RawTools

RawTools extracts and analyzes information from Thermo Orbitrap raw mass spectrometry files to provide metrics for proteomics data quality assessment and instrument performance optimization.

Key Features:

• Data Extraction Capabilities: Extracts meta-data, scan details, quantification metrics, and identification data directly from Thermo Orbitrap raw files.
• Output Generation: Generates summarized and detailed plain text outputs reporting scan rates, durations, duty cycle characteristics, precursor and reporter ion quantification, and chromatography performance metrics.
• Diagnostic Module: Includes a diagnostic module with an optional "preview" database search that provides performance metrics to inform system optimization.
• Cross-Platform Compatibility: Implemented in C# and uses the Thermo RawFileReader library to parse raw files on Windows, MacOS, and Linux.
• Performance Evaluation: Processes individual and large collections of raw MS files to identify problematic instrument performance characteristics.

Scientific Applications:

• Proteomics experiment optimization: Supports optimization of mass spectrometry acquisition parameters for Thermo Orbitrap–based proteomics experiments.
• Instrument performance monitoring: Enables assessment and longitudinal monitoring of instrument performance via metrics extracted from raw files.
• Quality control and troubleshooting: Identifies problematic characteristics in instrument performance to aid QC and troubleshooting of MS data acquisition.
• Data characterization for downstream analysis: Provides detailed scan- and quantification-level metrics to inform downstream identification and quantification workflows.

Methodology:

Parses Thermo Orbitrap raw files using the Thermo RawFileReader library in a C# implementation to produce summarized and detailed plain text outputs, with an optional "preview" database search in the diagnostic module.