Added mods to msfragger and neutral loss dictionary

wilhelm-lab · Sep 20, 2024 · 6e8ca39 · 6e8ca39
1 parent 847ddce
commit 6e8ca39
Showing 1 changed file with 50 additions and 57 deletions.
diff --git a/spectrum_fundamentals/constants.py b/spectrum_fundamentals/constants.py
@@ -115,6 +115,9 @@
     "K[230]": "K[UNIMOD:737]",
     "K[305]": "K[UNIMOD:2016]",
     "K[214]": "K[UNIMOD:214]",
+    "R[157]": "R[UNIMOD:7]",
+    "Q[129]": "Q[UNIMOD:7]",
+    "N[115]": "N[UNIMOD:7]",
     "n[230]": "[UNIMOD:737]-",
     "n[305]": "[UNIMOD:2016]-",
     "n[214]": "[UNIMOD:214]-",
@@ -139,14 +142,7 @@
 PARTICLE_MASSES = {"PROTON": 1.007276467, "ELECTRON": 0.00054858}
 
 # masses of different atoms
-ATOM_MASSES = {
-    "H": 1.007825035,
-    "C": 12.0,
-    "O": 15.9949146,
-    "N": 14.003074,
-    'S': 31.9720712,
-    'P': 30.9737619
-}
+ATOM_MASSES = {"H": 1.007825035, "C": 12.0, "O": 15.9949146, "N": 14.003074, "S": 31.9720712, "P": 30.9737619}
 
 MASSES = {**PARTICLE_MASSES, **ATOM_MASSES}
 MASSES["N_TERMINUS"] = MASSES["H"]
@@ -287,59 +283,56 @@
 
 
 AA_Neutral_losses = {
-    'R': ['NH3', 'CH2N2', 'C3H9N3'],
-    'N': ['NH3', 'CH3NO', 'C2H5NO', 'C3H5NO'],
-    'D': ['H2O', 'CO2', 'C2H4O2'],
-    'C': ['CH2S'],
-    'E': ['H2O', 'C2H4O2'],
-    'Q': ['NH3', 'CH3NO', 'C2H5NO', 'C3H5NO'],
-    'I': ['C2H4'],
-    'L': ['C3H6', 'C4H8'],
-    'K': ['C2H5N', 'C4H9N', 'C4H11N', 'C3H9N'],
-    'M': ['C2H4S', 'C3H6S'],
-    'M[UNIMOD:35]': ['CH4SO', 'C3H8SO', 'C3H6SO'],
-    'S': ['H2O', 'CH4O'],
-    'T': ['H2O', 'C2H4O'],
-    'W': ['C8H7N', 'C9H9N'],
-    'V': ['C3H6'],
-    '[]-': ['NH3'],
-    '-[]': ['H2O'],
+    "R": ["NH3", "CH2N2", "C3H9N3"],
+    "N": ["NH3", "CH3NO", "C2H5NO", "C3H5NO"],
+    "D": ["H2O", "CO2", "C2H4O2"],
+    "C": ["CH2S"],
+    "E": ["H2O", "C2H4O2"],
+    "Q": ["NH3", "CH3NO", "C2H5NO", "C3H5NO"],
+    "I": ["C2H4"],
+    "L": ["C3H6", "C4H8"],
+    "K": ["C2H5N", "C4H9N", "C4H11N", "C3H9N"],
+    "M": ["C2H4S", "C3H6S"],
+    "M[UNIMOD:35]": ["CH4SO", "C3H8SO", "C3H6SO"],
+    "S": ["H2O", "CH4O"],
+    "T": ["H2O", "C2H4O"],
+    "W": ["C8H7N", "C9H9N"],
+    "V": ["C3H6"],
+    "[]-": ["NH3"],
+    "-[]": ["H2O"],
 }
 
-Mod_Neutral_losses = {
-    'R[UNIMOD:7]': ['CHNO'],
-    'S[UNIMOD:21]': ['H3O4P']
-}
+Mod_Neutral_losses = {"R[UNIMOD:7]": ["CHNO"], "S[UNIMOD:21]": ["H3O4P"]}
 
