MSTune: A Data-Driven Approach to Parameter Tuning Using Grid Search and Differential Evolution for Gas Chromatography–Mass Spectrometry-Based Compound Identification

Background/Objectives: In gas chromatography–mass spectrometry (GC-MS) library-based compound identification, spectrum preprocessing and associated tuning parameters critically influence identification performance. These parameters are conventionally optimized using grid search, which requires predefined parameter spaces and becomes computationally inefficient as dimensionality increases, often failing to identify optimal values because of discretization. Differential evolution (DE), a population-based metaheuristic optimization algorithm, provides a flexible alternative through efficient global exploration of the parameter space. This study compared the performance of DE and grid search for optimizing compound identification. Methods: Cosine similarity was applied to the NIST GC-MS library. DE was used to maximize either cross-validated accuracy or mean reciprocal rank (MRR). Results were compared with those from a grid search over five equally spaced parameter values. Identification performance was evaluated using accuracy, MRR, and area under the receiver operating characteristic curve (AUC). Results: When all four parameters were optimized simultaneously, DE achieved slightly higher cross-validated accuracy and MRR than grid search, although the absolute differences were modest. More pronounced differences were observed in specific unidimensional tuning scenarios, particularly for the intensity weight factor. Simultaneous multidimensional parameter optimization yielded better performance than isolated parameter tuning. Conclusions: Grid search may be computationally advantageous when the parameter space is known and limited, whereas DE provides a more flexible approach for unknown or high-dimensional search spaces. Overall, DE achieved comparable identification performance to grid search, with modest improvements observed in some optimization settings. A command line Julia-based tool, MSTune, was developed for spectrum preprocessing parameter optimization and is publicly available on GitHub.