Spectral relative standard deviation: a practical benchmark in metabolomics.
@article{Parsons2009SpectralRS,
title={Spectral relative standard deviation: a practical benchmark in metabolomics.},
author={Helen M. Parsons and Drew R Ekman and Timothy W. Collette and Mark R. Viant},
journal={The Analyst},
year={2009},
volume={134 3},
pages={
478-85
}
}Metabolomics datasets, by definition, comprise of measurements of large numbers of metabolites. Both technical (analytical) and biological factors will induce variation within these measurements that is not consistent across all metabolites. Consequently, criteria are required to assess the reproducibility of metabolomics datasets that are derived from all the detected metabolites. Here we calculate spectrum-wide relative standard deviations (RSDs; also termed coefficient of variation, CV) for…
Tables from this paper
144 Citations
Direct infusion mass spectrometry metabolomics dataset: a benchmark for data processing and quality control
- Computer ScienceScientific data
- 2014
This dataset represents a systematic evaluation of the reproducibility of a multi-batch DIMS metabolomics study of cardiac tissue extracts, designed to test the efficacy of a batch-correction algorithm and will enable others to evaluate novel data processing algorithms.
Between-person comparison of metabolite fitting for NMR-based quantitative metabolomics.
- ChemistryAnalytical chemistry
- 2011
Overall, the effect of the person was less than the experimental group (in this case, sampling method) for almost all of the metabolites, and robust peak assignments are required in advance of manual deconvolution, when the widest range of metabolites is desired.
Characterising and correcting batch variation in an automated direct infusion mass spectrometry (DIMS) metabolomics workflow
- BiologyAnalytical and Bioanalytical Chemistry
- 2013
A purpose-designed, eight-batch DIMS metabolomics study using nanoelectrospray (nESI) Fourier transform ion cyclotron resonance mass spectrometric analyses of mammalian heart extracts is conducted, and a computational workflow that includes total-ion-current filtering, QC-robust spline batch correction and spectral cleaning is developed and implemented that reduces analytical variation and increases the proportion of significant peaks.
Missing values in mass spectrometry based metabolomics: an undervalued step in the data processing pipeline
- Computer ScienceMetabolomics
- 2011
The k-nearest neighbour imputation method (KNN) was identified as the optimal missing value estimation approach for direct infusion mass spectrometry datasets using direct infusion Fourier transform ion cyclotron resonance mass spectromaetry data.
Bioinformatics for mass spectrometry-based metabolomics.
- BiologyMethods in molecular biology
- 2011
This work describes the strategies to translate crude MS information into features characteristics of metabolites, and resources available to guide scientists along the metabolomics pipeline to fulfill increasing appetite for more accurate and larger view of the metabolome while providing sufficient data generation throughput.
Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis
- BiologyCurrent bioinformatics
- 2012
A state-of-the-art overview of the data processing tools available is provided, with their advantages and disadvantages, and comparisons are made to guide the reader.
A modified data normalization method for GC-MS-based metabolomics to minimize batch variation
- Biology, Computer ScienceSpringerPlus
- 2014
This study used a reference sample as a normalization standard for test samples within the same batch, and each metabolite value is expressed as a ratio relative to its counterpart in the reference sample to demonstrate normalization to a single reference standard has the potential to minimize batch-to-batch data variation.
Two-dimensional J-resolved NMR spectroscopy: review of a key methodology in the metabolomics toolbox.
- ChemistryPhytochemical analysis : PCA
- 2010
A basic introduction to the 2D JRES NMR experiment is provided and strategies for spectral acquisition and processing in the context of metabolomics applications are discussed, with some key recommendations: acquisition using a double spin-echo sequence with excitation sculpting; processing using the SEM window function, tilting and symmetricising, optionally followed by a skyline projection.
Understanding the variability of compound quantification from targeted profiling metabolomics of 1D-1H-NMR spectra in synthetic mixtures and urine with additional insights on choice of pulse sequences and robotic sampling
- BiologyMetabolomics
- 2013
This study explores the underlying source of quantification variability (tube insertion, spectra acquisition, and profiling) as well as a number of other factors, such as temporal consistency of repeated NMR scans, human consistency in repeated profiles, and human versus machine sampling.
References
SHOWING 1-10 OF 60 REFERENCES
Normalization method for metabolomics data using optimal selection of multiple internal standards
- BiologyBMC Bioinform.
- 2007
The NOMIS method proved superior in its ability to reduce the effect of systematic error across the full spectrum of metabolite peaks and can be used in analytical development of metabolomics methods by helping to select best combinations of standard compounds for a particular biological matrix and analytical platform.
Improved classification accuracy in 1- and 2-dimensional NMR metabolomics data using the variance stabilising generalised logarithm transformation
- Environmental ScienceBMC Bioinformatics
- 2007
It is demonstrated that the glog and extended glog transforms stabilise the technical variance in NMR metabolomics datasets and improves the discrimination between sample classes and has resulted in higher classification accuracies compared to unscaled, autoscaled or Pareto scaled data.
Analytical precision, biological variation, and mathematical normalization in high data density metabolomics
- BiologyMetabolomics
- 2005
A mathematical approach is developed to normalize this break and use partial least squares projection to latent structure discriminant analysis to confirm validity of this normalization approach, which helps enable longer term high data density studies by removing a critical source of systemic variation.
Evaluation of metabolite extraction strategies from tissue samples using NMR metabolomics
- Chemistry, BiologyMetabolomics
- 2006
Considering both yield and reproducibility of the hydrophilic metabolites as well as recovery of thehydrophobic metabolites, it is concluded that the methanol/chloroform/water extraction is the preferred method.
Improved methods for the acquisition and interpretation of NMR metabolomic data.
- PhysicsBiochemical and biophysical research communications
- 2003
Analytical reproducibility in (1)H NMR-based metabonomic urinalysis.
- BiologyChemical research in toxicology
- 2002
The excellent analytical reproducibility and robustness of metabonomic techniques demonstrated here are highly competitive compared to the best proteomic analyses and are in significant contrast to genomic microarray platforms, both of which are complementary techniques for predictive and mechanistic toxicology.
Solvent-dependent metabolite distribution, clustering, and protein extraction for serum profiling with mass spectrometry.
- Biology, ChemistryAnalytical chemistry
- 2006
Novel data analysis software, XCMS, was used to monitor all metabolite features detected from an array of serum extraction methods, with application to metabolite profiling using electrospray liquid chromatography/mass spectrometry (ESI-LC/MS).
NMR-based metabolomics: a powerful approach for characterizing the effects of environmental stressors on organism health.
- BiologyEnvironmental science & technology
- 2003
This discovery-based approach successfully identified novel metabolic biomarker profiles associated with withering syndrome in red abalone using a metabolomic approach that combines the metabolic profiling capabilities of nuclear magnetic resonance spectroscopy (NMR) with pattern recognition methods.
Direct sampling of organisms from the field and knowledge of their phenotype: key recommendations for environmental metabolomics.
- BiologyEnvironmental science & technology
- 2007
Direct field sampling is recommended for environmental metabolomics since it minimizes metabolic variability and enables stress-induced phenotypic changes to be observed, and it is recommended that species and phenotype of the study organism must be known for meaningful interpretation of metabolomics data.
Evaluation of metabolic variation in normal rat strains from a statistical analysis of 1H NMR spectra of urine.
- Biology, ChemistryJournal of pharmaceutical and biomedical analysis
- 2004
