Validation

mzTab-M files can be validated at multiple levels, from basic structural compliance to full semantic correctness against controlled vocabularies and quantification reporting rules.

Validation Approach

Validation in mzTab-M is structured around validation profiles that reflect the level of identification and quantification evidence present in a file. A file is validated against the profile that matches its mzTab-mode and mzTab-type declarations.

Validation Levels

Minimal

Checks mandatory fields, correct section ordering, and tab-delimited structure.

Structural

Adds cross-reference consistency (SML ↔ SMF ↔ SME links), column cardinality, and assay/study-variable definitions.

Semantic

Adds controlled vocabulary term resolution — all [param] entries are checked against their declared ontologies.

Tools

  • Web Validator — browser-based, no installation required.

  • jmzTab-m CLI — command-line validation with detailed error reporting and machine-readable output.

Validation Output

The validator produces a structured list of validation messages, each with:

  • A severity level (ERROR, WARN, INFO)

  • A line number and column reference

  • An error code from the mzTab-M error code registry

  • A human-readable description

Files containing ERROR-level messages do not conform to the specification. WARN-level messages indicate deviations from best practices.