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Related Concept Videos

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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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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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 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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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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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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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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ProSight Lite: graphical software to analyze top-down mass spectrometry data.

Ryan T Fellers1, Joseph B Greer, Bryan P Early

  • 1Department of Chemistry, Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern, University, Evanston, IL, USA.

Proteomics
|April 2, 2015
PubMed
Summary
This summary is machine-generated.

ProSight Lite is a free software tool that aids top-down proteomics by matching mass spectrometry data to protein sequences. It helps identify post-translational modifications (PTMs) and glycosylations, facilitating data analysis and hypothesis testing.

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Area of Science:

  • Proteomics
  • Biochemistry
  • Computational Biology

Background:

  • Top-down proteomics frequently involves identifying and localizing post-translational modifications (PTMs) and other mass shifts on protein sequences.
  • Efficient data analysis is crucial for hypothesis testing in these experiments.

Purpose of the Study:

  • To introduce ProSight Lite, a free software tool designed to simplify the analysis of mass spectrometric data in top-down proteomics.
  • To facilitate the matching of observed ion masses to candidate protein sequences, aiding in the identification and localization of PTMs.

Main Methods:

  • ProSight Lite matches a single candidate protein sequence against mass spectrometric observations.
  • It supports the application of fixed or variable modifications, including PTMs and specific glycosylations.
  • The software generates scores and lists of matching fragments.

Main Results:

  • The application provides multiple scoring metrics for assessing the quality of sequence matches.
  • It generates a list of matching fragments to support the identification of modifications.
  • Fragmentation maps can be exported in PNG or SVG formats for publication.

Conclusions:

  • ProSight Lite offers a user-friendly solution for analyzing top-down proteomics data.
  • The tool assists researchers in hypothesis testing for PTMs and glycosylations.
  • It is freely available for download and runs on Windows 7 or higher.