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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...
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...
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...
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 Spectrometers01:16

Mass Spectrometers

This lesson details the instrumentation of a mass spectrometer—a physical instrument to perform mass spectrometry on analyte molecules and record the characteristic mass spectra. This is achieved via three chief functions:

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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

Current trends in computational inference from mass spectrometry-based proteomics.

Bobbie-Jo M Webb-Robertson1, William R Cannon

  • 1Department of Computational Biology & Bioinformatics, Pacific Northwest National Laboratory, P.O. BOX 999, Richland, WA 99352, USA. bj@pnl.gov

Briefings in Bioinformatics
|June 23, 2007
PubMed
Summary

This review explores computational methods in proteomics, focusing on mass spectrometry. It highlights advancements in peptide and protein identification, quantification, and functional inference for systems biology applications.

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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

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Last Updated: Jul 14, 2026

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

Published on: August 19, 2025

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
10:37

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Area of Science:

  • Proteomics
  • Computational Biology
  • Systems Biology

Background:

  • Mass spectrometry is a key technology for high-throughput proteomic analysis.
  • Computational methods are essential for peptide/protein identification, quantification, and functional inference in proteomics.
  • Proteomics applications in systems biology require understanding the functional proteome and molecular interactions.

Purpose of the Study:

  • To provide an overview of recent computational methods in proteomics.
  • To discuss the impact of these methods on core computational challenges.
  • To address challenges in protein and peptide identification, quantification, and functional inference.

Main Methods:

  • Review of recently developed computational methods.
  • Analysis of computational approaches for peptide and protein identification from mass spectra.
  • Examination of computational strategies for proteome quantification and functional inference.

Main Results:

  • Recent computational methods have advanced peptide and protein identification.
  • New techniques improve the accuracy and throughput of proteome quantification.
  • Computational tools are enhancing the understanding of protein modifications and interactions.

Conclusions:

  • Computational methods are critical for addressing key challenges in proteomics.
  • Advancements in computational approaches are driving progress in systems biology.
  • This review highlights the impact of new methods on the future of proteomic analysis.