PROTICdb

ProTICdb manages storage, annotation, enrichment, querying, and programmatic access for mass spectrometry (MS)-based proteomic data to support comparative proteomics analyses.

Key Features:

• Data Handling and Storage: Archives MS-based proteomic data including quantification metrics and maintains independence from specific data-generation tools.
• Ontology-Based Annotation: Employs ontology terms to describe biological samples and proteomics data for standardized annotation.
• Automated Data Enrichment: Integrates a Taverna workflow to automatically retrieve information related to identified proteins by querying external databases.
• Sophisticated Querying Capabilities: Provides a "Query Builder" for constructing complex database queries.
• Graphical Data Display: Supports graphical representation of stored proteomic data for visualization and interpretation.
• Programmatic Access: Exposes a Java client API and RESTful web services for programmatic access and integration into research workflows.

Scientific Applications:

• Comparative Proteomics: Enables comparison of proteomes across different experimental conditions and methodologies.
• Example Application: Facilitates analysis such as comparing proteins extracted from maize leaf samples using four extraction methods analyzed via a label-free shotgun approach.

Methodology:

Integration of bioinformatics tools with an embedded Taverna workflow for automatic enrichment via external database queries, and use of ontology terms for dataset annotation.