Peptide PTM Search Localization ModLS Localization ModLS Score Corroborating Evidence Supp. Figure DSRPSQAAGDNQ GDEAKEQTFSGGTSQDTK Dimethyl R3 K17 45 Many b/y ions S1 MDSTEPPYSQKR Dimethyl R11 K10 18 b-11 ion Miscleavage S2 QSGYGGQTKPIFR Methyl R13 K9 14 Many b/y ions Miscleavage S3

Table 2: Examples of ModLS localization with automatic specificity expansion on the Uhlmann et al. [13] methylation dataset. Initial search was performed for Arg methylations only. ModLS corrects the localization of the PTM for 3 example peptides. All peptides have corroborating evidence by manual inspection of spectra and/or location of missed tryptic cleavage. Full localization detail is given in the indicated supplementary figures S1-S3.