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Related Concept Videos

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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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Related Experiment Video

Updated: Jun 21, 2026

Histone Modification Screening using Liquid Chromatography, Trapped Ion Mobility Spectrometry, and Time-Of-Flight Mass Spectrometry
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Histone Modification Screening using Liquid Chromatography, Trapped Ion Mobility Spectrometry, and Time-Of-Flight Mass Spectrometry

Published on: January 12, 2024

Rapid Histone Post-Translational Modification Analysis Using Alternative Proteases and Tandem Mass Tags.

Natalie P Turner1, Sabyasachi Baboo1, Patrick Garrett1

  • 1Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, California 92037, United States of America.

Analytical Chemistry
|June 19, 2026
PubMed
Summary
This summary is machine-generated.

We developed RIPUP, a rapid histone PTM workflow, significantly improving PTM identification and quantitative accuracy. This method uncovers a "dark epigenome" of previously undetected modifications, accelerating epigenetic research.

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Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis
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Extraction of Histones from Clinical Specimens for Epigenetic Profiling by Mass Spectrometry
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Published on: November 21, 2025

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Last Updated: Jun 21, 2026

Histone Modification Screening using Liquid Chromatography, Trapped Ion Mobility Spectrometry, and Time-Of-Flight Mass Spectrometry
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Published on: January 12, 2024

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis
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Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis

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Extraction of Histones from Clinical Specimens for Epigenetic Profiling by Mass Spectrometry
10:54

Extraction of Histones from Clinical Specimens for Epigenetic Profiling by Mass Spectrometry

Published on: November 21, 2025

Area of Science:

  • Epigenetics and Molecular Biology
  • Proteomics
  • Biochemistry

Background:

  • Histone post-translational modifications (PTMs) are crucial for gene regulation but analyzing them via mass spectrometry is hampered by complex sample preparation.
  • Current workflows are time-consuming and limit the comprehensive identification and quantification of histone PTMs.

Purpose of the Study:

  • To develop a streamlined, rapid, and highly efficient workflow for histone PTM analysis using mass spectrometry.
  • To improve the coverage and quantitative accuracy of histone PTM identification, particularly for previously undetected modifications.

Main Methods:

  • Development of RIPUP (Rapid Identification of histone PTMs in Underivatized Peptides), a multiprotease sample preparation workflow.
  • Systematic evaluation of Arg-C Ultra and recombinant Chymotrypsin proteases, with and without derivatization (propionic anhydride) and TMT labeling.
  • Utilized the HiP-Frag computational framework for unrestrictive PTM identification.

Main Results:

  • RIPUP reduces sample preparation time to hours, enhancing PTM coverage and quantitative accuracy.
  • Arg-C Ultra with TMT labeling surpassed trypsin-based methods in total PTM detection and identified a significant number of succinylation and glutarylation sites.
  • The workflow successfully quantified numerous significant peptidoforms in response to nicotinamide treatment and identified diverse PTMs in rat hippocampal tissue.

Conclusions:

  • RIPUP offers a rapid, high-efficiency platform for histone PTM discovery, overcoming limitations of traditional methods.
  • The workflow enables the identification of a largely undetected "dark epigenome" and accelerates the discovery of epigenetic mechanisms.
  • This platform facilitates the timely progression from PTM identification to therapeutic target validation in epigenetics research.