 

The Peak Picking option in the Analysis pull-down menu allows peak picking in an interactive way. Activating this menu option switches the button panel into the Peak Picking mode, the mouse cursor to Peak Picking Zoom mode and opens a dialog box (Fig. 4.10). 

In this dialog box the Peaks sign, the Peaks Label and the parameter PC, which determines the sensitivity of the peak picking algorithm may be specified. Furthermore, the Interpolation and Multiplicity mode can be set which increases the accuracy of the peak picking and lists the multiplicity information respectively. 

The buttons in the peak picking button panel have several functions  

Edit Cursor Allows you to edit (delete, add multiplicity information) currently displayed peak labels. During this operation the cursor will only move to marked peaks. 

Most operating software offers the facility to pick out the peak maxima in the spectrum and store the results in a file and/or label the peaks on the paper hardcopy. This is a very useful facility and greatly eases the task of interpretation. Coupled with peak-picking, there is usually a facility to store peak heights and areas in the same data file. This may be of use for quantitative work, although it remains preferable to analyse peaks personally when quantitation is required. Peak areas are to be preferred for such analyses, as areas better compensate for matrix effects (interactions). 

The result that is reported as the peak wavenumber is frequently the wavenumber value of the maximum discrete point, which rarely corresponds to the exact center of the band. It is not uncommon for these values to be reported to four or five decimal places, as this is how well the wavenumber of each datum is recorded however this number of digits is well beyond the realistic accuracy of most experiments. The use of the maximum data point for the wavenumber position of a band is suitable only for noncritical information. The actual band center may be considerably displaced from the maximum data point. For example, in a typical spectrum measured at 4-cm resolution, data points are typically computed at 2-cm intervals. Under these conditions simple peak-picking algorithms would not readily detect band shifts of about 0.5 cm . In practice, the wavenumber of the maxima of bands in the spectra of condensed-phase spectra measured at a resolution of 2 or 4 cm should only be reported to 1 cm .  

For a spectrum that is digitized at constant intervals, Vcg can be computed by the following summation  

It can be shown that the two approaches yield very similar values for the band center of symmetrical bands. The principal difference is that in the center-of-gravity approach, all points are weighted equally, whereas in the polynomial approach the weighting of a given point depends on its position relative to the band center. For asymmetrical bands, the two approaches yield slightly different values for the band center. 

The accurate determination of bandwidths can also be very important for example, in biochemical infrared spectrometry or in the smdy of polymorphs. Although bandwidths are often quoted at half-height, it may often be more informative to make the determination at some other fraction/of the peak height. The peak height may be defined as max — ref. where ref is an arbitrarily selected zero point and Vmax = Vref. The fractional width Av/ may be calculated as 

Under carefully controlled conditions, wavenumber measurements may be precise to 0.01 cm (discussed below), but usually only when a sample is left undisturbed in the sample compartment. Even if the sample is simply removed and reinserted between measurements, the repeatability is often worse than 0.01 cm . Several reasons can be advanced to explain why band shifts occur. First, the temperature of the sample may change between measurements, which leads to small spectral shifts. Second, it was noted in Section 2.6 that changes in the effective solid angle of the beam through the interferometer can lead to small wavenumber shifts. Because the cell may represent a field (Jacquinot) stop, if a cell is not placed in exactly the same position for successive measurements, bands will appear to shift from one measurement to the next. Furthermore, if the cell is slightly tilted and the angle changes appreciably from one measurement to the next, the beam may be refracted to a different position on the detector, which also shifts the wavenumber scale. Loose or insecure sample mounts should be avoided if users require the wavenumbers of absorption band maxima to be repeatable to better than 0.1 cm .  

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On the basis of automated peak picking and integration procedure, after less than 2 h, the enantiomeric purity was established. R S ratio was 34.4 65.6, which is close to the values obtained from the 1H or 13C NMR spectra. 

