File size: 7,365 Bytes
ef3002d
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
{
  "input_dim": 11,
  "hidden_dims": [
    50,
    50
  ],
  "dropout": 0.3,
  "learning_rate": 0.0001,
  "weight_decay": 0.001,
  "max_epochs": 1000,
  "batch_size": 1024,
  "n_iter_no_change": 10,
  "tol": 0.0001,
  "seed": 42,
  "val_early_stopping_max_psms": null,
  "val_subsample_seed": null,
  "feature_columns": [
    "ion_matches",
    "ion_match_intensity",
    "irt_error",
    "margin",
    "median_margin",
    "entropy",
    "z-score",
    "min_token_probability",
    "std_token_probability",
    "mass_error_da"
  ],
  "feature_names": [
    "Fragment Match Features",
    "iRT Feature",
    "Beam Features",
    "Token Score Features",
    "Mass Error (Da)"
  ],
  "features": {
    "Fragment Match Features": {
      "_target_": "winnow.calibration.features.fragment_match.FragmentMatchFeatures",
      "mz_tolerance_ppm": 20,
      "mz_tolerance_da": null,
      "learn_from_missing": false,
      "intensity_model_name": "Prosit_2025_intensity_22PTM",
      "max_precursor_charge": 6,
      "max_peptide_length": 30,
      "unsupported_residues": [
        "[UNIMOD:5]",
        "[UNIMOD:385]",
        "(+25.98)"
      ],
      "model_input_constants": null,
      "model_input_columns": {
        "collision_energies": "collision_energy",
        "fragmentation_types": "frag_type"
      },
      "koina_server_url": "localhost:8500",
      "koina_ssl": false,
      "excluded_columns": [
        "complementary_ion_count",
        "max_ion_gap",
        "spectral_angle",
        "xcorr"
      ]
    },
    "iRT Feature": {
      "_target_": "winnow.calibration.features.retention_time.RetentionTimeFeature",
      "train_fraction": 0.1,
      "min_train_points": 5,
      "learn_from_missing": false,
      "seed": 42,
      "irt_model_name": "Prosit_2025_irt_22PTM",
      "max_peptide_length": 30,
      "unsupported_residues": [
        "[UNIMOD:5]",
        "[UNIMOD:385]",
        "(+25.98)"
      ],
      "koina_server_url": "localhost:8500",
      "koina_ssl": false
    },
    "Beam Features": {
      "_target_": "winnow.calibration.features.beam.BeamFeatures",
      "excluded_columns": [
        "edit_distance"
      ]
    },
    "Token Score Features": {
      "_target_": "winnow.calibration.features.token_score.TokenScoreFeatures"
    },
    "Mass Error (Da)": {
      "_target_": "winnow.calibration.features.mass_error.MassErrorDaFeature",
      "residue_masses": {
        "G": 57.021464,
        "A": 71.037114,
        "S": 87.032028,
        "P": 97.052764,
        "V": 99.068414,
        "T": 101.04767,
        "C": 103.009185,
        "L": 113.084064,
        "I": 113.084064,
        "N": 114.042927,
        "D": 115.026943,
        "Q": 128.058578,
        "K": 128.094963,
        "E": 129.042593,
        "M": 131.040485,
        "H": 137.058912,
        "F": 147.068414,
        "R": 156.101111,
        "Y": 163.063329,
        "W": 186.079313,
        "U": 150.953633,
        "O": 237.147727,
        "K[UNIMOD:1]": 170.105528,
        "K[UNIMOD:3]": 354.172561,
        "C[UNIMOD:4]": 160.030649,
        "Q[UNIMOD:7]": 129.042594,
        "R[UNIMOD:7]": 157.085127,
        "N[UNIMOD:7]": 115.026943,
        "S[UNIMOD:21]": 166.998359,
        "T[UNIMOD:21]": 181.014009,
        "Y[UNIMOD:21]": 243.02966,
        "E[UNIMOD:27]": 111.032028,
        "Q[UNIMOD:28]": 111.032029,
        "K[UNIMOD:34]": 142.110613,
        "R[UNIMOD:34]": 170.116761,
        "M[UNIMOD:35]": 147.0354,
        "P[UNIMOD:35]": 113.047679,
        "K[UNIMOD:36]": 156.126263,
        "R[UNIMOD:36]": 184.132411,
        "K[UNIMOD:37]": 170.141913,
        "N[UNIMOD:43]": 317.1223,
