DeepCCS: Context-aware prediction of peptide collisional cross section increases peptide recovery for out-of-distribution data-independent acquisition (DIA) datasets

Trapped ion mobility spectrometry (TIMS) extends conventional LC-MS/MS proteomic workflows with an additional ion mobility dimension. Next to the benefits of signal separation, the implementation of TIMS in Bruker timsTOF instruments has demonstrated that collisional cross section (CCS) values of peptides are highly reproducible and can be used as orthogonal coordinates to retention time and ion m/z values for targeted data extraction in data-independent acquisition (DIA) workflows, or as additional metric for rescoring in spectrum-centric database searches.