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Related Concept Videos

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...
¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)01:20

¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)

When proton-coupled carbon-13 spectra are simplified by a broadband proton decoupling technique, structural information about the coupled protons is lost. Distortionless enhancement by polarization transfer (DEPT) is a technique that provides information on the number of hydrogens attached to each carbon in a molecule. While the DEPT experiment utilizes complex pulse sequences, the pulse delay and flip angle are specifically manipulated. The resulting signals have different phases depending on...
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...
Mass Spectrometry: Isotope Effect01:13

Mass Spectrometry: Isotope Effect

Most elements exist in nature as a mixture of isotopes. The isotopes differ in weight due to their respective number of neutrons. The molecular weight of a molecule is different depending on the specific isotope of its elements involved. As a result, the mass spectrum of the molecule exhibits peaks from the same fragment at multiple positions. The positions of these mass signals depend on the mass differences between isotopes. Furthermore, the intensity of these signals is dependent on the...
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...

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Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
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Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments

Published on: January 20, 2022

Features-based deisotoping method for tandem mass spectra.

Zheng Yuan1, Jinhong Shi, Wenjun Lin

  • 1Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK, Canada S7N5A9.

Advances in Bioinformatics
|January 21, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces a novel algorithm for deisotoping tandem mass spectra, improving peptide and protein identification. The new method enhances accuracy by analyzing isotopic cluster relationships and features, outperforming existing software.

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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
  • Mass Spectrometry
  • Bioinformatics

Background:

  • Accurate determination of fragment ion monoisotopic masses is crucial for peptide and protein identification in high-resolution tandem mass spectrometry.
  • Existing deisotoping algorithms may struggle with low-intensity fragment ions, impacting identification accuracy.

Purpose of the Study:

  • To develop and evaluate a new algorithm for deisotoping bottom-up tandem mass spectra.
  • To improve the accuracy and reliability of peptide and protein identification by enhancing deisotoping performance.

Main Methods:

  • Construction of isotopic-cluster graphs to represent relationships between isotopic clusters.
  • Development of a scoring function combining non-intensity and intensity features of fragment ions.
  • Application of dynamic programming to identify the highest-scoring path of reliable isotopic clusters.

Main Results:

  • The proposed deisotoping algorithm demonstrated superior performance compared to YADA and MS-Deconv.
  • Spectra processed by the new method yielded higher average Mascot scores and F-scores for identified peptides.
  • The algorithm effectively utilizes non-intensity features to retain low-intensity fragment ions.

Conclusions:

  • The novel deisotoping algorithm significantly improves peptide and protein identification from high-resolution tandem mass spectra.
  • This method offers a more robust approach to analyzing complex mass spectrometry data.
  • The enhanced accuracy in deisotoping leads to more reliable proteomic analyses.