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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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Mass Spectrometry: Isotope Effect01:13

Mass Spectrometry: Isotope Effect

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Most elements exist in nature as a mixture of isotopes. The isotopes differ in weight due to their respective number of neutrons. The molecular weight of a molecule is different depending on the specific isotope of its elements involved. As a result, the mass spectrum of the molecule exhibits peaks from the same fragment at multiple positions. The positions of these mass signals depend on the mass differences between isotopes. Furthermore, the intensity of these signals is dependent on the...
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Chemical Ionization (CI) Mass Spectrometry01:21

Chemical Ionization (CI) Mass Spectrometry

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The molecular ion peak of a molecule in the mass spectrum provides vital information for molecular identification. However, conventional electron impact ionization can lead to the rapid dissociation of some molecular ions before they reach the detector. A milder ionization method is required to increase the lifetime of such ionized analyte molecules. Chemical ionization (CI) is a gas-phase protonation reaction useful for mass-analyzing analyte molecules that are easily protonated to yield the...
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Mass Spectrometry: Alkene Fragmentation00:59

Mass Spectrometry: Alkene Fragmentation

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Alkenes lose one electron from the unsaturated π bond upon ionization and form stable molecular ions. Further fragmentation of alkenes occurs through three different reaction pathways. The most prominent fragmentation is the cleavage at the allylic position. The resultant allylic carbocation is resonance stabilized. In the mass spectra of terminal alkenes, this fragment appears at a mass-to-charge ratio of 41. In the internal alkenes, where there are two choices of allylic cleavage, the...
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EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data.

Zuo-Fei Yuan1, Simone Sidoli1, Dylan M Marchione2

  • 1Epigenetics Institute, Department of Biochemistry and Biophysics , Perelman School of Medicine University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States.

Journal of Proteome Research
|May 24, 2018
PubMed
Summary

EpiProfile 2.0 accurately quantifies histone post-translational modifications (PTMs) using liquid chromatography-tandem mass spectrometry. This advanced software enhances epigenetic research in biology and medicine by providing precise measurements of these crucial epigenetic marks.

Keywords:
acylationepigeneticshistonemutationspost-translational modificationquantification

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Area of Science:

  • Epigenetics and molecular biology
  • Biomedical research and translational medicine

Background:

  • Epigenetic marks, including DNA methylation and histone post-translational modifications (PTMs), are critical for regulating chromatin structure and gene expression.
  • Accurate quantification of diverse histone PTMs presents a significant challenge due to their wide abundance range and complexity.

Purpose of the Study:

  • To introduce EpiProfile 2.0, an enhanced software for precise quantification of histone peptides using liquid chromatography-tandem mass spectrometry (LC-MS/MS).
  • To improve the accuracy and scope of histone mark analysis in epigenetic studies.

Main Methods:

  • EpiProfile 2.0 utilizes data-independent acquisition with precursor and fragment extracted ion chromatography for accurate chromatographic profiling and isobaric peptide discrimination.
  • The software incorporates intelligent retention time prediction for robust peak detection.
  • It supports various analytical approaches, including label-free and isotopic labeling, diverse organisms, disease-related mutations, and unusual PTMs.

Main Results:

  • EpiProfile 2.0 provides accurate quantification of histone peptides, enhancing the reliability of epigenetic mark measurements.
  • The software effectively discriminates isobaric peptides and handles a wide dynamic range of PTM abundance.
  • It demonstrates versatility across different experimental conditions and sample types.

Conclusions:

  • EpiProfile 2.0 is a universal and accurate platform for LC-MS/MS-based quantification of histone marks.
  • This software is expected to significantly advance epigenetic research in fundamental biology and translational medicine.
  • EpiProfile 2.0 is freely available, promoting wider adoption and accelerating discoveries in epigenetics.