The use of 1-pass and multi-pass cIM routines resulted in the identification of unique peptide populations, which were used to improve bottom-up LC-MS data quality under both deuterated and non-deuterated conditions. Consequently, we recommend performing both 1-pass and multi-pass peptide mapping prior to HDX-MS analyses to fully exploit instrument performance and maximise nondeuterated peptide databases. As with the aforementioned data processing strategy, this would also benefit from dynamic switching between 1-pass and multi-pass throughout HDMS E experiments, as both 1-pass and multi-pass data could be acquired simultaneously to increase analytical throughput.