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Related Concept Videos

Mass Analyzers: Overview01:13

Mass Analyzers: Overview

The mass analyzer is a crucial component of the mass spectrometer. In the ionization chamber, the vaporized sample is bombarded with a high-energy electron beam to generate a radical cation and further fragment into neutral molecules, radicals, and cations. A series of negatively charged accelerator plates accelerate the cations into the mass analyzer. The mass analyzer separates ions according to their mass-to-charge (m/z) ratios and then directs them to the detector. The common types of mass...
Mass Analyzers: Common Types01:19

Mass Analyzers: Common Types

The quadrupole mass analyzer consists of four cylindrical metal rods arranged in a diamond carrying a DC voltage and a radio-frequency AC voltage. The motion of ions through the quadrupole depends on the field strength, causing only ions of a certain m/z to resonate successfully and strike the detector at a given field strength. Though the transmission rate for these analyzers is high, the exact elemental composition of the sample is not determined because of low resolution; however, they are...
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...
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...
Inductively Coupled Plasma–Mass Spectrometry (ICP–MS): Overview01:19

Inductively Coupled Plasma–Mass Spectrometry (ICP–MS): Overview

In inductively coupled plasma–mass spectrometry (ICP–MS), an inductively coupled plasma (ICP) torch is used as an atomizer and ionizer. Solid samples are dissolved and volatilized before being introduced into the high-temperature argon plasma, while solution samples are nebulized and passed through the high-temperature argon plasma. Plasma dissociates the analytes and ionizes their component atoms to form a mixture of positive ions and molecular species. The positive ions are then passed on to...
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 24, 2026

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
12:11

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Directed sample interrogation utilizing an accurate mass exclusion-based data-dependent acquisition strategy (AMEx).

Emily L Rudomin1, Steven A Carr, Jacob D Jaffe

  • 1The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

Journal of Proteome Research
|April 7, 2009
PubMed
Summary
This summary is machine-generated.

Accurate mass exclusion (AMEx) improves proteomic analysis by preventing redundant sampling of high-intensity ions. This novel method enhances peptide identification, leading to better protein characterization in complex mixtures.

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Enhanced Sample Multiplexing of Tissues Using Combined Precursor Isotopic Labeling and Isobaric Tagging (cPILOT)
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Enhanced Sample Multiplexing of Tissues Using Combined Precursor Isotopic Labeling and Isobaric Tagging (cPILOT)

Published on: May 1, 2017

Related Experiment Videos

Last Updated: Jun 24, 2026

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
12:11

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Enhanced Sample Multiplexing of Tissues Using Combined Precursor Isotopic Labeling and Isobaric Tagging (cPILOT)
09:06

Enhanced Sample Multiplexing of Tissues Using Combined Precursor Isotopic Labeling and Isobaric Tagging (cPILOT)

Published on: May 1, 2017

Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biochemistry

Background:

  • Thorough sampling is crucial for characterizing complex proteomic mixtures using mass spectrometry.
  • Conventional data-dependent acquisition (DDA) methods often lead to redundant sampling of intense ions and missed identification of low-intensity precursors.

Purpose of the Study:

  • To introduce and evaluate a novel method, accurate mass exclusion-based data-dependent acquisition (AMEx), for enhanced proteomic sampling.
  • To assess the efficacy of AMEx in increasing peptide and protein identifications compared to standard DDA.

Main Methods:

  • Development of AMEx, which uses identified peptide masses to create an exclusion list for subsequent analyses.
  • Performing concatenated analytical runs on a complex cell lysate using both AMEx and standard DDA on an ESI-Orbitrap instrument.

Main Results:

  • AMEx significantly increased the total number of validated peptide identifications compared to standard DDA.
  • The additional peptides identified using AMEx were predominantly from low-intensity precursor ions.
  • Increased peptide identifications led to a greater number of identified proteins and improved protein sequence coverage.

Conclusions:

  • AMEx is an effective strategy for improving the depth and accuracy of proteomic characterization.
  • This method enhances the ability to identify low-abundance peptides, providing a more comprehensive view of proteomic samples.
  • AMEx offers a valuable advancement for mass spectrometry-based proteomics research.