ArticleJournal of cheminformatics2021
patRoon: open source software platform for environmental mass spectrometry based non-target screening.
Article in Journal of cheminformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 1 of them a synthesis that pooled it.
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Who cites it
55 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
- Streamlining feature elaboration and statistics analysis in metabolomics: the GetFeatistics R-package.Journal of integrative bioinformatics · 2026Article
- Metabonaut: an open educational resource for learning reproducible, script-based untargeted LC-MS/MS metabolomics.Metabolomics : Official journal of the Metabolomic Society · 2026Review
- pyMSscreen: an interactive interface for automated quality control and prescreening in mass spectrometry workflows.Journal of cheminformatics · 2026Article
- Differentiation of White and Red Galangal Rhizomes by Pseudo-Targeted LC-MS/MS Metabolomics.Chemistry & biodiversity · 2026Article
- Browsing FAIR Transformation Product Information with FAIR-TPs.ACS environmental Au · 2026Article
- Persistence Assessment of Chemicals: Trajectories toward New Approach Methodologies (P-NAMs).Environmental science & technology · 2026Review
- Tracking the Metabolites of Health and Disease Using Artificial Intelligence.Diseases (Basel, Switzerland) · 2026Review
- MassBank: an open and FAIR mass spectral data resource.Nucleic acids research · 2026Article
- Dynamic expression of the zebrafish (Danio rerio) proteome across early larval development.Comparative biochemistry and physiology. Part D, Genomics & proteomics · 2025Article
- Not One Method to Rule Them All: A Comparative Study of Chromatographic Platforms (RP-LC-, HILIC-, SFC-, and IC-HRMS) for Water Analysis.Analytical chemistry · 2025Article
- A stochastic approach for parameter optimization of feature detection algorithms for non-target screening in mass spectrometry.Analytical and bioanalytical chemistry · 2025Article
- Leveraging open cheminformatics tools for non-targeted metabolomics analysis of C. elegans: a workflow comparison and application to strains related to xenobiotic metabolism and neurodegeneration.Analytical and bioanalytical chemistry · 2025Article
- Unraveling non-target screening variability for LC-HRMS data: a chemometric comparative analysis of river water samples impacted by treated wastewater.Analytical and bioanalytical chemistry · 2025Article
- Review
- Practical Guidance on Selecting Analytical Methods for PFAS in Semiconductor Manufacturing Wastewater.ACS measurement science au · 2025Review
- Improving Regions of Interest Multivariate Curve Resolution: Development of an Empirical Metric System through the Study of Passive Sampling Extracts of Wastewater in Antarctica.Analytical chemistry · 2025Article
- Shinyscreen: mass spectrometry data inspection and quality checking utility.Journal of cheminformatics · 2025Article
- [A review and research prospects on the application of the XCMS mass-spectrometry data-processing software in the environmental science field].Se pu = Chinese journal of chromatography · 2025Review
- Prioritization of Unknown LC-HRMS Features Based on Predicted Toxicity Categories.Environmental science & technology · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Mass spectrometry based non-target analysis is increasingly adopted in environmental sciences to screen and identify numerous chemicals simultaneously in highly complex samples. However, current data processing software either lack functionality for environmental sciences, solve only part of the workflow, are not openly available and/or are restricted in input data formats. In this paper we present patRoon, a new R based open-source software platform, which provides comprehensive, fully tailored and straightforward non-target analysis workflows. This platform makes the use, evaluation and mixing of well-tested algorithms seamless by harmonizing various common (primarily open) software tools under a consistent interface. In addition, patRoon offers various functionality and strategies to simplify and perform automated processing of complex (environmental) data effectively. patRoon implements several effective optimization strategies to significantly reduce computational times. The ability of patRoon to perform time-efficient and automated non-target data annotation of environmental samples is demonstrated with a simple and reproducible workflow using open-access data of spiked samples from a drinking water treatment plant study. In addition, the ability to easily use, combine and evaluate different algorithms was demonstrated for three commonly used feature finding algorithms. This article, combined with already published works, demonstrate that patRoon helps make comprehensive (environmental) non-target analysis readily accessible to a wider community of researchers.
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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.