Bruker nmr spectral data import

bruker-nmr-spectral-data-import

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Summary

Import Bruker NMR spectral data files into an R data frame, then convert to a Spectra object for downstream metabolite identification and quantification. This is a required preprocessing step in the ASICS pipeline for 1H NMR metabolomics analysis.

When to use

You have raw Bruker NMR spectral files (from a Bruker instrument) in a directory and need to prepare them for automated metabolite identification and quantification using ASICS. This step is mandatory before running metabolite quantification, as the Spectra object is the required input format for ASICS analysis.

When NOT to use

• Input spectral data are already in a different format (mzML, NetCDF, text CSV) — use format-specific importers instead
• Data have already been imported and converted to a Spectra object — proceed directly to ASICS quantification
• You are using a non-Bruker NMR instrument or vendor format — this function is specific to Bruker file structures

Inputs

• Bruker NMR spectral data files (raw instrument output in Bruker directory format)
• Directory path to Bruker files (character string)

Outputs

• Data frame with imported spectral data (rows = chemical shift bins, columns = samples)
• Spectra object (S4 class required for downstream ASICS quantification)

How to apply

Load the ASICS R package and use the importSpectraBruker() function to import all Bruker spectral files from a specified directory into a data frame. Specify the full path to the directory containing the Bruker files. Once imported, immediately create a Spectra object from the resulting data frame using the createSpectra() function. This object structure is required by downstream ASICS quantification functions. Verify that the Spectra object contains the expected number of samples and that spectral data are properly formatted before proceeding to quantification.

Related tools

• ASICS (R package providing importSpectraBruker() and createSpectra() functions for Bruker import and Spectra object creation; also performs downstream metabolite identification and quantification) — https://github.com/GaelleLefort/ASICS
• R (Execution environment for ASICS package and all import/preprocessing functions)

Examples

library(ASICS); dir_path <- system.file('example_spectra', package='ASICS'); data_frame <- importSpectraBruker(dir_path); spectra_obj <- createSpectra(data_frame)

Evaluation signals

• Data frame returned by importSpectraBruker() contains numeric matrix with correct dimensions (rows = chemical shift points, columns = number of samples)
• Spectra object is successfully created without errors using createSpectra()
• Spectra object class is confirmed (S4 class with expected slots for spectral data and sample metadata)
• No missing values or NaN entries in the imported spectral intensity data
• Chemical shift scale and spectral range are consistent with expected 1H NMR parameters (e.g., 0–10 ppm typical range)

Limitations

• Function is specific to Bruker instrument file format; incompatible with other vendor formats (Varian, JEOL, Bruker JCAMP-DX)
• Requires correct directory structure as output by Bruker instruments; manually reorganized or corrupted Bruker files may fail to import
• No changelog or version history available in the provided context, limiting traceability of format support changes

Evidence

• [other] Data are imported in a data frame from Bruker files with the importSpectraBruker function: "Data are imported in a data frame from Bruker files with the importSpectraBruker function"
• [other] Spectra object is required step for quantification: "from the data frame, a Spectra object is created. This is a required step for the quantification"
• [other] ASICS enables automated identification and quantification of metabolites in 1H NMR spectra: "fully automated procedure to identify and quantify metabolites in $^1$H 1D-NMR spectra of biological mixtures"
• [other] ASICS is an R package: "The R package ASICS is a fully automated procedure to identify and quantify metabolites"