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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
Published on: August 19, 2025
Mass spectrometry-based proteomics: basic principles and emerging technologies and directions
Susan K Van Riper1, Ebbing P de Jong, John V Carlis
1Department of Biomedical Informatics and Computational Biology, University of Minnesota, 321 Church St SE/6-155 Jackson Hall, Minneapolis, MN, 55455, USA. vanr0014@umn.edu
Advances in Experimental Medicine and Biology
|February 5, 2013
Summary
Proteomics, the study of proteins, uses mass spectrometry (MS) to analyze radiation
Area of Science:
- Biochemistry and Molecular Biology
- Radiation Biology
- Analytical Chemistry
Background:
- Proteins are vital biomolecules and primary targets of radiation damage in biological systems.
- Understanding radiation's impact on proteins is crucial for assessing cellular and tissue effects.
- Comprehensive proteome characterization requires methods to quantify protein levels, identify modifications, and map complexes.
Purpose of the Study:
- To review the current state of mass spectrometry (MS)-based proteomics.
- To highlight emerging technologies in MS-proteomics relevant to radiation biology research.
- To provide insights for researchers investigating radiation's biological effects.
Main Methods:
- Mass spectrometry (MS) coupled with sample fractionation and automated data analysis.
- Focus on advancements in: (1) instrumental methods, (2) computational peptide identification, and (3) label-free quantification.
Main Results:
- The chapter provides an overview of current MS-proteomics capabilities.
- Emerging technologies in instrumentation, data analysis, and quantification are discussed.
- These advancements enhance the ability to perform system-wide proteome characterization.
Conclusions:
- Mass spectrometry-based proteomics is a powerful platform for studying radiation effects.
- Emerging technologies in MS-proteomics offer improved analytical capabilities.
- These advancements are essential for researchers aiming to understand the biological consequences of radiation exposure.
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