ArticleBioinformatics (Oxford, England)2016
Warpgroup: increased precision of metabolomic data processing by consensus integration bound analysis.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research software.Metabolomics : Official journal of the Metabolomic Society · 2023Pooled it
- PeakDetective: A Semisupervised Deep Learning-Based Approach for Peak Curation in Untargeted Metabolomics.Analytical chemistry · 2023Article
- A Protocol for Untargeted Metabolomic Analysis: From Sample Preparation to Data Processing.Methods in molecular biology (Clifton, N.J.) · 2021Article
- MetaClean: a machine learning-based classifier for reduced false positive peak detection in untargeted LC-MS metabolomics data.Metabolomics : Official journal of the Metabolomic Society · 2020Article
- Chemical Discovery in the Era of Metabolomics.Journal of the American Chemical Society · 2020Review
- The ABRF Metabolomics Research Group 2016 Exploratory Study: Investigation of Data Analysis Methods for Untargeted Metabolomics.Metabolites · 2020Article
- The metaRbolomics Toolbox in Bioconductor and beyond.Metabolites · 2019Review
- Hepatocyte-Macrophage Acetoacetate Shuttle Protects against Tissue Fibrosis.Cell metabolism · 2019Article
- Analytical Methods for Detection of Plant Metabolomes Changes in Response to Biotic and Abiotic Stresses.International journal of molecular sciences · 2019Review
- Trace Phosphate Improves ZIC-pHILIC Peak Shape, Sensitivity, and Coverage for Untargeted Metabolomics.Journal of proteome research · 2018Article
- Sorting cells alters their redox state and cellular metabolome.Redox biology · 2018Article
- LipiDex: An Integrated Software Package for High-Confidence Lipid Identification.Cell systems · 2018Article
- Two complementary reversed-phase separations for comprehensive coverage of the semipolar and nonpolar metabolome.Analytical and bioanalytical chemistry · 2018Article
- Systems-Level Annotation of a Metabolomics Data Set Reduces 25 000 Features to Fewer than 1000 Unique Metabolites.Analytical chemistry · 2017Article
- The evolution of lipidomics through space and time.Biochimica et biophysica acta. Molecular and cell biology of lipids · 2017Review
- Computational Metabolomics: A Framework for the Million Metabolome.Chemical research in toxicology · 2016Review
- Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats.Analytical chemistry · 2016Article
- Lactate metabolism is associated with mammalian mitochondria.Nature chemical biology · 2016Article
- Inaccurate quantitation of palmitate in metabolomics and isotope tracer studies due to plastics.Metabolomics : Official journal of the Metabolomic Society · 2016Article
- Bar Coding MS(2) Spectra for Metabolite Identification.Analytical chemistry · 2016Article
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Authors and funding
3 authors.
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Abstract
motivationCurrent informatic techniques for processing raw chromatography/mass spectrometry data break down under several common, non-ideal conditions. Importantly, hydrophilic liquid interaction chromatography (a key separation technology for metabolomics) produces data which are especially challenging to process. We identify three critical points of failure in current informatic workflows: compound specific drift, integration region variance, and naive missing value imputation. We implement the Warpgroup algorithm to address these challenges.
resultsWarpgroup adds peak subregion detection, consensus integration bound detection, and intelligent missing value imputation steps to the conventional informatic workflow. When compared with the conventional workflow, Warpgroup made major improvements to the processed data. The coefficient of variation for peaks detected in replicate injections of a complex Escherichia Coli extract were halved (a reduction of 19%). Integration regions across samples were much more robust. Additionally, many signals lost by the conventional workflow were 'rescued' by the Warpgroup refinement, thereby resulting in greater analyte coverage in the processed data. AVAILABILITY AND: I: MPLEMENTATION: Warpgroup is an open source R package available on GitHub at github.com/nathaniel-mahieu/warpgroup. The package includes example data and XCMS compatibility wrappers for ease of use. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: nathaniel.mahieu@wustl.edu or gjpattij@wustl.edu.
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