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Related Concept Videos

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:
Mass Spectrum: Interpretation01:24

Mass Spectrum: Interpretation

An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a soft-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.To...
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: 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 Spectrum01:23

Mass Spectrum

A mass spectrum is the graphical representation of the relative abundance of the charged fragments in an analyte plotted against their mass-to-charge ratio (m/z). The plot's x-axis represents the ratio of the mass of the charged fragment to the number of charges it carries. The y axis of the plot represents the relative abundance of each charged species. The relative abundance is calculated from the signal intensity of each charged species recorded at the detector. The most intense signal (the...

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Related Experiment Video

Updated: Jun 25, 2026

Analyzing Large Protein Complexes by Structural Mass Spectrometry
15:35

Analyzing Large Protein Complexes by Structural Mass Spectrometry

Published on: June 19, 2010

Analysis of mass spectrometry data using sub-spectra.

Wouter Meuleman1, Judith Y M N Engwegen, Marie-Christine W Gast

  • 1Bioinformatics and Statistics, Department of Molecular Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands. w.meuleman@tudelft.nl

BMC Bioinformatics
|February 12, 2009
PubMed
Summary

Analyzing individual sub-spectra from Surface-Enhanced Laser Desorption/Ionisation (SELDI) mass spectrometry improves peak detection. This novel approach enhances sensitivity and provides confidence measures for identified peaks, outperforming traditional methods.

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Area of Science:

  • Biochemistry
  • Analytical Chemistry
  • Biophysics

Background:

  • Surface-Enhanced Laser Desorption/Ionisation (SELDI) mass spectrometry combines sub-spectra from multiple laser firings.
  • This summation process can obscure low-abundance or unevenly distributed peptides due to noise variation.
  • Analyzing sub-spectra individually is proposed to overcome these limitations.

Purpose of the Study:

  • To develop a novel framework for analyzing SELDI mass spectrometry sub-spectra individually.
  • To introduce a significance test for attaching confidence measures to detected peaks.
  • To improve the sensitivity and accuracy of peptide identification in SELDI analysis.

Main Methods:

  • Individual analysis of SELDI mass spectrometry sub-spectra.
  • Development of a framework incorporating a significance test for peak validation.
  • Introduction of 'peak-bags' to detail sub-spectral contributions to identified peaks.

Main Results:

  • The sub-spectral approach achieves higher sensitivity and a lower False Discovery Rate (FDR) compared to other methods.
  • A confidence measure can be assigned to detected peaks based on their signal strength across sub-spectra.
  • Peak-bags provide detailed information on sub-spectral contributions.

Conclusions:

  • The proposed method offers superior control in distinguishing signal from noise in SELDI data.
  • This approach enhances overall performance compared to existing SELDI analysis techniques.
  • The method implicitly deconvolutes peaks, offering insights into peak distribution and shape.