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Related Concept Videos

Mass Spectrometers01:16

Mass Spectrometers

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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:
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Mass Spectrometry: Overview01:19

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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...
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Mass Spectrum01:23

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A mass spectrum is the graphical representation of the relative abundance of the charged fragments in an analyte plotted against their mass-to-charge ratio (m/z). The plot's x-axis represents the ratio of the mass of the charged fragment to the number of charges it carries. The y axis of the plot represents the relative abundance of each charged species. The relative abundance is calculated from the signal intensity of each charged species recorded at the detector. The most intense signal (the...
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Mass Spectrum: Interpretation01:24

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An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a soft-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.To...
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Mass Spectrometry: Molecular Fragmentation Overview01:20

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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.
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Mass Analyzers: Overview01:13

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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...
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Updated: Feb 19, 2026

Sample Preparation Strategies for Mass Spectrometry Imaging of 3D Cell Culture Models
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JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals.

Jebediah Rosen1, Kyle Handy1, André Gillan1

  • 1Department of Computer Science, University of Montana, 32 Campus Drive, Missoula, 59812, MT, USA.

BMC Bioinformatics
|November 8, 2017
PubMed
Summary
This summary is machine-generated.

JS-MS is a new, modular JavaScript application for 3D visualization of mass spectrometry (MS) data. This tool offers dependency-free, cross-platform viewing, enhancing custom MS data processing and evaluation.

Keywords:
3-D visualizationJavaScript mass spectrometry parsingMass spectrometry JavaScriptMass spectrometry data processingMass spectrometry visualization

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Area of Science:

  • Analytical Chemistry
  • Biochemistry
  • Computational Biology

Background:

  • Mass spectrometry (MS) data processing tools are limited.
  • No stand-alone, cross-platform 3-D visualizer for MS data exists.
  • Existing visualization toolkits have dependencies and are not suited for custom MS data processing.

Purpose of the Study:

  • To develop a novel, stand-alone, cross-platform 3-D visualizer for mass spectrometry data.
  • To create a modular JavaScript client application for viewing MS data.
  • To improve custom MS data processing and evaluation capabilities.

Main Methods:

  • Developed JS-MS, a modular JavaScript client application.
  • Implemented a dependency-free, browser-based, cross-platform installation.
  • Created a modular Java backend with a streaming.mzML parser.
  • Utilized API-based serving of MS data to the viewer.

Main Results:

  • JS-MS provides a dependency-free, browser-based, one-click, cross-platform install.
  • Offers improved navigation interfaces for MS data visualization.
  • Demonstrates API-based serving of MS data through a novel streaming.mzML parser.
  • Enables custom MS data processing and evaluation with fast, 3-D visualization.

Conclusions:

  • JS-MS facilitates custom MS data processing and evaluation.
  • Provides fast, 3-D visualization with improved navigation and no dependencies.
  • JS-MS is publicly available under a GPLv2 license at github.com/optimusmoose/jsms.