Source-linked AI summary
NMRProcFlow: A graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics
Daniel Jacob, Catherine Deborde, Marie Lefebvre, Mickael Maucourt, Anick Moing
TL;DR
Because 1D NMR metabolomics processing often requires expert visual interpretation, NMRProcFlow provides an interactive graphical tool that displays spectra alongside experimental-factor levels. The authors report that this visualization links experimental design with subsequent statistical analyses and facilitates interaction between biologists and NMR spectroscopists.
Problem
Automatic phasing across diverse sample sources and analytical protocols was considered unsatisfactory without manual readjustment.
Source: Results and Discussion · p. 4Method
NMRProcFlow is an interactive graphical 1D NMR processing tool whose viewer displays spectra alongside experimental-factor levels.
Source: Results and Discussion · p. 3, Figure Captions · p. 7Results
The authors report that visualizing factor levels within spectra links experimental design with subsequent statistical analyses and facilitates interaction between biologists and NMR spectroscopists.
Source: Results and Discussion · p. 3Takeaways & Limitations
For metabolic fingerprinting, NMRProcFlow exports data matrices compatible with online statistical tools including BioStatFlow and MetaboAnalyst 3.0.
Source: Results and Discussion · p. 5The current version accepts only pre-processed raw spectra in Bruker format, requiring Fourier transform and phase correction beforehand.
Source: Results and Discussion · p. 3
Abstract
from arXiv · showhide
Concerning NMR-based metabolomics, 1D spectra processing often requires an expert eye for disentangling the intertwined peaks, and so far the best way is to proceed interactively with a spectra viewer. NMRProcFlow is a graphical and interactive 1D NMR (1H \& 13C) spectra processing tool dedicated to metabolic fingerprinting and targeted metabolomic, covering all spectra processing steps including baseline correction, chemical shift calibration, alignment. It does not require programming skills. Biologists and NMR spectroscopists can easily interact and develop synergies by visualizing the NMR spectra along with their corresponding experimental-factor levels, thus setting a bridge between experimental design and subsequent statistical analyses.
Keywords
The paper’s keywords are NMR-based metabolomics, NMR viewer, spectra processing, and graphical user interface.
Keywords
- The listed keywords are NMR-based metabolomics, NMR viewer, spectra processing, and Graphical Unit Interface.Source: Keywords · p. 1
Introduction
Growing volumes of data from high-throughput OMICS techniques have prompted a trend toward more automated processing.
- Growing high-throughput OMICS data volumes have prompted a trend toward processing data as automatically as possible.Source: Introduction · p. 2
Implementation
NMRProcFlow is implemented as two Dockerized applications that share data and communicate through AJAX web services. Its processing and viewing components use distinct technologies, while online and virtual-appliance deployment options support users who prefer not to install the software or need local data security.
Implementation
- NMRspec and NMRviewer run as separate Dockerized applications, sharing a data volume and communicating through AJAX web services.Docker was chosen to facilitate software setup.Source: Implementation · p. 2
- NMRspec is primarily implemented in R (R Core Team 2013), with some algorithms in C++ via Rcpp in the Rnmr1D module; its GUI uses event-driven R Shiny.Source: Implementation · p. 3
- NMRviewer uses a client-server architecture, storing spectra as binary data and generating PNG images directly with Gnuplot to minimize data reading, writing, and transfers.The binary-data approach avoids time-consuming text-to-binary conversion.Source: Implementation · p. 3
- NMRProcFlow is available online to avoid installation and as virtual appliances for VMware and VirtualBox to support local setup and protect confidential data.The passage gives clinical data as an example of confidential data.Source: Implementation · p. 3
Results and Discussion
NMRProcFlow combines interactive 1D NMR viewing and processing with workflows for targeted and fingerprinting metabolomics. It links spectra to experimental factors and supports processing through export of data for quantification or statistical analysis.
Results and Discussion
- The interactive viewer overlays or stacks spectra, colors them by experimental-factor levels, and applies region-specific processing to full datasets or factor-level subsets.Unlike the compared GUI tools, it supports specifying factor levels in the viewer and capturing ppm regions for processing; users can choose alignment methods suited to each region, including Parametric Time Warping when peak counts match.Source: Results and Discussion · p. 3
- NMRProcFlow accepts pre-processed Bruker spectra; automatic phasing is not included, while spectra acquired with different pulse sequences can be compared.Pre-processing requires Fourier transform and phase correction; the authors planned future nmrML support. They note that automatic phasing may require manual adjustment across diverse samples and protocols.Source: Results and Discussion · pp. 3–4
- For targeted metabolomics, users select ppm ranges for integration and locally correct baseline to reduce macromolecule effects and intense-peak interference in neighboring regions.The qHNMR workbook combines sample, bucket, SNR, data-matrix, and pre-calculated quantification tabs; editing default sample or bucket information updates quantifications.Source: Results and Discussion · p. 4
- For metabolic fingerprinting, Adaptive Intelligent Binning recursively identifies bin edges, addressing information loss and shift artifacts of equal-width bins (up to 0.05 ppm; Cloarec et al. 2005; De Meyer et al. 2008).The algorithm requires minimal user input and avoids arbitrary parameters or reference spectra.Source: Results and Discussion · p. 4
- Buckets can be filtered by Signal-to-Noise ratio during computation or at output, and exported matrices are compatible with BioStatFlow and MetaboAnalyst 3.0.The SNR filtering option was used in previous collaborative work.Source: Results and Discussion · pp. 4–5
- Experts can build reusable processing workflows interactively, then run them in batch on similar spectra sets or reproducible use cases following the same SOPs.Batch execution is available through a command-line tool or workflow-management systems, including Workflow4Metabolomics.Source: Results and Discussion · p. 5
Figure Captions
The captions identify NMRProcFlow’s interactive, visualization-based workflow for 1D NMR processing and note that its implementation comprises two applications.
- The captions describe an interactive, visualization-based workflow for 1D NMR processing and an implementation comprising two applications.Source: Figure Captions · p. 7
Supplementary Information
NMRProcFlow’s online documentation supplements the article with detailed feature descriptions and help on issues not covered there. A shortcut list provides quick access to viewer demonstrations and resources for processing methods and workflows.
Supplementary Information
- The online documentation offers detailed feature descriptions and help on issues not covered in the article.The article presents a shortcut list to help readers quickly access specific supplementary items.Source: Supplementary Information · p. 8
- S1 links to the spectra viewer and an online test of the viewer.The links are provided at nmrprocflow.org/c2 and nmrprocflow.org/testviewer.Source: Supplementary Information · p. 8
- The shortcuts link resources on alignment, baseline correction, targeted metabolomics, intelligent bucketing and fingerprinting, SNR, and batch workflow replay.They include a comparison of Least-Square and Parametric Time Warping, global and local baseline correction examples, and a quantification spreadsheet workbook.Source: Supplementary Information · p. 8