ThermoRawFileParser

ThermoRawFileParser converts Thermo RAW mass spectrometer files into open proteomics formats to enable downstream identification and quantification analyses.

Key Features:

• File format conversion: Converts Thermo RAW files to Mascot Generic Format (MGF) and the HUPO-PSI standard mzML.
• Scalability: Supports processing of increasing sample numbers and large per-run data volumes using elastic compute resources such as Linux-based clusters and cloud infrastructures.
• Cross-platform open-source implementation: Provides a cross-platform, open-source converter for integration into computational proteomics pipelines.
• Workflow interoperability: Integrates with workflow systems such as Galaxy and Nextflow for pipeline-based analyses.
• Quantitative fidelity benchmarking: Generates mzML files whose quantitative results have been benchmarked and validated against msconvert.

Scientific Applications:

• Proteomics data preprocessing: Converts proprietary Thermo RAW data into MGF and mzML for downstream peptide/protein identification and quantification.
• Large-scale proteomics: Enables analysis of high-throughput studies that produce many samples or large files per run in cluster- or cloud-based environments.
• Pipeline integration: Serves as a conversion component within Galaxy- or Nextflow-based proteomics workflows.

Methodology:

Performs direct conversion of Thermo RAW files to MGF and HUPO-PSI mzML; conversion outputs and quantitative fidelity have been benchmarked against msconvert.