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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 electrospray 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...
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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 Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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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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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 low-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

Mass Spectrometry: Molecular Fragmentation Overview

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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.
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...
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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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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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MSnbase, Efficient and Elegant R-Based Processing and Visualization of Raw Mass Spectrometry Data.

Laurent Gatto1, Sebastian Gibb2, Johannes Rainer3

  • 1Computational Biology Unit, de Duve Institute, Université catholique de Louvain, Brussels, 1200, Belgium.

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The MSnbase R/Bioconductor package (version 2) now efficiently handles large mass spectrometry datasets using on-disk infrastructure. This enables streamlined data processing, method development, and visualization for complex experiments.

Keywords:
BioconductorRmass spectrometrymetabolomicsproteomicsreproducible researchsoftwarevisualization

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Mass Spectrometry Data Analysis

Background:

  • Mass spectrometry generates large, complex datasets.
  • Efficient data handling and processing are crucial for biological insights.
  • Existing tools may face limitations with large-scale experiments.

Purpose of the Study:

  • Introduce version 2 of the MSnbase R/Bioconductor package.
  • Highlight the new on-disk infrastructure for handling large datasets.
  • Demonstrate the package's utility in data processing, method development, and visualization.

Main Methods:

  • Development of an on-disk infrastructure within the MSnbase package.
  • Implementation of data manipulation, processing, and visualization functionalities.
  • Utilizing R/Bioconductor framework for package development.

Main Results:

  • Successful implementation of version 2 of MSnbase.
  • Demonstrated capability to manage large mass spectrometry experiments on commodity hardware.
  • Showcased elegant data processing, method development, and visualization workflows.

Conclusions:

  • The enhanced MSnbase package (v2) provides robust infrastructure for large-scale mass spectrometry data.
  • On-disk capabilities facilitate efficient analysis on standard hardware.
  • The package supports advanced data processing and visualization in bioinformatics.