File size: 6,230 Bytes
c97ac7e db023d0 c97ac7e db023d0 c97ac7e db023d0 c97ac7e db023d0 c97ac7e db023d0 c97ac7e db023d0 c97ac7e db023d0 c97ac7e db023d0 c97ac7e db023d0 c97ac7e db023d0 c97ac7e | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 | AA_MASSES_DICT = {
"<pad>": 0.0,
"<mask" + ">": 0.0,
"<mask_token>": 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
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