PIQMIe

PIQMIe integrates peptide and non-redundant protein identifications and semi-quantitative mass spectrometry-based quantitations across multiple experiments into a lightweight relational database to support comparative analyses and biological annotation.

Key Features:

• Semi-quantitative MS data handling: Processes semi-quantitative proteomics data derived from mass spectrometry-based experiments.
• Identification and quantitation integration: Integrates peptide and non-redundant protein identifications and quantitations across multiple experimental datasets.
• Biological enrichment: Enriches integrated protein data with additional biological information related to the proteins.
• Relational database storage: Organizes integrated data into a lightweight relational database that supports dedicated analyses and queries.
• Analytical interoperability: Supports dedicated analyses using tools such as R and enables user-driven queries against the database.
• Programmatic access: Provides a RESTful web service for programmatic data retrieval to enable automated and large-scale analyses and integration into workflows.
• Statistical evaluation support: Facilitates statistical evaluations of differential protein- and pathway-level regulations using established bioinformatics methods.

Scientific Applications:

• Comparative proteomics: Comparative analysis of semi-quantitative proteomics datasets to identify differential protein abundance across experiments.
• Cross-dataset aggregation: Aggregation of peptide and non-redundant protein identifications and quantitations from multiple experiments for combined analyses.
• Functional and pathway analysis: Enrichment and annotation of proteins to support pathway- and cellular process-level evaluations.
• Workflow integration: Programmatic integration into bioinformatics workflows and automated large-scale analyses via the RESTful web service.
• EMF exposure study application: Enabled analysis of semi-quantitative mass spectrometry data from human fibroblasts, osteosarcomas, and mouse embryonic stem cells exposed to ELF 50 Hz, UMTS 2.1 GHz, and WiFi 5.8 GHz, reporting that less than 1% of the proteome showed small abundance changes and no significant perturbation at the cellular process or pathway level.

Methodology:

Integrates peptide and protein identifications and quantitations, enriches proteins with biological information, organizes data in a lightweight relational database, supports analyses using R and user-driven queries, exposes data via a RESTful web service, and supports statistical evaluations of differential protein- and pathway-level regulations using established bioinformatics methods.