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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...
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...
High-Resolution Mass Spectrometry (HRMS)01:15

High-Resolution Mass Spectrometry (HRMS)

The resolution of a mass spectrometer depends on the efficiency of separating ions with different ion masses. The mass of an atom is approximated to the sum of the masses of protons and neutrons inside, considering the masses of protons and neutrons as equal. However, the masses of the proton (1.6726 × 10−24 g) and neutron (1.6749 × 10−24 g) are not truly equal. There is a minor error in the expression of atomic masses relative to the simplest atom of hydrogen. For example, the mass of helium...
Rapid Identification of Pathogens01:25

Rapid Identification of Pathogens

MALDI-TOF MS has transformed clinical microbiology by offering a rapid and reliable method for pathogen identification. The traditional approach to microbial identification typically involves time-consuming culture techniques and biochemical tests, which can delay the initiation of appropriate antimicrobial therapy. MALDI-TOF MS avoids these delays by using characteristic ribosomal protein mass patterns of microbial cells, enabling accurate species-level identification within minutes.Principle...

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Related Experiment Video

Updated: Jul 6, 2026

A Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Platform for Investigating Peptide Biosynthetic Enzymes
11:32

A Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Platform for Investigating Peptide Biosynthetic Enzymes

Published on: May 4, 2020

High-Performance Computing in Tandem Mass Spectrometry (MS/MS) Peptide Identification.

Chuang Li1, Qiang He2, Tao Chen3

  • 1School of Computer Science, Hunan University of Technology and Business, Changsha, China.

Methods in Molecular Biology (Clifton, N.J.)
|July 4, 2026
PubMed
Summary

SW-Tandem accelerates peptide identification using high-performance computing (HPC) on the Sunway TaihuLight supercomputer. This framework enhances computational efficiency and accuracy for large-scale proteomics research.

Keywords:
BioinformaticsHigh-performance computingMS/MSParallel computingPeptide identification

More Related Videos

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

Related Experiment Videos

Last Updated: Jul 6, 2026

A Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Platform for Investigating Peptide Biosynthetic Enzymes
11:32

A Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Platform for Investigating Peptide Biosynthetic Enzymes

Published on: May 4, 2020

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
  • Bioinformatics
  • Computational Biology

Background:

  • Tandem mass spectrometry (MS/MS) generates large datasets for proteomics, posing computational challenges for peptide identification.
  • Conventional database search methods struggle with expanding protein repositories and complex spectra.
  • High-performance computing (HPC) offers parallelization and optimization for large-scale data analysis.

Purpose of the Study:

  • To introduce SW-Tandem, an efficient framework for peptide identification.
  • To leverage HPC for parallelizing the spectrum dot product scoring algorithm.
  • To improve computational performance and accuracy in large-scale proteomics.

Main Methods:

  • Implementation of SW-Tandem on the Sunway TaihuLight supercomputer.
  • Parallelization of the spectrum dot product scoring algorithm.
  • Incorporation of memory-access optimization, double buffering, and vectorization techniques.

Main Results:

  • SW-Tandem demonstrated marked improvements in computational performance.
  • The framework maintained high identification accuracy.
  • SW-Tandem significantly accelerated peptide identification compared to state-of-the-art methods across multiple nodes.

Conclusions:

  • SW-Tandem effectively addresses computational challenges in large-scale proteomics.
  • Integrating HPC with algorithmic enhancements advances bioinformatics research.
  • The framework shows potential for future large-scale biological data analysis.