- Metabolomics approaches
- General introduction
- Metabolic Fingerprinting
- Targeted Metabolomics
- Processing methods
- Quick Tutorial
- 1- Data preparation phase
- 2- View the spectra
- 3 - Interactive data processing
- 4 - Spectra Processing
- 5 - Bucketing
- 6 - Data Export
- 7 - Restore a session
- 8 - Batch mode execution
An easy GUI tool dedicated to 1D NMR spectra processing (1H & 13C)
NMRProcFlow is an open source software that greatly helps spectra processing. It was built by involving NMR spectroscopists eager to have a quick and easy tool to use.
Given the nature of the 1D NMR spectra and due to the diversity of problems encountered during the various stages of processing:
- baseline correction,
- ppm calibration,
- removal of solvents and other contaminants
- re-alignment of areas having high variations in chemical shifts between spectra, ...
and depending on:
- the biological context (humans, plants, micro-organisms),
- the type of sample source (tissue or biofluid like plasma, urine, plant extracts ...),
- the analytical protocol (choice of NMR sequence, use of additives for calibration and / or quantification, use of buffer solution to stabilize pH, etc ...).
It is essential to process this type of data, with an interactive interface that enables spectra visualization.
The expert's eyes are crucial to select the parameters, and to validate the treatments
Apart for very well-mastered and very reproducible use cases (see Batch mode execution), the implementation of NMR spectra processing workflows executed in batch mode (regarding as a black-box) seems to us very hazardous, and can produce output aberrations. So, it is crucial to proceed in an interactive way with a NMR spectra viewer to allow the expert eye to disentangle the intertwined peaks.
Major concerns having (initially) motivated the design and having served as a roadmap :
- Ease the data preparation phase in order to be loaded via the web interface
- View the spectra according to the experimental conditions, or separately,
- Allow user to apply interactive data processing procedures to all the spectra, either to the whole ppm range with the same set of parameters or to only a selected ppm range with specific set of parameters for each ppm range,
- Export a data matrix to establish statistical analysis ( (un)targeted approaches) with a statistical tool (such as BioStatFlow, MetaboAnalyst ...) so that the file manipulations are minimized.
- Allow user to replay the same processing workflow (e.g. few months later) on the same dataset or a similar one
NMRProcFlow open source software provides a complete set of tools for processing and visualizing of 1D NMR data, within an interactive interface based on a spectra visualization.