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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...
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 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 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 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...

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Related Experiment Video

Updated: May 22, 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

Speeding up tandem mass spectral identification using indexes.

Xiaowen Liu1, Alessandro Mammana, Vineet Bafna

  • 1Department of Computer Science and Engineering, University of California, San Diego, California 92093, USA. xil018@cs.ucsd.edu

Bioinformatics (Oxford, England)
|May 1, 2012
PubMed
Summary

New algorithms improve the speed of identifying peptides and proteins with post-translational modifications (PTMs) using tandem mass spectrometry (MS/MS). These methods enhance PTM identification in proteomics research.

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Area of Science:

  • Proteomics
  • Biochemistry
  • Computational Biology

Background:

  • Tandem mass spectrometry (MS/MS) is a standard technique in proteomics.
  • Identifying post-translational modifications (PTMs) from MS/MS spectra remains a significant challenge.

Purpose of the Study:

  • To develop novel scoring functions and algorithms for PTM identification in MS/MS data.
  • To improve the efficiency and accuracy of peptide and protein identification in proteomics.

Main Methods:

  • Definition of two scoring functions: match scores and diagonal scores.
  • Formulation of two spectral identification problems based on these scores.
  • Development of several index-based algorithms for efficient spectral identification.

Main Results:

  • The proposed index-based algorithms significantly enhance computational speed compared to existing methods.
  • Theoretical and experimental analyses validate the improved performance of the new algorithms.
  • Effective identification of peptides and proteins with PTMs from MS/MS spectra.

Conclusions:

  • The developed index-based algorithms offer a substantial speed improvement for PTM identification.
  • These advancements contribute to more efficient and accurate proteomics studies.
  • The new scoring functions and algorithms address a key challenge in tandem mass spectral analysis.