Interactive Software for Interpreting and Curating High‐Resolution Electron Ionization Mass Spectra

Gas chromatography coupled with electron ionization and high-resolution mass spectrometry (GC-EI-HRMS) has been increasingly used in analytical chemistry in recent years. Databases (libraries) of such mass spectra are emerging, and various studies require processing batches of such data. This necessitates the development of user-friendly software for curation and batch processing of such data sets. In this work, we propose the "gchrmsexplain" software specifically developed for this purpose. It includes both a graphical user interface and a command-line interface. The software receives a peak list as input and finds a formula for each peak using in silico fragmentation or combinatorial enumeration. The isotopic pattern is checked. The fraction of the ion current due to the annotated peaks is calculated. The absolute error in determining m/z can be specified in either millidaltons or parts per million. Batch processing is possible. The software was applied to six publicly available GC-EI-HRMS data sets: RECETOX (exposome and metabolome libraries), HREI-MSDB, library from Castro's work (2022), and two subsets of MassBank EU. In total, these data sets contain 1811 mass spectra. Impurity peaks, systematic errors in m/z, and completely incorrect mass spectra were detected. It was shown that some of the data sets contain low-quality mass spectra. It was demonstrated that the presented software can be used for the curation of such data. The software is free and available online: https://github.com/mtshn/gchrmsexplain.