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Related Concept Videos

Mass Analyzers: Overview01:13

Mass Analyzers: Overview

The mass analyzer is a crucial component of the mass spectrometer. In the ionization chamber, the vaporized sample is bombarded with a high-energy electron beam to generate a radical cation and further fragment into neutral molecules, radicals, and cations. A series of negatively charged accelerator plates accelerate the cations into the mass analyzer. The mass analyzer separates ions according to their mass-to-charge (m/z) ratios and then directs them to the detector. The common types of mass...
C4 Pathway and CAM01:27

C4 Pathway and CAM

Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
C4 Pathway
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Mitochondrial Protein Sorting01:39

Mitochondrial Protein Sorting

Mitochondria are double-membrane organelles of the eukaryotes involved in cellular metabolism, signaling, ATP synthesis, and programmed cell death.  Each of these processes requires specific proteins and enzymes that must be correctly sorted to the right mitochondrial subcompartment for the proper functioning of the organelle.
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Cotranslational Protein Translocation01:20

Cotranslational Protein Translocation

Translocation of proteins across membranes is an ancient process that occurs even in bacteria and archaebacteria. In fact, the components of the translocation machinery are still conserved between prokaryotes and eukaryotes.
Sec61 channel partners for cotranslational translocation
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Indirect Motor Pathways01:22

Indirect Motor Pathways

The indirect motor or extrapyramidal pathways originate in the brainstem, the lower portion of the brain that connects it to the spinal cord. They consist of several distinct tracts, each with specialized functions. The four main tracts of the indirect motor pathways are the vestibulospinal tract, the reticulospinal tract, the tectospinal tract, and the rubrospinal tract.
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Direct Motor Pathways

The direct motor pathways, also known as the pyramidal tracts, are a group of neural pathways that originate in the brain and descend through the spinal cord. They control the voluntary movement of the body. There are two major direct motor pathways: the corticospinal and the corticobulbar tracts.
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Updated: Jul 5, 2026

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
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A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

MassTRIX: mass translator into pathways.

Karsten Suhre1, Philippe Schmitt-Kopplin

  • 1Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany. karsten.suhre@helmholtz-muenchen.de

Nucleic Acids Research
|April 30, 2008
PubMed
Summary
This summary is machine-generated.

Mass spectrometry (MS) advances enable precise metabolomics detection, but metabolite annotation remains challenging. MassTRIX offers a genomic context approach for accurate high-precision MS data annotation, integrating biological information for better interpretation.

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Area of Science:

  • Metabolomics
  • Bioinformatics
  • Systems Biology

Background:

  • Recent advances in mass spectrometry (MS) allow for precise detection of numerous metabolites in various organisms.
  • Accurate metabolite annotation based on measured masses is a significant challenge in metabolomics.
  • Existing methods often lack biological and genomic context, leading to uncertain metabolite identification.

Purpose of the Study:

  • To address the challenge of accurate metabolite annotation in high-precision mass spectrometry data.
  • To develop a tool that integrates genomic context into metabolite identification.
  • To provide a hypothesis-driven approach for interpreting metabolomic data.

Main Methods:

  • Development of the MassTRIX web server for MS data annotation.
  • Integration of accurate mass measurements with genomic information.
  • Visualization of identified metabolites within KEGG pathway maps, colored by genomic context.
  • Option to incorporate gene transcription or gene complement data.

Main Results:

  • MassTRIX provides a hypothesis-driven framework for high-precision MS data annotation.
  • The tool visualizes identified metabolites in their genomic context on KEGG pathways.
  • Users can interpret metabolic states by considering potential and real enzymatic capacities, especially with transcriptomics data.

Conclusions:

  • MassTRIX facilitates more confident and context-aware metabolite annotation from high-precision MS data.
  • The integration of genomic and transcriptomic data enhances the interpretation of an organism's metabolic state.
  • The freely accessible MassTRIX web server supports the metabolomics research community.