ProHits

ProHits manages, stores, searches, and analyzes mass spectrometry (MS) data to support identification and analysis of protein‑protein interactions from affinity purification coupled with mass spectrometric identification (AP‑MS).

Key Features:

• Data Management Module: Performs backup, raw file conversion, database searches, instrument‑specific storage, and assigns unique identifiers to folders and files for tracking.
• Analyst Module: Organizes data by project, bait, experiment, and sample, supports gel‑based and gel‑free approaches, and retrieves bait gene names, species‑specific sequences, and annotations.
• Admin Office Module: Manages projects, instruments, user permissions, and protein databases.
• ProHits Lite: Accepts and integrates pre‑computed search results from core MS facilities and external data management systems.
• Client Implementation: Implements a PHP‑based client interfacing with a MySQL database on a dedicated server.
• Search Engine Integration: Integrates with Mascot, X!Tandem, and the TransProteomics Pipeline (TPP) via linked search engine servers for database searching.
• Data Conversion: Uses ProteoWizard converters to automatically convert raw MS files into formats appropriate for downstream analysis.

Scientific Applications:

• AP‑MS protein‑protein interaction discovery: Supports affinity purification coupled to MS workflows for identifying novel protein interactions.
• Raw MS data archiving and retrieval: Provides instrument‑specific storage and unique identifiers for long‑term archival and tracking of raw MS files.
• Database‑driven protein identification: Enables Mascot, X!Tandem, and TPP‑based peptide/protein identification workflows and result integration.

Methodology:

ProHits assigns unique identifiers and organizes instrument‑specific raw files and experimental metadata (project/bait/experiment/sample), uses ProteoWizard for raw file conversion, performs database searches via linked Mascot, X!Tandem, and TPP servers, and stores information in a PHP client interfacing with a MySQL database.