Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Mass Spectrometry: Complex Analysis

Mass Spectrometry: Complex Analysis

Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...

You might also read

Related Articles

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

Sort by

Same author

Hydrogen-Deuterium Back-Exchange for High-Resolution Mass-Spectrometry-Based Metabolite Characterization.

Analytical chemistry·2026

Same author

Reply to Z Yu and F Qin.

The American journal of clinical nutrition·2026

Same author

Enhancing Clinical Note Generation with ICD-10, Clinical Ontology Knowledge Graphs, and Chain-of-Thought Prompting Using GPT-4.

Journal of computational biology : a journal of computational molecular cell biology·2026

Same author

A Qualitative Assessment of Preoperative Educational Needs Among Adolescent Metabolic and Bariatric Surgery Patients and Parents or Guardians.

Childhood obesity (Print)·2026

Same author

Ontology-Aligned Representation of Adverse Events in a Multiple Myeloma Clinical Trial.

Studies in health technology and informatics·2026

Same author

Generation of Interactive Knowledge Graphs to Enable Research of the Effects of Trauma Center Organization on Patient Outcomes.

Knowledge graphs and semantic web : 7th international conference, KGSWC 2025, Leipzig, Germany, November 26-28, 2025 : proceedings. KGSWC (Conference) (7th : 2025 : Leipzig, Germany)·2026

Search research articles

Related Experiment Video

Updated: Jun 22, 2026

A Strategy for Sensitive, Large Scale Quantitative Metabolomics

A Strategy for Sensitive, Large Scale Quantitative Metabolomics

Published on: May 27, 2014

An Automated Workflow Composition System for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing.

Xinsong Du^1,2, Farhad Dastmalchi³, Matthew A Diller³

¹Division of General Internal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.

Journal of the American Society for Mass Spectrometry

|October 24, 2023

Summary

Automated workflow composition (AWC) systems can streamline liquid chromatography-mass spectrometry (LC-MS) metabolomics data processing. This study demonstrates AWC feasibility, generating novel and executable workflows for complex biological data analysis.

More Related Videos

2 in 1: One-step Affinity Purification for the Parallel Analysis of Protein-Protein and Protein-Metabolite Complexes

2 in 1: One-step Affinity Purification for the Parallel Analysis of Protein-Protein and Protein-Metabolite Complexes

Published on: August 6, 2018

An Integrated Workflow of Identification and Quantification on FDR Control-Based Untargeted Metabolome

An Integrated Workflow of Identification and Quantification on FDR Control-Based Untargeted Metabolome

Published on: September 20, 2022

Related Experiment Videos

Last Updated: Jun 22, 2026

A Strategy for Sensitive, Large Scale Quantitative Metabolomics

A Strategy for Sensitive, Large Scale Quantitative Metabolomics

Published on: May 27, 2014

2 in 1: One-step Affinity Purification for the Parallel Analysis of Protein-Protein and Protein-Metabolite Complexes

2 in 1: One-step Affinity Purification for the Parallel Analysis of Protein-Protein and Protein-Metabolite Complexes

Published on: August 6, 2018

An Integrated Workflow of Identification and Quantification on FDR Control-Based Untargeted Metabolome

An Integrated Workflow of Identification and Quantification on FDR Control-Based Untargeted Metabolome

Published on: September 20, 2022

Area of Science:

Computational Biology
Bioinformatics
Analytical Chemistry

Background:

Liquid chromatography-mass spectrometry (LC-MS) metabolomics generates high-dimensional data requiring complex informatics for analysis.
Developing customized computational workflows for LC-MS metabolomics data processing presents a significant challenge for researchers.
Ontology-based automated workflow composition (AWC) offers a promising solution for creating adaptable computational pipelines.

Purpose of the Study:

To assess the feasibility of using an ontology-based AWC system for LC-MS metabolomics data processing.
To develop and evaluate computational workflows for high-dimensional metabolomics data using the Automated Pipeline Explorer (APE).

Main Methods:

Utilized the Automated Pipeline Explorer (APE) to construct an AWC system tailored for LC-MS metabolomics data.
Applied the AWC system across three distinct use cases to predict data processing workflows.
Performed manual review and assessed the executability and computational viability of the generated workflows.

Main Results:

APE predicted a total of 145 data processing workflows across the three use cases.
Identified six traditional and six novel workflows, with one-third of novel workflows found to be executable.
Achieved a 45% computational viability rate for predicted workflows when selecting the top six per use case.

Conclusions:

The study successfully demonstrates the feasibility of developing an AWC system for automating LC-MS metabolomics data processing.
Ontology-based AWC systems like APE can generate both novel and executable workflows, simplifying complex data analysis.
This approach has the potential to enhance efficiency and reproducibility in metabolomics research.