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Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification
Published on: August 17, 2015
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Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics
Ulrike Kusebauch1, Eric W Deutsch1, David S Campbell1
1Institute for Systems Biology, Seattle, Washington.
Current Protocols in Bioinformatics
|June 19, 2014
Summary
PeptideAtlas, SRMAtlas, and PASSEL are web resources for proteomics research. These databases provide accessible tools for submitting, searching, and downloading mass spectrometry data for protein discovery and quantification.
Area of Science:
- Proteomics
- Bioinformatics
- Mass Spectrometry
Background:
- Proteomics research relies on robust data repositories for protein identification and quantification.
- Existing resources may lack standardization or comprehensive data integration.
- Accessible, user-friendly platforms are crucial for advancing proteomic discovery.
Purpose of the Study:
- To describe the utility of PeptideAtlas, SRMAtlas, and PASSEL for proteomics research.
- To provide guidance on data submission, searching, collation, and download.
- To highlight these resources as valuable tools for the scientific community.
Main Methods:
- Utilizing standardized mass spectrometry data analysis with statistical validation.
- Compiling shotgun proteomic data into PeptideAtlas.
- Generating high-quality, complete proteome SRM assays for SRMAtlas.
- Compiling selected reaction monitoring data into PASSEL.
Main Results:
- PeptideAtlas, SRMAtlas, and PASSEL offer integrated, web-accessible platforms.
- Standardized data processing ensures high-quality, reliable proteomic information.
- Resources provide intuitive search functionalities and data visualization options.
Conclusions:
- PeptideAtlas, SRMAtlas, and PASSEL significantly support proteomics discovery and targeted research.
- These freely available resources facilitate data sharing and analysis.
- The described protocols enhance the usability and accessibility of proteomic data.
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