Examples of net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.FragmentIon

Package net.sf.mzmine.modules.peaklistmethods.identification.mascot.data

Examples of net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.FragmentIon

net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.FragmentIon

      for (int i = indexFirstIonLossNH3; i < bIons.length; i++) {
        // b-ion minus 'NH3'
        mass = bIons[i].getMass() - lossMass;
        if (doubleCharged)
          mass /= 2.0;
        bIonsLossH20.add(new FragmentIon(mass, ionType, i + 1));
      }
    }
    return bIonsLossH20;
  }

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      double nitrogenMass) {
    Vector<FragmentIon> precursorIons = new Vector<FragmentIon>();
    double H2O = (hydrogenMass) * 2 + oxygenMass;
    double NH3 = nitrogenMass + (hydrogenMass * 3);
    if (precursorMass != 0.0) {
      precursorIons.add(new FragmentIon(precursorMass,
          FragmentIonType.PRECURSOR, 0));
      double mass = precursorMass - (H2O / charge);
      precursorIons.add(new FragmentIon(mass,
          FragmentIonType.PRECURSOR_H2O, 0));
      mass = precursorMass - (NH3 / charge);
      precursorIons.add(new FragmentIon(mass,
          FragmentIonType.PRECURSOR_NH3, 0));
    }
    return precursorIons.toArray(new FragmentIon[0]);
  }

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    for (int i = 0; i < sequence.length(); i++) {
      char c = sequence.charAt(i);
      switch (c) {
        case 'A' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("A"),
              FragmentIonType.IMMONIUM_A, 0));
          break;
        case 'R' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("R"),
              FragmentIonType.IMMONIUM_R, 0));
          break;
        case 'N' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("N"),
              FragmentIonType.IMMONIUM_N, 0));
          break;
        case 'D' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("D"),
              FragmentIonType.IMMONIUM_D, 0));
          break;
        case 'C' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("C"),
              FragmentIonType.IMMONIUM_C, 0));
          break;
        case 'E' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("E"),
              FragmentIonType.IMMONIUM_E, 0));
          break;
        case 'Q' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("Q"),
              FragmentIonType.IMMONIUM_Q, 0));
          break;
        case 'G' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("G"),
              FragmentIonType.IMMONIUM_G, 0));
          break;
        case 'H' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("H"),
              FragmentIonType.IMMONIUM_H, 0));
          break;
        case 'I' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("I"),
              FragmentIonType.IMMONIUM_I, 0));
          break;
        case 'L' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("L"),
              FragmentIonType.IMMONIUM_L, 0));
          break;
        case 'K' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("K"),
              FragmentIonType.IMMONIUM_K, 0));
          break;
        case 'M' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("M"),
              FragmentIonType.IMMONIUM_M, 0));
          break;
        case 'F' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("F"),
              FragmentIonType.IMMONIUM_F, 0));
          break;
        case 'P' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("P"),
              FragmentIonType.IMMONIUM_P, 0));
          break;
        case 'S' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("S"),
              FragmentIonType.IMMONIUM_S, 0));
          break;
        case 'T' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("T"),
              FragmentIonType.IMMONIUM_T, 0));
          break;
        case 'W' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("W"),
              FragmentIonType.IMMONIUM_W, 0));
          break;
        case 'Y' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("Y"),
              FragmentIonType.IMMONIUM_Y, 0));
          break;
        case 'V' :
          immoniumIons.add(new FragmentIon(defaultMasses.get("V"),
              FragmentIonType.IMMONIUM_V, 0));
          break;
      }
    }

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Related Classes of net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.FragmentIon

net.sf.mzmine.util.PeptideUtils

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