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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 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...
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...
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...

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Related Experiment Video

Updated: Jun 10, 2026

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

Protein Information and Knowledge Extractor: Discovering biological information from proteomics data.

J Alberto Medina-Aunon1, Alberto Paradela, Marcus Macht

  • 1Proteomics Facility, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain.

Proteomics
|August 14, 2010
PubMed
Summary

The Protein Information and Knowledge Extractor (PIKE) tool automates biological data collection for proteomics research. This bioinformatics solution streamlines the process of gathering and organizing protein information from public databases, reducing manual effort.

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Last Updated: Jun 10, 2026

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

mRNA Interactome Capture from Plant Protoplasts
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mRNA Interactome Capture from Plant Protoplasts

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

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Proteomics research requires extensive data collection from public repositories for identified proteins.
  • Manual data gathering is infeasible due to the complexity and volume of biological information.
  • Automated methods are essential for efficient data procurement in large-scale proteomic studies.

Purpose of the Study:

  • To develop an automated tool for extracting and organizing biological data for identified proteins.
  • To address the challenge of manual database validation in proteomics.
  • To facilitate the analysis and organization of protein information for biological and molecular research.

Main Methods:

  • Developed the Protein Information and Knowledge Extractor (PIKE) tool.
  • PIKE accesses multiple public information systems and databases.
  • Input: protein database accession codes; Output: summarized protein information in various file formats.

Main Results:

  • PIKE automatically retrieves relevant and updated information for a given set of proteins.
  • The tool summarizes data, enabling information sharing with other software.
  • Significantly reduces the time and effort required for manual database validation.

Conclusions:

  • PIKE represents a significant advancement in automated information procurement for proteomics.
  • The tool streamlines data collection and organization, supporting complex biological questions.
  • Facilitates large-scale proteomic studies by reducing manual data handling.