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Related Concept Videos

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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Proteomics01:33

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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.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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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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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 Spectrum01:23

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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

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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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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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Spectral library searching in proteomics.

Johannes Griss1,2

  • 1Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Austria.

Proteomics
|December 1, 2015
PubMed
Summary
This summary is machine-generated.

Spectral library searching is a key proteomics method for identifying tandem mass spectra. This review covers search engines, spectral libraries, and clustering algorithms for advanced data analysis.

Keywords:
BioinformaticsSpectral librariesSpectral library searchingSpectrum clustering

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Area of Science:

  • Proteomics
  • Computational Biology
  • Mass Spectrometry

Background:

  • Spectral library searching is a well-established technique in proteomics.
  • Accurate identification of tandem mass spectra is crucial for protein and peptide identification.

Purpose of the Study:

  • To provide a comprehensive overview of spectral library search engines.
  • To summarize resources for spectral libraries and tools for their expansion.
  • To discuss spectrum clustering algorithms for novel proteomics data analysis.

Main Methods:

  • Review of existing spectral library search engines.
  • Summary of spectral library resources.
  • Presentation of tools for simulating spectra.
  • Discussion of spectrum clustering algorithms.

Main Results:

  • Identification of distinct features of various spectral library search engines.
  • Cataloging of available spectral library resources.
  • Highlighting of tools for augmenting experimental spectral libraries.
  • Exploration of spectrum clustering for new analytical approaches.

Conclusions:

  • Spectral library searching is a mature and vital method in proteomics.
  • The reviewed resources and algorithms offer diverse options for spectral library-based proteomics analysis.
  • Spectrum clustering presents promising avenues for future proteomics data interpretation.