AA_MASSES_DICT = { "": 0.0, "": 0.0, "": 0.0, "A": 71.0371138, # Alanine "R": 156.1011110, # Arginine "N": 114.0429274, # Asparagine "D": 115.0269431, # Aspartic acid "C": 160.0306482, # Cysteine (carbamidomethylated, standard in ProteomeTools) "C(unmod)": 103.0091845, # Unmodified Cysteine "E": 129.0425931, # Glutamic acid "Q": 128.0585775, # Glutamine "G": 57.0214637, # Glycine "H": 137.0589119, # Histidine "I": 113.0840640, # Isoleucine "L": 113.0840640, # Leucine "K": 128.0949630, # Lysine "M": 131.0404846, # Methionine "F": 147.0684139, # Phenylalanine "P": 97.0527639, # Proline "S": 87.0320284, # Serine "T": 101.0476785, # Threonine "W": 186.0793130, # Tryptophan "Y": 163.0633286, # Tyrosine "V": 99.0684139, # Valine # --- Post-Translational Modifications (PTMs): Residue-Level --- # Methionine Oxidation (+15.9949 Da, UNIMOD:35) "M(ox)": 147.0353992, "M(+15.99)": 147.0353992, "M(+15.995)": 147.0353992, "M[UNIMOD:35]": 147.0353992, # Cysteine Carboxyamidomethylation (+57.0215 Da, UNIMOD:4) "C(cam)": 160.0306482, "C(+57.02)": 160.0306482, "C(+57.021)": 160.0306482, "C[UNIMOD:4]": 160.0306482, # Asparagine Deamidation (+0.9840 Da, UNIMOD:7) "N(deam)": 115.0269434, "N(+0.98)": 115.0269434, "N(+.98)": 115.0269434, "N[UNIMOD:7]": 115.0269434, # Glutamine Deamidation (+0.9840 Da, UNIMOD:7) "Q(deam)": 129.0425935, "Q(+0.98)": 129.0425935, "Q(+.98)": 129.0425935, "Q[UNIMOD:7]": 129.0425935, # Serine Phosphorylation (+79.9663 Da, UNIMOD:21) "S(ph)": 166.9983594, "S(+79.97)": 166.9983594, "S(p)": 166.9983594, "S[UNIMOD:21]": 166.9983594, # Threonine Phosphorylation (+79.9663 Da, UNIMOD:21) "T(ph)": 181.0140095, "T(+79.97)": 181.0140095, "T(p)": 181.0140095, "T[UNIMOD:21]": 181.0140095, # Tyrosine Phosphorylation (+79.9663 Da, UNIMOD:21) "Y(ph)": 243.0296596, "Y(+79.97)": 243.0296596, "Y(p)": 243.0296596, "Y[UNIMOD:21]": 243.0296596, # --- Post-Translational Modifications (PTMs): N-Terminal --- # N-terminal Acetylation (+42.0106 Da, UNIMOD:1) "[UNIMOD:1]": 42.010565, "(+42.01)": 42.010565, "[+42.01]": 42.010565, "(+42.0106)": 42.010565, # N-terminal Carbamylation (+43.0058 Da, UNIMOD:5) "[UNIMOD:5]": 43.005814, "(+43.01)": 43.005814, "[+43.01]": 43.005814, "(+43.0058)": 43.005814, # N-terminal Ammonia Loss (-17.0265 Da, UNIMOD:385) "[UNIMOD:385]": -17.026549, "(-17.03)": -17.026549, "[-17.03]": -17.026549, "(-17.0265)": -17.026549, } # Standard 20 amino acids in a stable alphabetical order. STANDARD_AMINO_ACIDS = sorted(list("ACDEFGHIKLMNPQRSTVWY")) # Primary residue-level PTM tokens. RESIDUE_PTM_TOKENS = [ "M(ox)", "C(cam)", "N(deam)", "Q(deam)", "S(ph)", "T(ph)", "Y(ph)", ] # N-terminal modification tokens. N_TERM_MODIFICATIONS = [ "(+42.01)", # Acetylation [UNIMOD:1] "(+43.01)", # Carbamylation [UNIMOD:5] "(-17.03)", # Ammonia Loss [UNIMOD:385] ] # Primary PTM tokens to include in extended vocabulary. TARGET_PTM_TOKENS = RESIDUE_PTM_TOKENS + N_TERM_MODIFICATIONS # Mapping from PTM token to unmodified parent amino acid for weight surgery. PTM_PARENT_MAP = { "M(ox)": "M", "C(cam)": "C", "N(deam)": "N", "Q(deam)": "Q", "S(ph)": "S", "T(ph)": "T", "Y(ph)": "Y", } # Mapping from canonical token to standard UNIMOD format string. CANONICAL_TO_UNIMOD_MAP = { "M(ox)": "M[UNIMOD:35]", "C(cam)": "C[UNIMOD:4]", "N(deam)": "N[UNIMOD:7]", "Q(deam)": "Q[UNIMOD:7]", "S(ph)": "S[UNIMOD:21]", "T(ph)": "T[UNIMOD:21]", "Y(ph)": "Y[UNIMOD:21]", "(+42.01)": "[UNIMOD:1]", "(+43.01)": "[UNIMOD:5]", "(-17.03)": "[UNIMOD:385]", } # Alternate delta and UNIMOD formatting aliases mapped to canonical token names. PTM_ALIAS_MAP = { # Methionine oxidation (+15.9949 Da, UNIMOD:35) "M[UNIMOD:35]": "M(ox)", "M[15.9949]": "M(ox)", "M[15.99]": "M(ox)", "M(+15.99)": "M(ox)", "M(+15.995)": "M(ox)", "M[+16]": "M(ox)", # Cysteine carboxyamidomethylation (+57.0215 Da, UNIMOD:4) "C[UNIMOD:4]": "C(cam)", "C[57.0215]": "C(cam)", "C[57.02]": "C(cam)", "C(+57.02)": "C(cam)", "C(+57.021)": "C(cam)", "C[+57]": "C(cam)", # Asparagine deamidation (+0.9840 Da, UNIMOD:7) "N[UNIMOD:7]": "N(deam)", "N[0.9840]": "N(deam)", "N[0.98]": "N(deam)", "N(+0.98)": "N(deam)", "N(+.98)": "N(deam)", "N[+1]": "N(deam)", # Glutamine deamidation (+0.9840 Da, UNIMOD:7) "Q[UNIMOD:7]": "Q(deam)", "Q[0.9840]": "Q(deam)", "Q[0.98]": "Q(deam)", "Q(+0.98)": "Q(deam)", "Q(+.98)": "Q(deam)", "Q[+1]": "Q(deam)", # Serine phosphorylation (+79.9663 Da, UNIMOD:21) "S[UNIMOD:21]": "S(ph)", "S[79.9663]": "S(ph)", "S(p)": "S(ph)", "S(+79.97)": "S(ph)", "S(+79.966)": "S(ph)", "S[+80]": "S(ph)", # Threonine phosphorylation (+79.9663 Da, UNIMOD:21) "T[UNIMOD:21]": "T(ph)", "T[79.9663]": "T(ph)", "T(p)": "T(ph)", "T(+79.97)": "T(ph)", "T(+79.966)": "T(ph)", "T[+80]": "T(ph)", # Tyrosine phosphorylation (+79.9663 Da, UNIMOD:21) "Y[UNIMOD:21]": "Y(ph)", "Y[79.9663]": "Y(ph)", "Y(p)": "Y(ph)", "Y(+79.97)": "Y(ph)", "Y(+79.966)": "Y(ph)", "Y[+80]": "Y(ph)", # N-terminal Acetylation (+42.0106 Da, UNIMOD:1) "[UNIMOD:1]": "(+42.01)", "[42.0106]": "(+42.01)", "[+42.01]": "(+42.01)", "(+42.0106)": "(+42.01)", "[+42]": "(+42.01)", # N-terminal Carbamylation (+43.0058 Da, UNIMOD:5) "[UNIMOD:5]": "(+43.01)", "[43.0058]": "(+43.01)", "[+43.01]": "(+43.01)", "(+43.0058)": "(+43.01)", "[+43]": "(+43.01)", # N-terminal Ammonia Loss (-17.0265 Da, UNIMOD:385) "[UNIMOD:385]": "(-17.03)", "[-17.0265]": "(-17.03)", "[-17.03]": "(-17.03)", "(-17.0265)": "(-17.03)", "[-17]": "(-17.03)", } # Monoisotopic mass of a proton (Da). M_H = 1.007276 # Monoisotopic mass of water (Da). M_H2O = 18.010565