diff --git a/spectrum_fundamentals/constants.py b/spectrum_fundamentals/constants.py index 69b4894..ded561c 100644 --- 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"], } #######################################