The simplicity and clarity of CONCISE has been retained in the automated rule generator which creates CONCISE interpretation rules for PAIRS based on a representative set of IR spectra. The rule generator uses peak position, intensity, and width tables produced by an automated peak picking routine. This method reduces the dependency on published frequency correlation data and enhances the usefulness of data already available. All work was done using the version of PAIRS running on a Nicolet 1180 minicomputer and programs generated have been optimized for this system. 

An E-map is computed for the best set and the peaks picked. We then use our knowledge of molecular dimensions and conformations to extract a trial structure. This is the first point at which chemical knowledge is used actively i.e. the direct methods procedure is model free until this point. The structure is completed and refined in the usual way. 

Peak-picking appears to be a domain largely occupied by instrument manufacturers. As a consequence, many of the algorithms remain unpublished. 

The role of peak-picking is to return only one position per peak, and in the presence of noise, this again poses problems. It is likely that most algorithms will start from a position of intensity maximum, and then search either side for the first point significantly lower, i.e., a multiplier of the noise. This defines a new peak region and the process could then be repeated. Some software additionally offers the facility of a horizontal threshold, above which values are returned and below which they are not. 

Zero filling the FID more than a factor of two does not contribute to information extraction and any features revealed by this are artefacts. In most instances, zero filling by a factor of two amounts to an interpolation procedure benefiting primarily peak-picking. There are other procedures which can allow peak-picking interpolation between data points and the one used by the author is a simple equation to fit the maximum intensity and one point either side to a parabola and compute the position of its maximum. Bruker peak-pick table positions for instance are not separated by a multiple of the digital resolution and it would seem that they use the same or an analogous procedure. 

Wiithrich et al published a tour de force on the Automated Peak-Picking and Peak Integration in Macromolecular Spectra (AUTOPSY). This work deals primarily with two-dimensional spectra, but the algorithms are equally... 

In the retesting and deconvolution phase of the procedure new compound mixtures were made based on the results of primary screening. These contained from nine to 14 compounds and no monoisotopic mass redundancy. Since most mass spectrometric peaks picked as hits in the primary screen contain more than one compound, and only one compound per peak is likely to be a binder, the nonmass redundant retest mixtures are unlikely to contain more than a few bona fide ligands, so once again target excess is maintained. Both the initial (round zero,... 

There are four general modes of operation for LC-NMR on-flow, direct stop-flow, time-sliced and loop collection/transfer. The mode selected will depend on the level and complexity of the analyte and also on the NMR information required. All modes of LC-NMR can be run under full automation for LC peak-picking, LC peak transfer to storage loops or NMR flow cell, and NMR detection [46],... 

Analysis This pull-down menu is only available for frequency domain data (spectra) and allows a few simple analytical tasks to be performed such as peak picking, calibration, integration or simple spectral analysis. 

Starts peak picking using the parameter PC last set during interactive peak picking (see section 4.6.2). 

Load the H spectrum of glucose D NMRDATA GLUCOSE 1D H GH 002999.1 R. Use the Peak Picking button in the button panel for peak picking. From the Display pull-down menu choose the Display Colors menu. In the dialog box that appears on the screen select different colors for the spectrum, the frame, the numbers and the peak labels. Peak picking will be explained in more detail in section 4.6.2. 

The Mouse Peak Picking mode allows you to define the x-and y-limits for the peak picking regions (Fig. 4.11). It is possible to pick peaks in many different regions of the spectrum using this option. 

A dialog box allows you to inspect and edit the peak picking parameters. 

A dialog box allows you to list, edit, load and save peak picking regions and to execute peak picking according to the entries. 

Erases all the individual peak picking regions and all the picked labels. A region is created that spans the complete spectrum. 

Relax.-> Allows the Peak Picking mode to be carried over into the Peak Picking -Relaxation mode. For peak picking in connection with relaxation studies, you are referred to Modern Spectral Analysis (volume 3 of this series). 

Fig. 4.11 Peak picking in the Mouse Peak Picking mode.

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