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Related Concept Videos

Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

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Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and signal-to-noise ratio for the analyte. 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 collision-induced...
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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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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 spectrometry is 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 material. The...
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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 elementary charge 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...
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Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
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Whole-body Mass Spectrometry Imaging by Infrared Matrix-assisted Laser Desorption Electrospray Ionization IR-MALDESI
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MassDash: A Web-Based Dashboard for Data-Independent Acquisition Mass Spectrometry Visualization.

Justin C Sing1,2, Joshua Charkow1,2, Mohammed AlHigaylan1,2

  • 1Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.

Journal of Proteome Research
|April 29, 2024
PubMed
Summary
This summary is machine-generated.

MassDash is new software for visualizing and validating Data-Independent Acquisition (DIA) mass spectrometry data. It allows interactive comparison of results from various automated tools on a personal computer.

Keywords:
data-independent-acquisitionmass-spectrometryoptimizationprototypingvalidationvisualization

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Area of Science:

  • Proteomics
  • Computational Biology
  • Data Visualization

Background:

  • Data-Independent Acquisition (DIA) mass spectrometry generates complex datasets requiring robust validation.
  • Increasing diversity of DIA analysis tools necessitates effective methods for result comparison and quality control.

Purpose of the Study:

  • To introduce MassDash, a novel cross-platform software for visualizing and validating DIA mass spectrometry data.
  • To enable interactive comparison of results from multiple automated DIA analysis tools.

Main Methods:

  • MassDash offers a web-based interface and Python package for interactive visualizations.
  • It processes peptides on-the-fly for simultaneous visualization across numerous runs.
  • Supports multidimensional visualizations including retention time, ion mobility, m/z, and intensity.

Main Results:

  • MassDash facilitates comparison of features and results from popular DIA tools like OpenSwath, DIA-NN, and dreamDIA.
  • Enables interactive visualization of peptides across dozens of runs on a personal computer.
  • Provides additional insights through multidimensional data exploration.

Conclusions:

  • MassDash enhances the validation process for automated DIA mass spectrometry software.
  • Its modular framework supports the development of new peak-picking algorithms.
  • The software is open-source and freely available, promoting broader adoption and development.