Description

This article explains how to improve macro settings in Spectrus Processor when processing noisy 1D NMR spectra. Use these recommendations when you need to automate peak picking, peak fitting, and integration across large datasets and cannot manually review every spectrum.

Solution

For low-quality or noisy 1D NMR data, add some processing steps prior to peak picking. An exponential weighting function, smoothing, and baseline correction can reduce noise-related artifacts and improve automated peak detection and fitting. For very noisy data, a higher line broadening value (recommended value:10 or 20) may help reduce noise, but it can also lower spectral resolution. Always test settings on representative spectra before using them for batch processing.

Recommended approach for noisy NMR data used in targeted profiling:

• Apply some pre-processing steps, such as an exponential weighting function, smoothing, and baseline correction. These steps can reduce noise-related artifacts and improve the reliability of automated peak detection and fitting.
• Focus the analysis on spectral regions with clearer and more informative signals instead of fitting the entire spectrum at once.
• Use stricter peak picking parameters to reduce detections caused by noise, such as increasing the noise factor or minimum signal-to-noise requirement.
• Limit the chemical shift range when possible so the macro evaluates only relevant regions.
• Use automatic peak fitting conservatively in regions where peaks are well resolved.
• Validate the macro on a representative subset of spectra before applying it to the complete dataset.

Example macro settings for noisy spectra:

Use the example below as a starting point. Adjust the parameters based on your data, and validate the results before batch processing.

FT(Operation = "Default") - applies Fourier Transform to FID
WindowFunction (Method = "Exponential"; LB = 10.0000) — applies an exponential weighting function.
BaseLine (Range = Full; Method = "Polynomial"; Order = 4) — applies baseline correction.
Smoothing (Order = "3"; Points = "5") — applies smoothing.
PeakPicking (Range = -1.7394..100; NoiseFactor = 30; Threshold = "SignalNoise"; MinSN = 5; PosPeaks = True; NegPeaks = False; EqualPosition = False; UseDerivation = False; UsePeakFiting = FALSE; IgnoreBroadWaterPeakBase = FALSE) — uses stricter peak picking for noisy regions.
PeakPicking (Range = 100..220; NoiseFactor = 8; Threshold = "SignalNoise"; MinSN = 8; PosPeaks = True; NegPeaks = False; EqualPosition = False; UseDerivation = False; UsePeakFiting = FALSE; IgnoreBroadWaterPeakBase = FALSE) — uses a separate peak picking command for higher chemical shift regions, if needed.
PeakFittingAuto (Range = Full; Function = "Gauss+Lorentz"; DefWidth = 0.7; DefLF = 0.5; VPos = 5; WidthRange = 1..1000; FitExt = 1; Tol = 5; MaxIt = 200) — applies automatic peak fitting. Use this only after confirming that the detected peaks represent real signals.
Integration (Method = "Auto"; DetectSign = True; NegSign = False; NoiseFactor = 10.0000; RefValue = 100.0000; RefType = "AllIntegrals"; CalibrationRange = 0..1; MinVolumePercent = 0.0000) — applies automatic integration settings for the selected region.

Use the workflow below to create or update a 1D NMR macro for automated processing:

1. Open the Macro Organizer using one of these methods: 
   Go to File > Macro > Organizer 
   
   Or click Organizer on the Macro toolbar. 
   
    
2. In the Macro Organizer dialog box, click New... to create a macro, or click Edit... to update an existing macro. For a 1D NMR macro, change the data type from ANY to 1D NMR.
3. In the Edit Macro dialog box, click Insert Macro Command. The Insert New Command dialog box opens and shows the available macro commands.
4. Select the command you want to add, and then click OK. The Edit Command: <CommandName> dialog box opens and shows the available settings for that command.
   
   Tip: If you are not familiar with the command line, perform the required actions in the Spectrus interface first. Then review the recorded actions in View > History. You can also create a macro from the recorded history.
   
5. Enter the required settings, and then click OK to add the command to the macro. To change command settings later, double-click the command in the macro command list.
   
6. Repeat the previous steps until you have added all required commands.
7. Click Settings, choose the macro execution options in the Macro Settings dialog box, and then click OK.
   
8. When the macro is ready, click OK. 
   Important: If you plan to apply the macro to a group of spectra, the macro must include at least one command that creates or saves an output. Examples include CopyToSketch, CopyToWindow, DatabaseLists, Execute, ExecuteChembasicApp, ExportDocument, ExportReportToPDF, ExportTable, Print, SaveDocument, or UpdateCurrentDatabase. Without one of these commands, you may not be able to view the results.
9. In the Save Macro File As dialog box, enter a name and location for the macro file (*.mcr), and then click Save. The macro is saved and the Edit Macro dialog box closes.
10. To use an existing *.mcr file, click Add... in the Macro Organizer dialog box, browse to the file, and select it. 
11. To show the macro on the Macro toolbar, make sure the checkbox next to the macro name is selected.