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Related Concept Videos

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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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.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
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Mass Spectrum01:23

Mass Spectrum

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A mass spectrum is the graphical representation of the relative abundance of the charged fragments in an analyte plotted against their mass-to-charge ratio (m/z). The plot's x-axis represents the ratio of the mass of the charged fragment to the number of charges it carries. The y axis of the plot represents the relative abundance of each charged species. The relative abundance is calculated from the signal intensity of each charged species recorded at the detector. The most intense signal (the...
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Mass Spectrum: Interpretation01:24

Mass Spectrum: Interpretation

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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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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 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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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 of Amines01:15

Mass Spectrometry of Amines

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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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Organic Solvent-Based Protein Precipitation for Robust Proteome Purification Ahead of Mass Spectrometry
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A Spectrum Graph-Based Protein Sequence Filtering Algorithm for Proteoform Identification by Top-Down Mass

Runmin Yang1,2, Daming Zhu1, Qiang Kou2

  • 1School of Computer Science and Technology, Shandong University.

Proceedings. IEEE International Conference on Bioinformatics and Biomedicine
|March 6, 2018
PubMed
Summary
This summary is machine-generated.

We developed a new algorithm for faster proteoform identification using mass spectrometry. This method efficiently filters protein databases, significantly speeding up the search for modified or mutated proteins.

Keywords:
Mass spectrometryfiltering algorithmspectrum graph

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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
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Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
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Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
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Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Database searching of top-down tandem mass spectra is crucial for identifying proteoforms.
  • Current methods are slow, especially for proteoforms with post-translational modifications or mutations.

Purpose of the Study:

  • To develop a novel, efficient, and sensitive algorithm for filtering protein sequence databases.
  • To accelerate the identification of proteoforms in complex biological samples.

Main Methods:

  • A new filtering algorithm generating spectrum graphs from subspectra of query spectra.
  • Searching these spectrum graphs against protein databases to identify candidate sequences.
  • Comparison with existing sequence tag and gaped tag approaches.

Main Results:

  • The proposed method bypasses the need for tag extraction, simplifying data processing.
  • Experimental results demonstrate high speed and sensitivity in protein sequence filtration.
  • Achieved significant improvements over traditional sequence tag methods.

Conclusions:

  • The novel spectrum graph-based filtering algorithm substantially enhances the speed and sensitivity of proteoform identification.
  • This approach offers a simplified and more efficient alternative for large-scale proteomic database searches.
  • Facilitates faster and more accurate analysis of proteoforms with modifications and mutations.