Data processing phase correction

At the end of the 2D experiment, we will have acquired a set of N FIDs composed of quadrature data points, with N /2 points from channel A and points from channel B, acquired with sequential (alternate) sampling. How the data are processed is critical for a successful outcome. The data processing involves (a) dc (direct current) correction (performed automatically by the instrument software), (b) apodization (window multiplication) of the <2 time-domain data, (c) Fourier transformation and phase correction, (d) window multiplication of the t domain data and phase correction (unless it is a magnitude or a power-mode spectrum, in which case phase correction is not required), (e) complex Fourier transformation in Fu (f) coaddition of real and imaginary data (if phase-sensitive representation is required) to give a magnitude (M) or a power-mode (P) spectrum. Additional steps may be tilting, symmetrization, and calculation of projections. A schematic representation of the steps involved is presented in Fig. 3.5. 

Field recovery samples are an important part of the quality control in DFR studies. Field fortifications allow the experimental data to be corrected for losses at all phases of the study from collection through sample transport and storage. Fresh laboratory fortifications monitor losses due to the analytical phase. This section details how the field recovery process was handled in the oxamyl tomato DFR study. 

The basic processing of ID and 2D data requires obligatory processing steps for transforming the raw data (FID) into a "readable spectrum, i.e. Fourier transformation and phase correction to produce a spectrum with absorptive lineshapes. Finally, a few additional step.s (calibration, peak picking, integration) as discussed in chapter 4 are required before the spectrum is eventually plotted. 

Load the raw data of the ID H experiment measured for peracetylated glucose D NMRDATA GLUCOSE 1D H GH 002001.FID and perform a Fourier transformation. Use either the FT button in the button panel or from the Process pull-down menu choose the FT option. In the DC Correction dialog box click on the No button. Note that the calculated spectrum is incorrectly phased. Use the dual display option to compare this spectrum, showing the ring protons, with the correctly phased spectrum D NMRDATA GLUCOSE 1 D H GH 002999.l R. Exit the dual display and from the Process pull-down menu choose the Phase Correction option. The... 

For 2D data which need no phase correction the PHmod parameter in FI, available in the General parameter setup dialog box opened via the Process pull-down menu, must be set to me if a magnitude, or to ps if a power spectrum should be calculated. Use the Help tool for more informations. 

Load the raw data obtained for peracetylated glucose with the 2D TOCSY experiment D NMRDATA GLUCOSE 2D HH GHHTO 001001.SER and perform a 2D FT following the guidelines given above. Enter the Manual phase correction option in the Process pull-down menu and perform a phase correction in F2 and Ft according to the procedure outlined above. Try to phase all peaks to positive absorption and store the spectrum (... 001001. RR). 

Correction, Window Function (Exponential LB = 1.0 Hz) and FT. In the frequency domain select Phase Correction (6th Order), Peak Picking (positive Peaks only X Range whole Spectrum) of the whole region. Save Spectrum (set Processing Number Increment = 1) and Plot Spectrum (set the plot parameters according to your preferences). Execute the automatic processing and if you are satisfied with the result, store this job for processing 1D C raw data as C.JOB. 

The data processing can be divided into three phases. Phase 1 is the removal of poor quality spectra with an automated routine. Phase 2 is the data preprocessing of the spectra, which passed the quality test. This usually entails some type of baseline correction and normalization process. Phase 3 is multivariate image reconstruction where the spectra are classified and reproduced as color points... 

The hardware and data-processing details of ID NMR data were discussed in Chapter 3 data sampling in the ADC, quadrature detection, the spectral window, weighting (window) functions, and phase correction. We will have to revisit each of these topics in the second (t, F ) dimension and some of them will take on added signihcance. 

Figure 2-11 Comparison of shapes of absorption (solid line) and dispersion (dotted line) signals. Spectra are usually phase corrected to give pure absorption-mode peaks. The arrows indicate the full width at half maximum. (Reprinted from J. C. Hoch and A. S. Stern, NMR Data Processing, 1996 by permission of Wiley-Liss, Inc., a subsidiary of John Wiley Sons, Inc.)...

Load the configuration file ch3234c.cfg. Run the simulation and process the data as in part a. Using the Numerical option correct the zero-order phase (Process I Phase Correction, phcO -40 and phc1 0). Ensure that the cursor is set on top of the peak at 3.75 ppm click the First Order button and adjust the phase of the off-resonance signals for the correct absorptive lineshape.-... 

The comparison of 2D spectra is often simplified by the decomposition or splitting of a 2D data matrix into a series of ID spectra. Time domain data can be used to optimize weighting functions prior to processing the 2D data matrix whilst frequency domain data can be used in the evaluation and development of modified pulse sequence. ID spectra can also be used to optimize the phase correction in a phase sensitive experiment. 

Load the configuration file ch52614.cfg and simulate the iH decoupled PENDANT-13C 1H spectrum of ethyl acrylate. Save the data as USER ch526, Name 52614 and Exp No. 1. Process the FID (Sl(r+i) 64k, wdw EM, LB 2.0 [Hz]). Apply a slight phase correction and then examine the spectrum for the sign of the signal amplitude. 

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