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Related Concept Videos

Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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Tandem Mass Spectrometry01:21

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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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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: Overview01:19

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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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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 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 soft-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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Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry
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SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra.

Mikhail Kolmogorov1, Xiaowen Liu2, Pavel A Pevzner1

  • 1Department of Computer Science and Engineering, UCSD , 9500 Gilman Drive, La Jolla, California, United States.

Journal of Proteome Research
|December 3, 2015
PubMed
Summary
This summary is machine-generated.

Top-down proteogenomics enhances genome annotation by discovering unannotated genes. This advanced approach, utilizing the SpectroGene software, overcomes limitations of traditional methods for bacterial genomes.

Keywords:
genome annotationprotein identificationproteogenomicstop-down mass spectrometry

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Area of Science:

  • Proteomics
  • Genomics
  • Bioinformatics

Background:

  • Proteogenomics integrates proteomic data with genomic information for genome annotation.
  • Traditional proteogenomic studies primarily used bottom-up mass spectrometry, limiting their scope.
  • Top-down mass spectrometry offers deeper proteome analysis but was underutilized in proteogenomics.

Purpose of the Study:

  • To demonstrate the utility of top-down proteogenomics for advancing genome annotation.
  • To address limitations of bottom-up proteogenomics in gene discovery.
  • To introduce SpectroGene, a novel software tool for genome annotation using top-down mass spectrometry data.

Main Methods:

  • Implementation of top-down mass spectrometry for proteogenomic analysis.
  • Development and application of the SpectroGene software tool.
  • Genome annotation using tandem mass spectra against a six-frame genome translation.

Main Results:

  • Top-down proteogenomics successfully identified previously unannotated genes in bacterial genomes.
  • SpectroGene facilitated genome annotation using top-down tandem mass spectra.
  • Searches against six-frame genome translations identified nearly all proteoforms found in traditional top-down proteomics.

Conclusions:

  • Top-down proteogenomics is a powerful approach for comprehensive genome annotation.
  • SpectroGene software enhances the discovery of novel genetic elements.
  • This method significantly expands the capabilities of proteogenomic analysis, particularly for microbial genomes.