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Related Concept Videos

Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

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Related Experiment Video

Updated: May 31, 2026

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
07:38

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

The effect of using an inappropriate protein database for proteomic data analysis.

Giselle M Knudsen1, Robert J Chalkley

  • 1Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America.

Plos One
|June 23, 2011
PubMed
Summary

Reanalysis of proteomic data found no evidence of Iridovirus or Nosema in honey bee samples. The identified peptides were actually from the honey bee (Apis mellifera), highlighting potential pitfalls in mass spectrometry analysis.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Apiculture

Background:

  • A previous study identified Iridovirus and Nosema peptides in honey bees.
  • The validity of these findings has been questioned.

Purpose of the Study:

  • To re-analyze a subset of the original proteomic data.
  • To investigate the origin of identified peptides.
  • To illustrate potential issues in mass spectrometry data analysis.

Main Methods:

  • Re-analysis of mass spectrometry data from a previous study.
  • Peptide identification and spectral analysis.

Main Results:

  • Many spectra identified as Iridovirus and Nosema proteins were re-assigned to Apis mellifera (honey bee) proteins.
  • No reliable evidence for Iridovirus or Nosema proteins was found in the re-analyzed data.

Conclusions:

  • The original findings of Iridovirus and Nosema in honey bees are not supported by this re-analysis.
  • Emphasizes the importance of rigorous data analysis and reporting in mass spectrometry-based proteomics.
  • Highlights the need for adherence to MS/MS data reporting guidelines to ensure data validity and facilitate peer review.