Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

1.9K
Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and signal-to-noise ratio for the analyte. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.
Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called collision-induced...
1.9K
MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

6.1K
Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.
Matrix-assisted laser desorption ionization (MALDI) is a commonly...
6.1K
Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

7.7K
Mass spectrometry is an analytical technique used to determine the molecular mass and molecular formula of a compound. The basic principle of mass spectrometry is to generate ions from the analyte molecule and measure these ion abundances against their molecular mass.  One common type of ionization, known as electrospray ionization or EI, bombards the analyte molecules in the gas phase with high-energy electron beams. The electron beams displace an electron from the molecule and leave...
7.7K
Mass Spectrometers01:16

Mass Spectrometers

7.7K
This lesson details the instrumentation of a mass spectrometer—a physical instrument to perform mass spectrometry on analyte molecules and record the characteristic mass spectra. This is achieved via three chief functions:
7.7K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Embrace Open, Collaborative, Discovery-Based Exposomics.

Environmental science & technology·2026
Same author

Mood Altering Waters: Multidimensional Profiling and Chiral Characterization of Antidepressants in Effluent-Impacted Waterways.

Environmental science & technology·2026
Same author

Browsing FAIR Transformation Product Information with FAIR-TPs.

ACS environmental Au·2026
Same author

Identification of persistent substructures in transformation products with zebrafish embryos using cheminformatics and a suspect screening approach.

Environmental science. Processes & impacts·2026
Same author

Mapping the human chemical exposome for public health.

Nature medicine·2026
Same author

MassBank: an open and FAIR mass spectral data resource.

Nucleic acids research·2025

Related Experiment Video

Updated: Nov 22, 2025

Identifying Per- and Polyfluorinated Chemical Species with a Combined Targeted and Non-Targeted-Screening High-Resolution Mass Spectrometry Workflow
09:04

Identifying Per- and Polyfluorinated Chemical Species with a Combined Targeted and Non-Targeted-Screening High-Resolution Mass Spectrometry Workflow

Published on: April 18, 2019

12.8K

patRoon: open source software platform for environmental mass spectrometry based non-target screening.

Rick Helmus1, Thomas L Ter Laak2,3, Annemarie P van Wezel2

  • 1Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands. r.helmus@uva.nl.

Journal of Cheminformatics
|January 7, 2021
PubMed
Summary

A new R-based open-source software, patRoon, simplifies environmental non-target analysis. It offers comprehensive workflows, harmonizes tools, and automates data processing for efficient chemical identification in complex samples.

Keywords:
Compound identificationComputational workflowsHigh resolution mass spectrometryNon-target analysis

More Related Videos

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry UPLC-MS
07:34

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry UPLC-MS

Published on: March 14, 2013

13.1K
Leaf Spray Mass Spectrometry: A Rapid Ambient Ionization Technique to Directly Assess Metabolites from Plant Tissues
06:43

Leaf Spray Mass Spectrometry: A Rapid Ambient Ionization Technique to Directly Assess Metabolites from Plant Tissues

Published on: June 21, 2018

8.9K

Related Experiment Videos

Last Updated: Nov 22, 2025

Identifying Per- and Polyfluorinated Chemical Species with a Combined Targeted and Non-Targeted-Screening High-Resolution Mass Spectrometry Workflow
09:04

Identifying Per- and Polyfluorinated Chemical Species with a Combined Targeted and Non-Targeted-Screening High-Resolution Mass Spectrometry Workflow

Published on: April 18, 2019

12.8K
Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry UPLC-MS
07:34

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry UPLC-MS

Published on: March 14, 2013

13.1K
Leaf Spray Mass Spectrometry: A Rapid Ambient Ionization Technique to Directly Assess Metabolites from Plant Tissues
06:43

Leaf Spray Mass Spectrometry: A Rapid Ambient Ionization Technique to Directly Assess Metabolites from Plant Tissues

Published on: June 21, 2018

8.9K

Area of Science:

  • Environmental chemistry
  • Analytical chemistry
  • Computational chemistry

Background:

  • Mass spectrometry-based non-target analysis is crucial for identifying chemicals in environmental samples.
  • Existing software often lacks environmental-specific functionality, is not open-source, or has limited data format compatibility.

Purpose of the Study:

  • To introduce patRoon, a novel R-based open-source software platform for comprehensive non-target analysis in environmental sciences.
  • To provide a streamlined, automated, and efficient workflow for processing complex environmental data.

Main Methods:

  • Development of patRoon, an R-based platform integrating various open-source tools.
  • Implementation of optimization strategies to reduce computational time.
  • Demonstration using open-access data from a drinking water treatment plant study.

Main Results:

  • patRoon offers a comprehensive, tailored, and straightforward non-target analysis workflow.
  • The platform seamlessly integrates and evaluates different algorithms.
  • Automated processing and time-efficient data annotation of environmental samples were demonstrated.

Conclusions:

  • patRoon makes advanced environmental non-target analysis more accessible to researchers.
  • The software facilitates the use, evaluation, and combination of analytical algorithms.
  • It addresses limitations of current software for environmental chemical analysis.