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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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DO-MS: Data-Driven Optimization of Mass Spectrometry Methods.

R Gray Huffman1,2, Albert Chen1,2, Harrison Specht1,2

  • 1Department of Bioengineering , Northeastern University , Boston , Massachusetts 02115 , United States.

Journal of Proteome Research
|May 14, 2019
PubMed
Summary
This summary is machine-generated.

We developed Data-driven Optimization of MS (DO-MS), an open-source platform for diagnosing and optimizing liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods. DO-MS interactive visualization significantly improved ion delivery for MS2 analysis by 370%.

Keywords:
MaxQuantRShinymethod developmentoptimizing mass spectrometryquality controlsingle-cell analysissingle-cell proteomics by mass spectrometryultrasensitive proteomicsvisualization

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Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biotechnology

Background:

  • Ultrasensitive liquid chromatography and tandem mass spectrometry (LC-MS/MS) methods, including single-cell proteomics by mass spectrometry (SCoPE-MS), rely on numerous interdependent parameters.
  • Interdependencies complicate the identification of specific issues and effective solutions within LC-MS/MS workflows.
  • Low MS2 signals can stem from various factors, such as suboptimal LC separation, ionization efficiency, apex targeting, ion transfer, or detection.

Purpose of the Study:

  • To develop a method for diagnosing problems in bottom-up LC-MS/MS analysis.
  • To create an open-source platform for interactive visualization and analysis of LC-MS/MS data.
  • To enable rational optimization of LC-MS/MS methods through data-driven insights.

Main Methods:

  • Developed Data-driven Optimization of MS (DO-MS), an open-source software platform.
  • Utilized existing data from software packages like MaxQuant.
  • Implemented interactive visualization of data from all levels of bottom-up LC-MS/MS analysis.
  • Focused on optimizing the sampling of elution peak apexes.

Main Results:

  • DO-MS effectively diagnosed specific problems within LC-MS/MS methods.
  • Optimization using DO-MS led to significant improvements, including a 370% increase in ion delivery efficiency for MS2 analysis.
  • The platform facilitates interactive data subsetting and high-quality figure generation.
  • DO-MS features a modular design for customization and expansion.

Conclusions:

  • DO-MS provides a powerful tool for diagnosing and optimizing LC-MS/MS performance.
  • Interactive data visualization is crucial for understanding and improving complex analytical workflows.
  • The platform enhances ion delivery efficiency, leading to more robust proteomic analyses.
  • DO-MS is user-friendly, easily installable, and extensible for future applications.