Appendix A Proteomics Terminology and Acronyms

Table 9 highlights interesting patterns observed in Figure 3. First, the same modification occurring at different residues can have varying effects on the peptide properties, implying that including amino acid PTM information is essential to achieve better predictions. Second, some modifications have the same Unimod ID and the same molecular structure but only differ in their stereo-chemistry (spatial arrangement of atoms), yet they impact the peptide properties differently. Such scenarios are present in modified sequences and require a proper representation of PTMs (via encoding and domain-specific features) to predict peptide properties accurately. Table 11 in Appendix Section D shows the impact of PTMs on retention time for the special cases from Table 9.