Proteios Software Environment

Proteios manages and analyzes proteomics experimental data to support proteome identification, quantification, annotation, and submission to public repositories.

Key Features:

• Local Data Repository: Provides a local repository for storing proteomics experimental data.
• Sample Tracking: Tracks samples throughout the analysis process.
• Project Sharing: Supports project sharing among multiple users.
• Automated Data Merging and Analysis: Automates merging of data from different sources and formats for downstream analysis.
• Quantitative Proteomics Workflows: Includes built-in support for several quantitative proteomics workflows.
• Integration with Search Engines: Integrates multiple search engines and facilitates automated combination of search results.
• False Discovery Rate Control: Applies predetermined false discovery rates when combining search results.
• Protein Annotation and Public Submission: Enables protein annotation and submission of results to public repositories.
• Programming Interface for Extensions: Provides a programming interface for developing local extensions.
• Database Access via Web Services: Supports database access via Web services.

Scientific Applications:

• Proteomics Data Management and Analysis: Manages and analyzes proteomics experimental data and workflows.
• Quantitative Proteomics: Supports workflows for protein quantification.
• Protein Identification and Validation: Combines search engine results and applies false discovery rate thresholds for protein identification.
• Protein Annotation and Deposition: Facilitates protein annotation and submission to public repositories.

Methodology:

Automated merging of heterogeneous data formats; integration and automated combination of multiple search engine results with application of predetermined false discovery rates; support for built-in quantitative proteomics workflows.