The spectral library, which was used in the analysis, was generated using Prosit (https://www.nature.com/articles/s41592-019-0426-7). More specifically the Prosit_intensity_hcd_2020 and Prosit_2019_irt intensity and retention time prediction models were used.

A list of peptide targets, with defined charge states and normalized collision energies was used as input for the prediction.