jmztab-m

jmztab-m implements the mzTab 2.0 (mzTab-M) format for metabolomics to read, write, and validate standardized metabolomics data including experimental metadata, small-molecule summaries across assays, mass spectrometry (MS) features for quantitation, and identification evidence.

Key Features:

• Format Design: Implements mzTab-M as a tab-delimited format that captures experimental metadata, assay-level small-molecule summaries, MS quantitation features, and identification evidence.
• Java reference implementation: Provides a Java library to read, write, and validate mzTab-M files as a reference implementation.
• Command-line validator: Includes a command-line validator to perform automated validation of mzTab-M files.
• Multi-language implementations: Provides additional implementations in Python and R to support integration into diverse computational workflows.
• Standards provenance: Serves as a reference implementation developed in collaboration with the Proteomics and Metabolomics Standards Initiatives and contributions from the Lipidomics Standards Initiative.

Scientific Applications:

• Metabolomics data standardization: Enables standardized reporting of metabolomics experiments using the mzTab-M schema.
• Small-molecule quantitation: Supports reporting of assay-level small-molecule summaries and MS-based quantitation features for comparative analyses.
• Identification evidence reporting: Records evidence for identification of individual or grouped features to support metabolite identification and downstream validation.
• Cross-domain interoperability: Facilitates standardized data exchange and interoperability between metabolomics and proteomics workflows.

Methodology:

Implements the mzTab-M tab-delimited format and provides a Java library to read, write, and validate mzTab-M files, together with a command-line validator and additional Python and R implementations.