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Updated: May 19, 2026
07:44
Identifying Protein-protein Interaction Sites Using Peptide Arrays
Published on: November 18, 2014
Interfaces to PeptideAtlas: a case study of standard data access systems
Sarah Killcoyne1, Jeremy Handcock, Thomas Robinson
1Institute for Systems Biology, Seattle, WA 98109, USA.
Briefings in Bioinformatics
|September 4, 2012
Summary
Public data access is crucial for scientific advancement. This study compares BioMart, caBIG, and Google Data Sources for accessing research data, highlighting suitability based on specific needs and tradeoffs.
Area of Science:
- Bioinformatics
- Data Science
- Scientific Data Management
Background:
- Public data sets are vital for scientific research, enabling new experiments and data validation.
- Platforms like PeptideAtlas, Ensembl, and The Cancer Genome Atlas (TCGA) provide access to and repositories for public data.
- Web protocols (e.g., HTTP) and web service APIs (e.g., REST, SOAP) are commonly used for data access.
Purpose of the Study:
- To examine and compare three common access mechanisms for web-accessible data: BioMart, caBIG, and Google Data Sources.
- To illustrate the implementation of these mechanisms using the PeptideAtlas repository.
- To review their suitability for common research use cases.
Main Methods:
- Implementation of BioMart, caBIG, and Google Data Sources over the PeptideAtlas data repository.
- Evaluation of each access mechanism based on specific research usage scenarios.
- Analysis of tradeoffs inherent in each technology, such as security versus speed.
Main Results:
- BioMart, caBIG, and Google Data Sources demonstrate varying suitability for different research data access needs.
- Each access mechanism presents distinct tradeoffs in design, impacting usability for specific applications.
- The choice of access technology depends on the specific requirements of the research task.
Conclusions:
- Understanding the specific requirements and tradeoffs of data access technologies is essential for effective selection.
- Different access mechanisms are optimized for different use cases, necessitating careful consideration.
- The PeptideAtlas repository serves as a practical platform for evaluating these data access tools.
Related Concept Videos
02:04Protein-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...
01:33Peptide 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...
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...
02:26Protein 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,...
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,...