        "K[UNIMOD:58]": 184.121178,
        "K[UNIMOD:64]": 228.111007,
        "K[UNIMOD:121]": 242.13789,
        "K[UNIMOD:122]": 156.089878,
        "N[UNIMOD:137]": 1330.46579,
        "N[UNIMOD:148]": 682.254496,
        "N[UNIMOD:159]": 1006.360143,
        "R[UNIMOD:188]": 162.12124,
        "K[UNIMOD:214]": 272.197026,
        "K[UNIMOD:259]": 136.109162,
        "R[UNIMOD:267]": 166.10938,
        "Y[UNIMOD:275]": 192.053493,
        "N[UNIMOD:305]": 1558.576797,
        "N[UNIMOD:307]": 1720.62962,
        "N[UNIMOD:308]": 1882.682444,
        "N[UNIMOD:309]": 1412.518888,
        "N[UNIMOD:310]": 1574.571711,
        "N[UNIMOD:311]": 1736.624535,
        "C[UNIMOD:312]": 222.013284,
        "K[UNIMOD:481]": 132.12007,
        "K[UNIMOD:737]": 357.257895,
        "S[UNIMOD:737]": 316.19496,
        "K[UNIMOD:747]": 214.095357,
        "K[UNIMOD:1289]": 198.136828,
        "K[UNIMOD:1363]": 196.121178,
        "N[UNIMOD:1408]": 2318.815368,
        "N[UNIMOD:1409]": 2027.719952,
        "N[UNIMOD:1410]": 2173.77786,
        "N[UNIMOD:1452]": 1168.412966,
        "N[UNIMOD:1462]": 1476.523699,
        "N[UNIMOD:1465]": 1492.518613,
        "N[UNIMOD:1467]": 1517.550248,
        "N[UNIMOD:1468]": 1533.545162,
        "N[UNIMOD:1477]": 1638.576522,
        "N[UNIMOD:1480]": 1654.571437,
        "N[UNIMOD:1481]": 1663.608157,
        "N[UNIMOD:1484]": 1679.603071,
        "N[UNIMOD:1487]": 1695.597986,
        "N[UNIMOD:1488]": 1703.614305,
        "N[UNIMOD:1496]": 1777.651084,
        "N[UNIMOD:1500]": 1800.629346,
        "N[UNIMOD:1504]": 1816.62426,
        "N[UNIMOD:1506]": 1824.640579,
        "N[UNIMOD:1509]": 1841.655895,
        "N[UNIMOD:1510]": 1849.672213,
        "N[UNIMOD:1511]": 1850.692615,
        "N[UNIMOD:1519]": 1923.708993,
        "N[UNIMOD:1529]": 1970.698488,
        "N[UNIMOD:1531]": 1978.677084,
        "N[UNIMOD:1532]": 1980.730457,
        "N[UNIMOD:1534]": 1986.693402,
        "N[UNIMOD:1537]": 2003.708718,
        "N[UNIMOD:1540]": 2021.757006,
        "N[UNIMOD:1541]": 2028.740353,
        "N[UNIMOD:1547]": 2044.735267,
        "N[UNIMOD:1549]": 2060.730182,
        "N[UNIMOD:1551]": 2068.746501,
        "N[UNIMOD:1555]": 2085.761816,
        "N[UNIMOD:1559]": 2101.756731,
        "N[UNIMOD:1562]": 2110.793451,
        "N[UNIMOD:1722]": 1647.613242,
        "N[UNIMOD:1746]": 1907.714078,
        "N[UNIMOD:1761]": 1152.418052,
        "N[UNIMOD:1763]": 1209.439515,
        "N[UNIMOD:1766]": 1314.470875,
        "N[UNIMOD:1768]": 1355.497424,
        "N[UNIMOD:1769]": 1371.492339,
        "N[UNIMOD:1771]": 1501.555333,
        "N[UNIMOD:1772]": 1615.598261,
        "N[UNIMOD:1773]": 1662.587755,
        "N[UNIMOD:1775]": 1761.656169,
        "N[UNIMOD:1776]": 1818.677633,
        "N[UNIMOD:1777]": 1865.667128,
        "N[UNIMOD:1778]": 1866.687529,
        "N[UNIMOD:1779]": 1898.677358,
        "N[UNIMOD:1780]": 1939.703908,
        "N[UNIMOD:1781]": 1964.735542,
        "N[UNIMOD:1782]": 2011.725037,
        "N[UNIMOD:1783]": 2012.745438,
        "N[UNIMOD:1784]": 2052.751586,
        "N[UNIMOD:1785]": 2069.766902,
        "N[UNIMOD:1840]": 2206.788091,
        "K[UNIMOD:1848]": 242.126657,
        "K[UNIMOD:1849]": 214.131742,
        "N[UNIMOD:1963]": 1962.682169,
        "N[UNIMOD:1964]": 1994.709721,
        "K[UNIMOD:2016]": 432.302109,
        "N[UNIMOD:2028]": 2975.042981,
        "N[UNIMOD:2029]": 2466.888927,
        "[UNIMOD:1]": 42.010565,
        "[UNIMOD:5]": 43.005814,
        "[UNIMOD:214]": 144.102063,
        "[UNIMOD:385]": -17.026549,
        "[UNIMOD:737]": 229.162932,
        "[UNIMOD:2016]": 304.207146,
        "(+25.98)": 25.980265
      },
      "isotope_error_range": [
        0,
        1
      ]
    }
  }
}