pygecko

pyGecko is an open-source Python library designed for the parsing, processing, and analysis of raw data from Gas Chromatography-Mass Spectrometry (GC-MS) and Gas Chromatography-Flame Ionization Detection (GC-FID). It addresses the bottleneck of manual data processing in high-throughput experimentation (HTE) by enabling automated or semi-automated handling of measurements and sequences. Key features include the interpretation of measurements within experimental contexts, automatic identification of internal standards, and compound identification based on retention times, molecular ion mass, fragments, and spectral comparison. For GC-FID measurements, it supports quantification relative to an internal standard. The library facilitates the integration of analytical methods into closed-loop systems and standardized storage of reaction data. Results, chromatograms, and spectra can be visualized and exported in standardized formats such as the Open Reaction Database (ORD) schema, mzML, and ANDI/AIA netCDF. pyGecko supports various file formats including .mzML, .mzXML, .D (Agilent), .RAW (Thermo), .cdf, .xy, and .CSV. It requires the msConvert tool from ProteoWizard for reading certain vendor files. The library is designed for easy integration into automated workflows and can be used as a standalone tool or a Python library, with documentation available online and example notebooks provided for quantitative analysis and spectral matching.