MzIdentML Converter

About This Tool

The mzIdentML Converter ingests mzIdentML files and outputs analysis-ready tables. It standardizes field names for identifications, including peptide sequences, protein references, scores, and modifications, so results can be fed into downstream analyses and repositories. Conceptually, the tool parses the mzIdentML structure, extracts PSMs and protein mappings, and re-exports them into flat formats that are easy to join with other data sources. It supports both single-file and batch workflows and preserves provenance metadata such as search engine and filtering criteria. Users benefit from a consistent export path that reduces manual reformatting and improves reproducibility across projects. Core features include schema validation, field mapping, decoy handling, and optional protein database cross-referencing. The converter is designed for reproducible pipelines and provides options to customize visible columns, include detailed modification information, and export in multiple formats for different analysis stages. Typical use cases include preparing data for statistical analysis, submitting identifications to public repositories, or powering dashboards with up-to-date results. The tool emphasizes robust error reporting, audit trails, and compatibility with mzIdentML versions 1.2 and 1.4, enabling researchers to standardize data exchange while preserving critical metadata and scoring information.

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