sdrf-pipelines

sdrf-pipelines validates and converts Sample Description Format (SDRF) files into workflow configuration files for MSstats, OpenMS, and MaxQuant and supports mzIdentML, mzML, and mzTab formats to standardize sample-to-data file metadata.

Key Features:

• Metadata validation and conversion: Validates SDRF files for metadata completeness and accuracy and converts them as part of the standardization process.
• Workflow configuration generation: Produces configuration files tailored for MSstats, OpenMS, and MaxQuant from validated SDRF metadata.
• Support for standard proteomics formats: Handles and preserves references to mzIdentML, mzML, and mzTab file formats during conversion.
• Sample-to-data file metadata standardization: Emphasizes capture and standardization of sample-to-data file relationships to improve dataset interoperability.

Scientific Applications:

• Reproducibility and reanalysis: Enables more reproducible proteomics analyses and facilitates reanalysis by ensuring sample-to-data file metadata are complete and machine-readable.
• Standards development and community adoption: Supports European Bioinformatics Community for Mass Spectrometry (EuBIC) efforts toward a standardized sample metadata format (PMID: 32786688).

Methodology:

Validation of metadata completeness, with emphasis on sample-to-data file information, and conversion of validated SDRF files into workflow-specific configuration files.