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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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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.
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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 Spectrometry: Molecular Fragmentation Overview01:20

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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.
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Peptide Identification Using Tandem Mass Spectrometry01:33

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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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Mass Spectrometry: Complex Analysis01:21

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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.
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Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products
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TopPIC Gateway: A Web Gateway for Top-Down Mass Spectrometry Data Interpretation.

In Kwon Choi1, Eroma Abeysinghe2, Eric Coulter2

  • 1Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis.

PEARC20 : Practice and Experience in Advanced Research Computing 2020 : Catch the Wave : July 27-31, 2020, Portland, or Virtual Conference. Practice and Experience in Advanced Research Computing (Conference) (2020 : Online)
|May 26, 2022
PubMed
Summary

A new web gateway simplifies proteoform analysis using the TopPIC suite for mass spectrometry. This tool provides accessible high-performance computing for researchers studying intact proteoforms.

Keywords:
Apache AiravataApplied computing → BioinformaticsInformation systems → Computing platformsProteomicsSciGaPScience GatewaysTop-down mass spectrometryXSEDE

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • Top-down mass spectrometry is crucial for identifying and quantifying intact proteoforms.
  • The TopPIC suite is a widely adopted software for interpreting top-down mass spectrometry data.
  • Access to high-performance computing resources can be a barrier for many researchers.

Purpose of the Study:

  • To present a web-based gateway for the TopPIC suite.
  • To enable broader access to computational resources for top-down mass spectrometry data analysis.
  • To support proteomics researchers and students with limited computing infrastructure.

Main Methods:

  • Developed a web gateway integrating the TopPIC suite (TopFD, TopPIC, TopMG, TopDiff).
  • Leveraged heterogeneous computing resources, including Indiana University's high-performance computing clusters and XSEDE's Jetstream Cloud.
  • Facilitated data analysis for top-down mass spectral data.

Main Results:

  • The gateway provides a user-friendly interface for complex proteomic data analysis.
  • It enables the use of distributed and cloud computing resources for TopPIC suite applications.
  • Researchers can now perform advanced proteoform analysis without direct supercomputer interaction.

Conclusions:

  • The TopPIC suite web gateway democratizes access to powerful computational tools for proteoform analysis.
  • It lowers the barrier for researchers and students to conduct sophisticated mass spectrometry data interpretation.
  • This resource enhances the capabilities of the proteomics community in studying intact proteoforms.