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Related Concept Videos

Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

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Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and signal-to-noise ratio for the analyte. 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 collision-induced...
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Peptide Identification Using Tandem Mass Spectrometry01:33

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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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Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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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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Mass Spectrometers01:16

Mass Spectrometers

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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:
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Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

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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 electrospray 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...
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Mass Analyzers: Overview01:13

Mass Analyzers: Overview

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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...
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Related Experiment Video

Updated: Aug 6, 2025

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry UPLC-MS
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Progressive search in tandem mass spectrometry.

Yoonsung Joh1, Kangbae Lee1, Hyunwoo Kim2

  • 1Department of Computer Science, Hanyang University, Seoul, 06978, Republic of Korea.

BMC Bioinformatics
|March 15, 2023
PubMed
Summary

High-throughput proteomics using tandem mass spectrometry is slowed by lengthy database searches. A new progressive search method significantly speeds up analysis of updated peptide databases, delivering identical results more efficiently.

Keywords:
AlgorithmsMass spectrometryProtein sequence analysisProteomics

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Analytical Chemistry

Background:

  • High-throughput proteomics relies on tandem mass spectrometry for accelerated analysis.
  • Current database search methods are time-consuming, with O(|S||D|) complexity, hindering up-to-date results.
  • Frequent database updates (0.5-2% changes) necessitate inefficient re-analysis from scratch, impacting result stability.

Purpose of the Study:

  • To develop an efficient method for updating tandem mass spectrometry analysis results.
  • To maintain result accuracy comparable to full database searches after updates.
  • To reduce the computational burden associated with evolving proteomics databases.

Main Methods:

  • Introduction of a 'progressive search' algorithm.
  • The method leverages the difference (ΔD) between old and new databases for targeted re-analysis.
  • Complexity is reduced to O(|S||ΔD|) on average.

Main Results:

  • Progressive search yields identical results to traditional scratch searches.
  • Achieved speedups of up to 53.9x for PSM (Peptide-Spectrum Match) updates.
  • Demonstrated speedups of up to 16.5x for combined PSM and E-value updates.

Conclusions:

  • Progressive search offers a novel and efficient approach for updated database analysis in proteomics.
  • This method significantly accelerates result generation compared to re-analyzing from scratch.
  • The progressive search tool is publicly available for use.