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Related Concept Videos

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...
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...
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...
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...
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...
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...

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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Fast multi-blind modification search through tandem mass spectrometry.

Seungjin Na1, Nuno Bandeira, Eunok Paek

  • 1Division of Computer Science and Engineering, Hanyang University, Seoul 133-791, Korea.

Molecular & Cellular Proteomics : MCP
|December 22, 2011
PubMed
Summary

MODa is a new algorithm for fast, unrestrictive post-translational modification (PTM) identification in proteomics. It significantly speeds up analysis and improves accuracy, potentially replacing older methods.

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Area of Science:

  • Proteomics and Mass Spectrometry
  • Bioinformatics and Computational Biology

Background:

  • Post-translational modifications (PTMs) are crucial for biological function, driving interest in their identification using MS/MS.
  • Current PTM identification methods often focus on unrestrictive searches, but face challenges with extended search times, false positives, and false negatives.

Purpose of the Study:

  • To introduce MODa, a novel multi-blind spectral alignment algorithm for fast and unrestrictive PTM searches.
  • To overcome the limitations of existing approaches in high-throughput proteomics analysis.

Main Methods:

  • Development of MODa, a multi-blind spectral alignment algorithm.
  • Application of MODa to human shotgun proteomics data for PTM identification.
  • Comparison of MODa's speed and sensitivity against existing PTM identification methods.

Main Results:

  • MODa achieves over an order of magnitude speedup compared to existing methods.
  • The algorithm allows unrestrictive PTM searches with no limitation on the number of modifications per peptide.
  • Analysis of human proteomics data revealed multiple mutations, diverse modifications including glycosylation, and evidence for novel modifications.

Conclusions:

  • MODa offers significant efficiency and sensitivity for unrestrictive PTM identification.
  • The algorithm has the potential to replace conventional restrictive identification methods in proteomics mass spectrometry.
  • MODa facilitates high-throughput analysis by addressing bottlenecks in speed and accuracy.