 Neutral_losses_Mass = {
- 'C2H4': (ATOM_MASSES['C']*2) + (ATOM_MASSES['H']*4),
- 'C2H4O': (ATOM_MASSES['C']*2) + (ATOM_MASSES['H']*4) + ATOM_MASSES['O'],
- 'C2H4O2': (ATOM_MASSES['C']*2) + (ATOM_MASSES['H']*4) + (ATOM_MASSES['O']*2),
- 'C2H4S': (ATOM_MASSES['C']*2) + (ATOM_MASSES['H']*4) + ATOM_MASSES['S'],
- 'C2H5N':  (ATOM_MASSES['C']*2) + (ATOM_MASSES['H']*5) + ATOM_MASSES['N'],
- 'CHNO': (ATOM_MASSES['C']) + (ATOM_MASSES['H']) + ATOM_MASSES['N'] + ATOM_MASSES['O'],
- 'C2H5NO': (ATOM_MASSES['C']*2) + (ATOM_MASSES['H']*5) + ATOM_MASSES['N'] + ATOM_MASSES['O'],
- 'C3H5NO': (ATOM_MASSES['C']*3) + (ATOM_MASSES['H']*5) + ATOM_MASSES['N'] + ATOM_MASSES['O'],
- 'C3H6': (ATOM_MASSES['C']*3) + (ATOM_MASSES['H']*6),
- 'C3H6S': (ATOM_MASSES['C']*3) + (ATOM_MASSES['H']*6) + ATOM_MASSES['S'],
- 'C3H6SO': (ATOM_MASSES['C']*3) + (ATOM_MASSES['H']*6) + ATOM_MASSES['S'] + ATOM_MASSES['O'],
- 'C3H8SO': (ATOM_MASSES['C']*3) + (ATOM_MASSES['H']*8) + ATOM_MASSES['S'] + ATOM_MASSES['O'],
- 'C3H9N': (ATOM_MASSES['C']*3) + (ATOM_MASSES['H']*9) + ATOM_MASSES['N'],
- 'C3H9N3': (ATOM_MASSES['C']*3) + (ATOM_MASSES['H']*9) + (ATOM_MASSES['N']*3),
- 'C4H11N': (ATOM_MASSES['C']*4) + (ATOM_MASSES['H']*11) + ATOM_MASSES['N'],
- 'C4H8': (ATOM_MASSES['C']*4) + (ATOM_MASSES['H']*8),
- 'C4H9N': (ATOM_MASSES['C']*4) + (ATOM_MASSES['H']*9) + ATOM_MASSES['N'],
- 'C8H7N': (ATOM_MASSES['C']*8) + (ATOM_MASSES['H']*7) + ATOM_MASSES['N'],
- 'C9H9N': (ATOM_MASSES['C']*9) + (ATOM_MASSES['H']*9) + ATOM_MASSES['N'],
- 'CH2N2': ATOM_MASSES['C'] + (ATOM_MASSES['H']*2) + (ATOM_MASSES['N']*2),
- 'CH2S': ATOM_MASSES['C'] + (ATOM_MASSES['H']*2) + ATOM_MASSES['S'],
- 'CH3NO': ATOM_MASSES['C'] + (ATOM_MASSES['H']*3) + ATOM_MASSES['N'] + ATOM_MASSES['O'],
- 'CH4O': ATOM_MASSES['C'] + (ATOM_MASSES['H']*4) + ATOM_MASSES['O'],
- 'CH4SO': ATOM_MASSES['C'] + (ATOM_MASSES['H']*4) + ATOM_MASSES['S'] + ATOM_MASSES['O'],
- 'CO2': ATOM_MASSES['C'] + (ATOM_MASSES['O']*2),
- 'H2O': (ATOM_MASSES['H']*2) + ATOM_MASSES['O'],
- 'NH3': ATOM_MASSES['N'] + (ATOM_MASSES['H']*3),
- 'H3O4P': (ATOM_MASSES['H']*3) + (ATOM_MASSES['O']*4) + ATOM_MASSES['P']
+    "C2H4": (ATOM_MASSES["C"] * 2) + (ATOM_MASSES["H"] * 4),
+    "C2H4O": (ATOM_MASSES["C"] * 2) + (ATOM_MASSES["H"] * 4) + ATOM_MASSES["O"],
