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feat: update residue config to extended set #219

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113 changes: 107 additions & 6 deletions winnow/configs/residues.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,21 +24,122 @@ residue_masses:
"R": 156.101111
"Y": 163.063329
"W": 186.079313
"U": 150.953633
"O": 237.147727
# Modifications
"M[UNIMOD:35]": 147.035400 # Oxidation
"K[UNIMOD:1]": 170.105528
"K[UNIMOD:3]": 354.172561
"C[UNIMOD:4]": 160.030649 # Carboxyamidomethylation
"N[UNIMOD:7]": 115.026943 # Deamidation
"Q[UNIMOD:7]": 129.042594 # Deamidation
"R[UNIMOD:7]": 157.085127 # Arginine citrullination
"P[UNIMOD:35]": 113.047679 # Proline hydroxylation
"N[UNIMOD:7]": 115.026943 # Deamidation
"S[UNIMOD:21]": 166.998028 # Phosphorylation + 79.966
"T[UNIMOD:21]": 181.01367 # Phosphorylation + 79.966
"Y[UNIMOD:21]": 243.029329 # Phosphorylation + 79.966
"C[UNIMOD:312]": 222.013284 # Cysteinylation
"E[UNIMOD:27]": 111.032028 # Glu -> pyro-Glu
"Q[UNIMOD:28]": 111.032029 # Gln -> pyro-Gln
"E[UNIMOD:27]": 111.032028 # Glu -> pyro-Glu
"Q[UNIMOD:28]": 111.032029 # Gln -> pyro-Gln
"K[UNIMOD:34]": 142.110613
"R[UNIMOD:34]": 170.116761
"M[UNIMOD:35]": 147.035400 # Oxidation
"P[UNIMOD:35]": 113.047679 # Proline hydroxylation
"K[UNIMOD:36]": 156.126263
"R[UNIMOD:36]": 184.132411
"K[UNIMOD:37]": 170.141913
"N[UNIMOD:43]": 317.122300
"K[UNIMOD:58]": 184.121178
"K[UNIMOD:64]": 228.111007
"K[UNIMOD:121]": 242.137890
"K[UNIMOD:122]": 156.089878
"N[UNIMOD:137]": 1330.465790
"N[UNIMOD:148]": 682.254496
"N[UNIMOD:159]": 1006.360143
"R[UNIMOD:188]": 162.121240
"K[UNIMOD:214]": 272.197026
"K[UNIMOD:259]": 136.109162
"R[UNIMOD:267]": 166.109380
"Y[UNIMOD:275]": 192.053493
"N[UNIMOD:305]": 1558.576797
"N[UNIMOD:307]": 1720.629620
"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 # Cysteinylation
"K[UNIMOD:481]": 132.120070
"K[UNIMOD:737]": 357.257895
"S[UNIMOD:737]": 316.194960
"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]": 2173.777860
"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]": 1816.624260
"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
# Terminal modifications
"[UNIMOD:1]": 42.010565 # Acetylation
"[UNIMOD:5]": 43.005814 # Carbamylation
"[UNIMOD:214]": 144.102063
"[UNIMOD:385]": -17.026549 # NH3 loss
"[UNIMOD:737]": 229.162932
"[UNIMOD:2016]": 304.207146
"(+25.98)": 25.980265 # Carbamylation & NH3 loss (legacy notation)
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