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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 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...
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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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In mass spectroscopy, amines undergo fragmentation to give parent ions with odd molecule weights. This observed mass spectrum follows the nitrogen rule; a molecule with an odd number of nitrogen atoms produces a molecular ion with an odd molecular weight. Amines undergo fragmentation through α cleavage, producing nitrogen-containing cations—iminium ions—and alkyl radicals. Mass spectra of aromatic and cyclic aliphatic amines exhibit strong molecular ion peaks, but acyclic...
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Most elements exist in nature as a mixture of isotopes. The isotopes differ in weight due to their respective number of neutrons. The molecular weight of a molecule is different depending on the specific isotope of its elements involved. As a result, the mass spectrum of the molecule exhibits peaks from the same fragment at multiple positions. The positions of these mass signals depend on the mass differences between isotopes. Furthermore, the intensity of these signals is dependent on the...
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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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The molecular ion peak of a molecule in the mass spectrum provides vital information for molecular identification. However, conventional electron impact ionization can lead to the rapid dissociation of some molecular ions before they reach the detector. A milder ionization method is required to increase the lifetime of such ionized analyte molecules. Chemical ionization (CI) is a gas-phase protonation reaction useful for mass-analyzing analyte molecules that are easily protonated to yield the...
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mineXpert: Biological Mass Spectrometry Data Visualization and Mining with Full JavaScript Ability.

Filippo Rusconi1,2

  • 1LCP, UMR CNRS 8000, Université Paris-Sud , Université Paris Saclay , Build. 349 , 91400 Orsay , France.

Journal of Proteome Research
|April 6, 2019
PubMed
Summary

Scientists can now visualize and analyze biological mass spectrometry data using open-source software. This tool, mineXpert, allows for detailed inspection and mining of MS1 mass spectral data without proprietary instrument software.

Keywords:
C++GPLv3+JavaScriptMS1 spectrumdata visualizationion mobilityisotopic clustermass spectrometrymetabolomicsmzMLproteomicssoftware

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Area of Science:

  • Biological mass spectrometry, encompassing proteomics, metabolomics, and structural biology.

Background:

  • Mass spectrometry (MS) data analysis, particularly MS1 spectral data, is crucial across various biological disciplines.
  • New data visualization methods are needed due to advancements like ion mobility-mass spectrometry.

Purpose of the Study:

  • To develop an open-source, desktop software for visualizing and analyzing MS1 mass spectral data.
  • To provide scientists with a tool for thorough data scrutiny, quality assessment, and data mining outside of instrument-specific software.

Main Methods:

  • Developed an MS1-only mass data visualization software supporting conventional and drift time data.
  • Integrated features for isotopic cluster calculations, mass peak deconvolution, and flexible data reporting.
  • Enabled task automation via a JavaScript environment and efficient handling of large, sparse datasets.

Main Results:

  • The software, mineXpert, allows visualization and analysis of MS1 mass spectral data, including drift time data.
  • Users can perform detailed data inspection, quality assessments, and quantitation measurements.
  • The software facilitates isotopic cluster calculations, deconvolution, and reporting, supporting data mining and discovery.

Conclusions:

  • mineXpert provides an open-source solution for inspecting and mining MS1 mass spectral data, independent of proprietary vendor software.
  • The software enhances accessibility for mass spectrometry users, enabling data analysis outside of core facilities.
  • Conversion to mzML format is required, with reference materials and tutorials available online.