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Related Concept Videos

Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

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...
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...
MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

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...
Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

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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Updated: May 14, 2026

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

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
PubMed
Summary
This summary is machine-generated.

Proteomics, the study of proteins, uses mass spectrometry (MS) to analyze radiation

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Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

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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.