Updated publication reference for PubMed record(s): 32639981. Dependent peptide searching is a method for detecting modified peptides using data from shotgun proteomics analyses. We have developed a set of tools for visualising the results of dependent-peptide searches (as performed in MaxQuant). The tools were developed using four sets of search results: two sets for a sample of N-ethylmaleimide-treated bovine serum albumin (BSA), and two sets for a corresponding control sample (replicates = different LC-MS/MS analyses). This submission includes our raw data, MaxQuant output files, and a *.fasta file containing the sequence of mature BSA. An accompanying *.csv file summarises the structure of the data set.