Enabling direct access to proprietary GC-MS data through black-box reconstruction of the Chromatec binary format

Proprietary data formats used by vendors of analytical instruments limit data portability, reproducibility, and reuse of raw data. When official application programming interfaces are unavailable, access to such data often relies on black-box reverse engineering, but the underlying strategies are rarely described in a systematic and transparent manner. In this work, we reconstructed the proprietary Chromatec .msdx binary format for gas chromatography - mass spectrometry (GC-MS) data, explicitly documented the reconstruction workflow, and implemented an open-source parser as the msdxr package for R. The parser was validated using test files corresponding to different acquisition modes, and the extracted data showed quantitative agreement with data exported from the vendor software. The utility of the package for GC-MS data handling was demonstrated using an environmental monitoring dataset comprising soil and water samples. A retrospective screening workflow based on automated prioritization of candidate files revealed signals tentatively assigned to polychlorinated biphenyls in previously acquired GC-MS data, without sample reanalysis or manual data conversion. The results show that reconstructing proprietary analytical data formats can support reproducible data handling, facilitate integration with advanced data-processing workflows, and increase the long-term value of datasets stored in vendor-specific formats.