The protein hits are numbered (prot_hit_num) according to the Protein Score (prot_score). In addition, the following information are available in the data set: protein accession name in the Swiss-Prot database (prot_acc), description (prot_desc), protein mass (prot_mass), percentage of protein sequence covered by assigned peptide matches (prot_cover), the assigned MS/MS spectrum number (pep_query), rank of peptide match (pep_rank), indication of first time (1) or not first time (0) the peptide is matched to a protein in the data set (pep_isbold), observed m/z value (pep_exp_mz), observed relative molecular mass (pep_exp_mr), observed charge state (pep_exp_z), calculated relative molecular mass (pep_calc_mr), pep_calc_mr - pep_exp_mr (pep_delta), first and last residue numbers in the matched peptide (pep_start and pep_end), number of missed trypsin cleavage sites (pep_miss), peptide match score (pep_score), peptide match expectation value (pep_expect), the sequence of the peptide (pep_seq) and the residue before (pep_res_before) and the residue after (pep_res_after) the peptide sequence in the protein, variable modifications (methionine oxidation and proline hydroxylation) in the peptide (pep_var_mod) and their position in the peptide sequence (pep_var_mod_pos), and emPAI value for the protein hit (emPAI). To access the data, click or select the words “Appendix 2.”