Accurate and Rational Collision Cross Section Prediction Using Voxel-Projected Area and Deep Learning

Ion mobility spectrometry–mass spectrometry (IMS-MS) enables rapid acquisition of collision cross section (CCS), a critical physicochemical property for analyte characterization. Despite CCS being theoretically defined as the rotationally averaged projected area of 3D atomic spheres, existing models have underutilized this geometric insight. Here, we present a projected area–based CCS prediction method (PACCS). It integrates voxel-projected area approximation, graph neural network (GNN)–extracted features, and m/z to achieve accurate and rational CCS prediction. A voxel-based algorithm efficiently calculates molecular projected areas by leveraging Fibonacci grids sampling and discretizing 3D conformers into voxel grids. PACCS demonstrates exceptional performance, achieving a median relative error (MedRE) of 1.03% and a coefficient of determination (R²) of 0.994 on the test set. External test set against AllCCS2, GraphCCS, SigmaCCS, CCSbase, and DeepCCS highlights the superiority of PACCS, with 80.1% of predictions exhibiting < 3% error. Notably, PACCS exhibits broad applicability across diverse molecular types, including environmental contaminants (R² = 0.954–0.979) and structurally complex phycotoxins (R² = 0.961), highlighting the superiority of PACCS in robustness and versatility. Computational efficiency is enhanced via parallelization, enabling large-scale CCS database generation (e.g., 5.9 million entries for ChEMBL within 10 h). Ablation studies confirm the pivotal role of voxel-projected areas (Pearson correlation coefficients > 0.988), while stability analyses reveal minimal sensitivity to conformational variability (standard deviation of R² is 0.00003). PACCS provides an open-source, scalable solution for expanding CCS databases, advancing compound identification in metabolomics and environmental analysis.