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Related Concept Videos

Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

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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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MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

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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...
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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 Analyzers: Overview01:13

Mass Analyzers: Overview

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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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Mass Spectrum01:23

Mass Spectrum

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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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Matrix-Assisted Laser Desorption Ionization (MALDI)01:08

Matrix-Assisted Laser Desorption Ionization (MALDI)

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Matrix-assisted laser desorption ionization (MALDI) is a powerful analytical technique used in mass spectrometry. It enables the identification and characterization of various biomolecules, including proteins, peptides, nucleic acids, and carbohydrates. MALDI is an ionization technique, widely employed in biological and medical research, as well as in fields like pharmacology and biochemistry.The analyte of interest, a biomolecule or a mixture of biomolecules, is mixed with a suitable matrix...
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MassVision: An Open-Source End-to-End Platform for AI-Driven Mass Spectrometry Imaging Analysis.

Amoon Jamzad1, Jade Warren1, Ayesha Syeda1

  • 1School of Computing, Queen's University, Kingston, Ontario K7L 2N8, Canada.

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|September 18, 2025
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MassVision is a new software platform that simplifies complex mass spectrometry imaging (MSI) data analysis. It offers an integrated, user-friendly solution for researchers to gain deeper biological insights from MSI data.

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Area of Science:

  • Biomedical imaging
  • Computational biology
  • Data science

Background:

  • Mass spectrometry imaging (MSI) generates rich spatial and spectral data for molecular analysis.
  • MSI data analysis is computationally intensive, requiring coding expertise and often fragmented workflows.
  • Current tools lack integration, hindering efficiency and accessibility for researchers.

Purpose of the Study:

  • To introduce MassVision, a comprehensive and user-friendly software platform for mass spectrometry imaging data analysis.
  • To address the computational and accessibility challenges in MSI data analysis.
  • To provide an integrated solution for end-to-end MSI workflows.

Main Methods:

  • MassVision is built on the 3D Slicer ecosystem, offering an intuitive interface.
  • Key functionalities include visualization, segmentation, colocalization, data merging, preprocessing, statistical analysis, and AI model deployment.
  • The platform supports high-throughput studies and multislide datasets.

Main Results:

  • MassVision demonstrated effectiveness in exploratory data analysis, ion identification, and tissue-type classification.
  • The platform seamlessly integrates various MSI data handling steps.
  • Case studies utilized both in-house and public MSI data from different modalities.

Conclusions:

  • MassVision lowers barriers for researchers with varying computational expertise in MSI analysis.
  • The platform facilitates the discovery of new biological insights and structures from MSI data.
  • MassVision provides a robust, integrated tool for advancing MSI data analysis and interpretation.