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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...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...

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Related Experiment Video

Updated: May 29, 2026

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides
08:37

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides

Published on: November 2, 2021

A face in the crowd: recognizing peptides through database search.

Jimmy K Eng1, Brian C Searle, Karl R Clauser

  • 1University of Washington, Department of Genome Sciences, Seattle, WA 98195, USA. engj@u.washington.edu

Molecular & Cellular Proteomics : MCP
|August 31, 2011
PubMed
Summary
This summary is machine-generated.

Peptide identification using tandem mass spectrometry (MS/MS) database searching is crucial for proteomics. This review explains MS/MS search mechanisms and how parameter settings influence peptide and protein identification results.

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Peptide-based Identification of Functional Motifs and their Binding Partners
14:28

Peptide-based Identification of Functional Motifs and their Binding Partners

Published on: June 30, 2013

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Last Updated: May 29, 2026

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides
08:37

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides

Published on: November 2, 2021

Peptide-based Identification of Functional Motifs and their Binding Partners
14:28

Peptide-based Identification of Functional Motifs and their Binding Partners

Published on: June 30, 2013

Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biochemistry

Background:

  • Peptide identification using tandem mass spectrometry (MS/MS) sequence database searching is a fundamental technique in proteomics.
  • Advances in instrumentation and software have made MS/MS data acquisition and peptide/protein identification routine.
  • Numerous MS/MS database search tools exist, sharing core algorithms but differing in specific features.

Purpose of the Study:

  • To revisit the fundamental mechanism of sequence database searching for peptide identification.
  • To discuss the impact of various parameter settings on the underlying search algorithms.
  • To provide insights for proteomics researchers utilizing MS/MS data.

Main Methods:

  • Review of existing literature on tandem mass spectrometry (MS/MS) database searching algorithms.
  • Analysis of the core components and distinctive features of various search tools.
  • Discussion of the influence of parameter optimization on search outcomes.

Main Results:

  • Sequence database searching is a key proteomics method for peptide identification.
  • MS/MS data acquisition and analysis are widely adopted due to technological advancements.
  • Different search algorithms share common principles but possess unique characteristics.

Conclusions:

  • Understanding MS/MS search mechanisms is vital for accurate peptide and protein identification.
  • Parameter settings significantly affect the results of database searches.
  • This review offers a foundational understanding for optimizing proteomics analyses.