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 Experiment Videos

Computing positional isotopomer distributions from tandem mass spectrometric data.

Ari Rantanen1, Juho Rousu, Juha T Kokkonen

  • 1Department of Computer Science, FIN-00014 University of Helsinki, Finland. ari.rantanen@cs.helsinki.fi

Metabolic Engineering
|March 21, 2003
PubMed
Summary

Positional isotopomer distributions (PID) can be discovered using tandem mass spectrometry. However, amino acid fragmentation limits exact PID determination in metabolic flux analysis.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

Predicting drug combination response surfaces.

npj drug discovery·2026
Same author

A cross-attentive multi-task graph learning framework for chemical reaction modeling.

Bioinformatics (Oxford, England)·2026
Same author

Advantage of analysing drug paraphernalia in cause-of-death investigations.

Forensic science international·2026
Same author

Extracting a COVID-19 signature from a multi-omic dataset.

Frontiers in bioinformatics·2025
Same author

Comprehensive interaction modeling with machine learning improves prediction of disease risk in the UK Biobank.

Nature communications·2025
Same author

CSGL: chemical synthesis graph learning for molecule representation.

Bioinformatics (Oxford, England)·2025

Area of Science:

  • Metabolomics
  • Systems Biology
  • Analytical Chemistry

Background:

  • Metabolite isotopomer distributions are crucial for metabolic flux analysis.
  • Tandem mass spectrometry (MS/MS) is a key technology in metabolomics.
  • Positional isotopomer distributions (PID) offer detailed metabolic information.

Purpose of the Study:

  • To describe the application of MS/MS with daughter ion scanning for PID discovery.
  • To evaluate the practical utility of this technique in metabolic flux computation.

Main Methods:

  • Utilized tandem mass spectrometry with daughter ion scanning.
  • Developed computational methods implemented in MATLAB (PIDC).
  • Investigated amino acid fragmentation patterns in MS/MS.

Related Experiment Videos

Main Results:

  • Daughter ion scanning provides more information than full scanning for PID.
  • Amino acid fragmentation limitations prevent exact PID determination in practice.
  • A MATLAB application, PIDC, was developed for PID calculation.

Conclusions:

  • MS/MS with daughter ion scanning is a promising technique for PID discovery.
  • Practical limitations in fragmentation currently hinder precise PID determination.
  • Further advancements are needed for accurate metabolic flux analysis using PID.