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Proteomics

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 Networks

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 Networks

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,...

Tagging and Fusion Proteins

Tagging and Fusion Proteins

Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...

Peptide Identification Using Tandem Mass Spectrometry

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-protein Interfaces

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

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

[Knowledge-based technologies in proteomics].

E A Ponomarenko, E V Il'gisonis, A V Lisitsa

Bioorganicheskaia Khimiia

|July 5, 2011

Summary

This summary is machine-generated.

Proteomic data analysis requires robust storage and processing. This review explores knowledge-based tools for extracting insights from large-scale proteomic datasets.

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Last Updated: May 31, 2026

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Area of Science:

Proteomics
Bioinformatics
Data Science

Context:

Proteomic technologies identify thousands of proteins, generating vast datasets.
Effective storage, dissemination, and analysis are crucial for knowledge discovery.
Controlled vocabularies like GeneOntology and Medical Subjects Headings aid data processing.

Purpose:

To review modern analytical tools for proteome research.
To highlight the importance of knowledge-based technologies in data interpretation.
To discuss the need for centralized proteomic data storage and revision.

Summary:

Proteomic data analysis relies on controlled vocabularies and centralized repositories (e.g., PRIDE, PeptideAtlas).
Knowledge-based technologies enable comparison of identified proteins with ontologies and pathways.
This paper surveys analytical tools leveraging these technologies for advanced proteome research.

Impact:

Facilitates more efficient and accurate interpretation of complex proteomic data.
Supports the development of advanced data extraction and knowledge discovery technologies.
Enhances the integration of proteomic findings with existing biological knowledge domains.