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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 Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
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 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,...

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Related Experiment Video

Updated: May 21, 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

Soybean Proteome Database 2012: update on the comprehensive data repository for soybean proteomics.

Hajime Ohyanagi1, Katsumi Sakata, Setsuko Komatsu

  • 1Tsukuba Division, Mitsubishi Space Software Co., Ltd, Tsukuba, Japan.

Frontiers in Plant Science
|June 5, 2012
PubMed
Summary

The enhanced Soybean Proteome Database now offers comprehensive protein data for functional analysis of soybean stress responses. This resource aids researchers in understanding plant resilience to flooding, salt, and drought conditions.

Keywords:
2-DE (two-dimensional polyacrylamide gels electrophoresis)Glycine max cv. Enreidatabasegel-free proteomics techniqueproteomicssoybean

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Related Experiment Videos

Last Updated: May 21, 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

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
14:51

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Area of Science:

  • Plant science
  • Proteomics
  • Bioinformatics

Background:

  • Flooding stress significantly impacts soybean production.
  • Existing databases lacked comprehensive functional analysis data for soybean stress responses.

Purpose of the Study:

  • To update and expand the Soybean Proteome Database (SPD) with enhanced protein data.
  • To facilitate functional analyses of soybean responses to various environmental stresses.

Main Methods:

  • Expanded database with 23 reference maps of soybean proteins from various organs and organelles.
  • Included proteomic data analyzed by both 2D-PAGE and gel-free techniques.
  • Integrated 'omics data (mRNAs, proteins, metabolites) with temporal profiles.

Main Results:

  • The updated SPD contains extensive protein annotations and analysis data for soybean.
  • New data includes protein fluctuations under flooding, salt, and drought stress.
  • An intuitive interface allows integrated browsing of multi-omics data and networks.

Conclusions:

  • The enhanced SPD provides a valuable resource for soybean functional genomics and stress response research.
  • The integrated 'omics data facilitates deeper understanding of plant adaptation mechanisms.
  • The database supports efficient data retrieval and network analysis for soybean researchers.