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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...
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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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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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Updated: Jun 28, 2026

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry
11:54

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.

Gelio Alves1, Aleksey Y Ogurtsov, Yi-Kuo Yu

  • 1National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA. alves@ncbi.nlm.nih.gov

BMC Genomics
|October 29, 2008
PubMed
Summary
This summary is machine-generated.

Researchers have developed enhanced databases and software (RAId_DbS) integrating amino acid variations and disease associations for 17 organisms. This tool aids in proteomics research by improving peptide identification and facilitating hypothesis generation for clinical studies.

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Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry
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Published on: April 1, 2017

Area of Science:

  • Bioinformatics
  • Proteomics
  • Genomics

Background:

  • Scientific literature provides valuable biological information, including disease markers.
  • Integrating literature data with analysis aids in identifying research controversies and forming hypotheses.
  • Individualized proteomics can be advanced by considering amino acid changes and disease associations.

Purpose of the Study:

  • To create comprehensive databases integrating single amino acid polymorphisms (SAPs), post-translational modifications (PTMs), and their disease associations.
  • To enhance peptide identification software (RAId_DbS) to utilize this integrated data for tandem mass spectrum analysis.
  • To facilitate hypothesis generation and discovery in proteomics by enabling targeted or exploratory searches.

Main Methods:

  • Integrated annotated single amino acid polymorphisms, post-translational modifications, and disease associations from various sources into organism-specific databases.
  • Augmented peptide identification software (RAId_DbS) to incorporate this integrated data during tandem mass spectrum analysis.
  • Developed search functionalities within RAId_DbS to either respect or ignore correlations of polymorphisms/modifications and to permit searches for novel polymorphisms.

Main Results:

  • Constructed enhanced databases for 17 organisms, incorporating detailed information on amino acid variations and disease links.
  • RAId_DbS software was successfully augmented to analyze tandem mass spectra using the enhanced databases.
  • The system allows for both targeted searches (respecting known correlations) and exploratory searches (ignoring correlations or allowing novel polymorphisms).

Conclusions:

  • Enhanced databases and the RAId_DbS software are available for 17 organisms.
  • The tool facilitates dynamic information retrieval for proteomics studies, potentially accelerating clinical laboratory research.
  • Access to RAId_DbS and databases is provided via a web link for download and use.