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Related Concept Videos

Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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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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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 electrospray 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...
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High-Resolution Mass Spectrometry (HRMS)01:15

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The resolution of a mass spectrometer depends on the efficiency of separating ions with different ion masses. The mass of an atom is approximated to the sum of the masses of protons and neutrons inside, considering the masses of protons and neutrons as equal. However, the masses of the proton (1.6726 × 10−24 g) and neutron (1.6749 × 10−24 g) are not truly equal. There is a minor error in the expression of atomic masses relative to the simplest atom of hydrogen. For...
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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 low-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.
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Updated: Jun 14, 2025

Isolation of Histone from Sorghum Leaf Tissue for Top Down Mass Spectrometry Profiling of Potential Epigenetic Markers
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pyMS-Vis, an Open-Source Python Application for Visualizing and Investigating Deconvoluted Top-Down Mass

James J Pesavento1, Megan S Bindra1, Udayan Das1

  • 1Saint Mary's College of California, Moraga, California 94575, United States.

Analytical Chemistry
|August 30, 2024
PubMed
Summary
This summary is machine-generated.

We developed an open-source Python application for analyzing liquid-chromatography top-down mass spectrometry (LC-TDMS) data. This tool quantifies proteoform abundances, revealing new insights into histone modifications in Chlamydomonas reinhardtii.

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Area of Science:

  • Proteomics
  • Biochemistry
  • Computational Biology

Background:

  • Top-down mass spectrometry (TDMS) is crucial for analyzing intact proteins and their modifications.
  • Liquid chromatography coupled with TDMS (LC-TDMS) enables the separation and analysis of complex proteoform mixtures.
  • Quantitative analysis of proteoforms, particularly histones, is essential for understanding cellular regulation.

Purpose of the Study:

  • To develop an open-source Python application for quantitative and qualitative analysis of LC-TDMS data.
  • To enable rapid and accurate quantification of proteoform abundances.
  • To facilitate the discovery of novel biological insights from complex proteomic datasets.

Main Methods:

  • Development of a user-friendly Python application for processing deconvoluted LC-TDMS data.
  • Implementation of functions for searching masses-of-interest, visualizing ion intensities, and quantifying relative abundances.
  • Application of the software to analyze histone proteoforms from Chlamydomonas reinhardtii.

Main Results:

  • The application significantly reduces analysis time from hours to minutes for proteoform quantification.
  • Quantitative analysis of Chlamydomonas histone proteoforms revealed new insights into alpha-amino termini processing.
  • Demonstrated the exclusive processing of alpha-amino termini in histone H2A family members.

Conclusions:

  • The developed Python application provides an efficient and accessible tool for LC-TDMS data analysis.
  • The software enables quantitative insights into proteoform dynamics, advancing biological discovery.
  • The open-source nature promotes customizability and broader adoption within the mass spectrometry community.