ArticlePLoS computational biology2020
ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- MIMI: Molecular Isotope Mass Identifier for stable isotope-labeled Fourier transform ultra-high mass resolution data analysis.BMC bioinformatics · 2026Article
- Molecular diversity of dissolved organic matter reflects macroecological patterns in river networks.Scientific reports · 2025Article
- Article
- Decomposing the molecular complexity and transformation of dissolved organic matter for innovative anaerobic bioprocessing.Nature communications · 2025Article
- FREDA: A Web Application for the Processing, Analysis, and Visualization of Fourier-Transform Mass Spectrometry Data.Rapid communications in mass spectrometry : RCM · 2025Article
- Organic molecules are deterministically assembled in variably inundated river sediments, but drivers remain unclear.Scientific reports · 2025Article
- Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient.Nature microbiology · 2024Article
- Article
- Thermal responses of dissolved organic matter under global change.Nature communications · 2024Article
- Rethinking Aerobic Respiration in the Hyporheic Zone under Variation in Carbon and Nitrogen Stoichiometry.Environmental science & technology · 2023Article
- MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data.Microbiome · 2023Article
- New algorithms demonstrate untargeted detection of chemically meaningful changing units and formula assignment for HRMS data of polymeric mixtures in the open-source constellation web application.Journal of cheminformatics · 2023Article
- Wildfire-dependent changes in soil microbiome diversity and function.Nature microbiology · 2022Article
- Ecological networks of dissolved organic matter and microorganisms under global change.Nature communications · 2022Article
- Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly.Frontiers in microbiology · 2022Article
- Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives.Life (Basel, Switzerland) · 2021Review
- Article
- Using metacommunity ecology to understand environmental metabolomes.Nature communications · 2020Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The high-resolution and mass accuracy of Fourier transform mass spectrometry (FT-MS) has made it an increasingly popular technique for discerning the composition of soil, plant and aquatic samples containing complex mixtures of proteins, carbohydrates, lipids, lignins, hydrocarbons, phytochemicals and other compounds. Thus, there is a growing demand for informatics tools to analyze FT-MS data that will aid investigators seeking to understand the availability of carbon compounds to biotic and abiotic oxidation and to compare fundamental chemical properties of complex samples across groups. We present ftmsRanalysis, an R package which provides an extensive collection of data formatting and processing, filtering, visualization, and sample and group comparison functionalities. The package provides a suite of plotting methods and enables expedient, flexible and interactive visualization of complex datasets through functions which link to a powerful and interactive visualization user interface, Trelliscope. Example analysis using FT-MS data from a soil microbiology study demonstrates the core functionality of the package and highlights the capabilities for producing interactive visualizations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.