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Related Concept Videos

Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

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Updated: May 23, 2026

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
14:58

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

A complex standard for protein identification, designed by evolution.

Marc Vaudel1, Julia M Burkhart, Daniela Breiter

  • 1Leibniz-Institut für Analytische Wissenschaften, ISAS, e.V., Dortmund, Germany.

Journal of Proteome Research
|April 12, 2012
PubMed
Summary
This summary is machine-generated.

The Pyrococcus furiosus proteome serves as a novel standard for evaluating proteomics identification workflows. It reliably detects false positives and true positives, improving algorithm accuracy.

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Last Updated: May 23, 2026

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
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Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

An Integrated Approach for Microprotein Identification and Sequence Analysis
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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

  • Proteomics
  • Bioinformatics
  • Mass Spectrometry

Background:

  • Shotgun proteomics relies on accurate peptide-spectrum matching.
  • Current reference samples for algorithm validation are often inadequate.
  • Novel algorithms require robust evaluation methods.

Purpose of the Study:

  • To introduce Pyrococcus furiosus proteome as a standard for validating proteomics identification algorithms.
  • To demonstrate its effectiveness in detecting both false and true positive peptide identifications.
  • To enable rigorous testing of proteomics workflows.

Main Methods:

  • Utilized the Pyrococcus furiosus proteome as a reference standard.
  • Applied standard proteomics identification workflows to the reference proteome.
  • Compared results against decoy databases and known true positives.

Main Results:

  • The Pyrococcus furiosus proteome effectively detects random hits, similar to decoy databases.
  • It provides hundreds of highly reliable true positive hits.
  • This standard enables detection of both false and true positives at the proteome scale.

Conclusions:

  • The Pyrococcus furiosus proteome is a superior standard for evaluating proteomics identification algorithms.
  • It offers a more comprehensive validation than traditional decoy approaches.
  • This method enhances the rigor and accuracy of peptide and protein identification in proteomics.