+    "C2H4O2": (ATOM_MASSES["C"] * 2) + (ATOM_MASSES["H"] * 4) + (ATOM_MASSES["O"] * 2),
+    "C2H4S": (ATOM_MASSES["C"] * 2) + (ATOM_MASSES["H"] * 4) + ATOM_MASSES["S"],
+    "C2H5N": (ATOM_MASSES["C"] * 2) + (ATOM_MASSES["H"] * 5) + ATOM_MASSES["N"],
+    "CHNO": (ATOM_MASSES["C"]) + (ATOM_MASSES["H"]) + ATOM_MASSES["N"] + ATOM_MASSES["O"],
+    "C2H5NO": (ATOM_MASSES["C"] * 2) + (ATOM_MASSES["H"] * 5) + ATOM_MASSES["N"] + ATOM_MASSES["O"],
+    "C3H5NO": (ATOM_MASSES["C"] * 3) + (ATOM_MASSES["H"] * 5) + ATOM_MASSES["N"] + ATOM_MASSES["O"],
+    "C3H6": (ATOM_MASSES["C"] * 3) + (ATOM_MASSES["H"] * 6),
+    "C3H6S": (ATOM_MASSES["C"] * 3) + (ATOM_MASSES["H"] * 6) + ATOM_MASSES["S"],
+    "C3H6SO": (ATOM_MASSES["C"] * 3) + (ATOM_MASSES["H"] * 6) + ATOM_MASSES["S"] + ATOM_MASSES["O"],
+    "C3H8SO": (ATOM_MASSES["C"] * 3) + (ATOM_MASSES["H"] * 8) + ATOM_MASSES["S"] + ATOM_MASSES["O"],
+    "C3H9N": (ATOM_MASSES["C"] * 3) + (ATOM_MASSES["H"] * 9) + ATOM_MASSES["N"],
+    "C3H9N3": (ATOM_MASSES["C"] * 3) + (ATOM_MASSES["H"] * 9) + (ATOM_MASSES["N"] * 3),
+    "C4H11N": (ATOM_MASSES["C"] * 4) + (ATOM_MASSES["H"] * 11) + ATOM_MASSES["N"],
+    "C4H8": (ATOM_MASSES["C"] * 4) + (ATOM_MASSES["H"] * 8),
+    "C4H9N": (ATOM_MASSES["C"] * 4) + (ATOM_MASSES["H"] * 9) + ATOM_MASSES["N"],
+    "C8H7N": (ATOM_MASSES["C"] * 8) + (ATOM_MASSES["H"] * 7) + ATOM_MASSES["N"],
+    "C9H9N": (ATOM_MASSES["C"] * 9) + (ATOM_MASSES["H"] * 9) + ATOM_MASSES["N"],
+    "CH2N2": ATOM_MASSES["C"] + (ATOM_MASSES["H"] * 2) + (ATOM_MASSES["N"] * 2),
+    "CH2S": ATOM_MASSES["C"] + (ATOM_MASSES["H"] * 2) + ATOM_MASSES["S"],
+    "CH3NO": ATOM_MASSES["C"] + (ATOM_MASSES["H"] * 3) + ATOM_MASSES["N"] + ATOM_MASSES["O"],
+    "CH4O": ATOM_MASSES["C"] + (ATOM_MASSES["H"] * 4) + ATOM_MASSES["O"],
+    "CH4SO": ATOM_MASSES["C"] + (ATOM_MASSES["H"] * 4) + ATOM_MASSES["S"] + ATOM_MASSES["O"],
+    "CO2": ATOM_MASSES["C"] + (ATOM_MASSES["O"] * 2),
+    "H2O": (ATOM_MASSES["H"] * 2) + ATOM_MASSES["O"],
+    "NH3": ATOM_MASSES["N"] + (ATOM_MASSES["H"] * 3),
+    "H3O4P": (ATOM_MASSES["H"] * 3) + (ATOM_MASSES["O"] * 4) + ATOM_MASSES["P"],
 }
 
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