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Published on: May 31, 2012
Using the Human Plasma PeptideAtlas to study human plasma proteins
Terry Farrah1, Eric W Deutsch, Ruedi Aebersold
1Institute for Systems Biology, Seattle, WA, USA. tfarrah@systemsbiology.org
Methods in Molecular Biology (Clifton, N.J.)
|April 7, 2011
Summary
The Human Plasma PeptideAtlas provides a unified resource for proteomics data from 91 studies. This database allows researchers to explore identified peptides and proteins, aiding in the discovery of biomarkers like cytokine receptors.
Area of Science:
- Proteomics
- Biochemistry
- Bioinformatics
Background:
- Large-scale proteomics studies generate vast amounts of data.
- Data heterogeneity from diverse laboratories and analysis pipelines hinders integration.
- A unified database is needed for efficient human plasma proteome exploration.
Purpose of the Study:
- To introduce the Human Plasma PeptideAtlas, a comprehensive database of human plasma and serum proteomics data.
- To demonstrate the utility of the database for identifying and analyzing specific proteins, such as cytokine receptors.
Main Methods:
- Aggregated LC-MS/MS shotgun proteomics data from 91 experiments.
- Standardized data processing using a uniform analysis pipeline.
- Web interface for searching, browsing, and visualizing peptide and protein identifications, spectra, and supporting information.
Main Results:
- The Human Plasma PeptideAtlas contains extensive proteomics data from human plasma and serum.
- The database enables users to search for identified peptides and proteins.
- Supporting information including chromosomal mapping, estimated abundances, and sequence alignments is readily available.
Conclusions:
- The Human Plasma PeptideAtlas serves as a valuable, accessible resource for the proteomics community.
- The database facilitates the exploration of the human plasma proteome, exemplified by the analysis of cytokine receptors.
- Standardized data processing ensures data quality and comparability across experiments.
