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Related Concept Videos

Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

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 electron 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 behind a...
Mass Spectrometers01:16

Mass Spectrometers

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:
MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

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...
Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at...
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. 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...
Mass Spectrometry: Complex Analysis01:21

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...

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Updated: Jun 23, 2026

Imaging of Biological Tissues by Desorption Electrospray Ionization Mass Spectrometry
06:21

Imaging of Biological Tissues by Desorption Electrospray Ionization Mass Spectrometry

Published on: July 12, 2013

TOPPView: an open-source viewer for mass spectrometry data.

Marc Sturm1, Oliver Kohlbacher

  • 1Center for Bioinformatics, Eberhard Karls University Tubingen, Sand 14, 72076 Tubingen, Germany. sturm@informatik.uni-tuebingen.de

Journal of Proteome Research
|May 12, 2009
PubMed
Summary
This summary is machine-generated.

TOPPView offers integrated visualization and analysis for mass spectrometry data in proteomics and metabolomics. This open-source tool supports various data types and simplifies complex data exploration for researchers.

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Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports

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Last Updated: Jun 23, 2026

Imaging of Biological Tissues by Desorption Electrospray Ionization Mass Spectrometry
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Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports

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Area of Science:

  • Proteomics and Metabolomics
  • Computational Biology
  • Data Visualization

Background:

  • Complex mass spectrometric data visualization is crucial for proteomics and metabolomics research.
  • Existing tools may lack integration or broad compatibility with diverse mass spectrometry data formats.

Purpose of the Study:

  • To introduce TOPPView, an integrated software solution for visualizing and analyzing mass spectrometric data.
  • To enable seamless data import from various mass spectrometers using standardized formats.
  • To facilitate efficient data analysis through a graphical user interface linked with the OpenMS Proteomics Pipeline (TOPP).

Main Methods:

  • Development of TOPPView as an integrated data visualization and analysis tool.
  • Implementation of support for standardized XML-based data exchange formats for broad compatibility.
  • Integration of the OpenMS Proteomics Pipeline (TOPP) analysis tools within the TOPPView graphical user interface.

Main Results:

  • TOPPView enables visualization and comparison of individual mass spectra and 2D LC-MS datasets.
  • The tool supports data import from any mass spectrometer via standardized formats.
  • Integrated TOPP analysis tools allow efficient data processing directly within TOPPView.

Conclusions:

  • TOPPView provides a comprehensive, user-friendly solution for mass spectrometry data visualization and analysis.
  • Its open-source nature and cross-platform compatibility enhance accessibility for researchers in proteomics and metabolomics.
  • The integration with TOPP streamlines complex data analysis workflows.