Submitted:
07 January 2024
Posted:
08 January 2024
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Abstract

Keywords:
Introduction
Direct current (DC) offset removal
Eddy current (EC) correction
- 1)
- Check the time and frequency domains for eddy current issues, focusing on distorted peaks (see Figure 4F).
- 2)
- If you detect eddy current effects and have the necessary resources, perform EC correction in the time domain.
- 3)
- If resources are limited, address the issue during domain transformation. Prioritize phase error correction and chemical shift calibration during frequency domain pre-processing.
FID shift and linear prediction
Weighting
Zero Filling
Domain Transformation
Conclusion/Discussion
- 1)
- DC Offset Correction: Prioritize investigating, estimating, and removing DC offsets. This can usually be done with phase cycling or a sufficiently long FID recording.
- 2)
- Eddy Current (EC) Correction: EC-induced distortion is a challenging pre-processing step. Investigate EC issues in both time and frequency domains. If specific conditions are met, EC correction is feasible. Otherwise, use wavelet transform instead of FT during domain transformation to address EC-affected signals.
- 3)
- FID Shift: In general, avoid FID shifts that result in information loss. Exceptions include intentional pre-acquisition delays for severe distortion, followed by backward LP. Forward LP is useful for extending the FID tail to enhance digital resolution, either on its own or before DC offset removal and zero filling.
- 4)
- Weighting: Weighing can enhance sensitivity or resolution, but not both at once. Only apply weighting if you’re confident it’s necessary, and use the same function for all spectra within an experiment to ensure comparability.
- 5)
- Zero Filling: Zero filling can boost digital FID resolution. It’s recommended if the ending FID values are close to zero. If not, consider applying forward LP before zero filling, provided DC offset is not an issue.
- 6)
- Domain Transformation: FT is the primary method for domain transformation and works well in most cases. However, for uncorrected EC effects, wavelet transform is a better alternative. While many NMR pre-processing software tools lack wavelet transform options, dedicated packages in languages like R and Python can perform this technique.
| Pre-processing step | Possible problems | Our recommendations |
| DC (Direct Current) offset removal | The DC offset might not be correctly estimated | Approach with two sets of scans is the best method. When this is not practical, we need a converged tail of FID to estimate DC offset and remove it. When recording time is too short, forward LP might be applied before DC offset estimation. |
| EC (Eddy Current) correction | Additional data or specific adjustments might not be available. | Reference FID, isolated solvent peak, and opposite magnetic inductions are especially useful to remove EC. When extra data and tools are not available, skip this step and take care of the problem in domain transformation. |
| FID shift and LP (Linear Prediction) | Might cause severe phasing problems, distortion and unrecoverable errors in FID data. | FID shift plus backward LP is useful to deal with serious distortion in the leading part of FID even though the process is still risky. Otherwise, we suggest no FID shift. But forward LP to extend tail is recommended when the data are recorded too short. |
| Weighting | Could distort data that cannot be recovered later. | Skip this step unless you know data very well and you are sure to improve sensitivity or to enhance resolution. |
| Zero filling | Too many zero additions might change true information. | Zero filling is generally recommended, but it is important to ensure that the ending values are already close to zero and that too many zeros are not added. Otherwise, forward LP is needed before zero filling. |
| Domain transformation | When prior knowledge is not available, and if there are many peaks in the FID, some methods might not work. | In general, FT is the best choice since it does not require additional information and it works well for multiple signals. However, wavelet transform is a better choice when an EC problem exists. |
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| Order | Pre-processing step | Purpose | Examples of software* |
| 1 | Free Induction Decay (FID) conversion | Read FID binary files and convert into text format | TopSpin, SpinWorks, ACD/LABS, NMRPipe, rNMR, Mnova, NMR Metabolomics Quantified |
| 2 | Direct Current (DC) offset removal | Remove DC offsets | TopSpin, SpinWorks, NMRPipe, rNMR |
| 3 | Eddy Current (EC) correction | Estimate and remove EC effect | eddy |
| 4 | FID shift and Linear Prediction (LP) | Remove distorted starting points, apply LP to impute missing points. | TopSpin, SpinWorks, ACD/LABS, NMRPipe, Mnova |
| 5 | Weighting | Multiply a nonlinear function | TopSpin, SpinWorks, ACD/LABS, NMRPipe, rNMR, Mnova, NMR Metabolomics Quantified |
| 6 | Zero filling | Add zeros to the end of FID | TopSpin, SpinWorks, ACD/LABS, NMRPipe, rNMR, Mnova, NMR Metabolomics Quantified |
| 7 | Domain transformation | Transform time domain FID to another domain | TopSpin, SpinWorks, ACD/LABS, NMRPipe, rNMR, Mnova, NMR Metabolomics Quantified |
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