Deep3DCCS: Geometry-Driven Collision Cross Section Prediction from Multi-View Molecular Projection Tensors

Collision cross section (CCS) measurements from ion mobility–mass spectrometry improve confidence in molecular identification in metabolomics and lipidomics and reduce false-positive annotations in untargeted analyses. However, experimental CCS coverage remains incomplete, and accurate computational prediction remains needed. Here, we present Deep3DCCS, a geometry-driven deep learning framework that predicts CCS from stacked multi-angle molecular projection tensors using a three-dimensional convolutional neural network operating across the projection-view and two spatial image dimensions. Three-dimensional molecular structures generated from SMILES strings were rotated around the x, y, and z-axes, converted into binary two-dimensional projections, and assembled into standardized multi-view tensors for CCS regression. Deep3DCCS was developed and evaluated using curated AllCCS and METLIN lipid CCS datasets containing 3948 molecule–adduct entries across [M – H]−, [M + H]+, and [M + Na]+ ions, and input optimization identified 32 × 32 pixel projections with five rotations per axis as a practical balance between prediction accuracy, model stability, and computational feasibility. In independent true-validation experiments, AllCCS-trained models achieved MRPE values of 3.27–3.79% on AllCCS validation data and 2.93–3.72% on METLIN validation data, whereas METLIN-trained models transferred less effectively to the broader AllCCS chemical space. Overall, these results support multi-view molecular projection tensors as a viable geometry-driven representation for CCS prediction and demonstrate that substantial CCS-relevant information can be learned directly from three-dimensional molecular morphology using a 3DCNN architecture, with low single-digit prediction errors across independent and cross-dataset validation experiments.