MEPDOXP

MEPDOXP stands for Modular Experimental Protocol for Data Exchange in Proteomics. It is a community-driven framework intended to standardize the description of proteomics experiments and facilitate sharing and reproducibility of data across laboratories. The central idea is to separate experimental protocol descriptions from raw data, using modular blocks that specify steps, parameters, and dependencies in a machine-readable form.

The protocol is organized into modules such as sample preparation, instrument settings, and data processing, each with defined inputs, outputs, and validation criteria. Metadata fields cover experimental design, reagents, instrument configurations, quality control metrics, and data provenance. Protocol descriptions can be serialized in JSON or YAML and linked to data files encoded in established formats such as mzML and mzIdentML. A reference implementation provides validators to check syntax and completeness and to generate human-readable glossaries from machine-readable definitions.

Adoption and impact: Several laboratories and research consortia have piloted MEPDOXP to enable cross-lab replication and meta-analysis. Journals increasingly encourage or require MEPDOXP-compliant method reporting, and repositories are emerging to host validated modules. Strengths include improved reproducibility, easier method sharing, and clearer provenance chains.

Limitations and future directions: Adoption is not universal, and the learning curve for authors and reviewers can be nontrivial. Ongoing work focuses on broader interoperability with established data standards such as ISA-Tab and the PSI formats, better integration with electronic lab notebooks and LIMS, and expansion of the module registry to cover more experimental workflows.