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 j = 0; j < i; j++) {
        bMass += peptideMasses[j];
      }
      bMass = bMass + hydrogenMass;


      bIons.add(new FragmentIon(bMass, FragmentIonType.B_ION, i));


    }


    return bIons;
  }

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       */
      for (int j = 0; j < i; j++) {
        yMass += peptideMasses[(peptideMasses.length - 1) - j];
      }
      yMass = yMass + ctermMass + (2 * hydrogenMass);
      yIons.add(new FragmentIon(yMass, FragmentIonType.Y_ION, i));
    }


    return yIons;
  }

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    double H2 = hydrogenMass * 2;


    for (int i = 0; i < bIons.length; i++) {
      // b-ion minus 'CO' plus 'H2'
      mass = bIons[i].getMass() - CO + H2;
      aIons.add(new FragmentIon(mass, FragmentIonType.A_ION, (i + 1)));
    }
    return aIons;
  }

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    double NH3 = nitrogenMass + (hydrogenMass * 3);


    for (int i = 0; i < bIons.length; i++) {
      // b-ion plus 'NH3'
      mass = bIons[i].getMass() + NH3;
      cIons.add(new FragmentIon(mass, FragmentIonType.C_ION, (i + 1)));
    }
    return cIons;
  }

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    double H2 = hydrogenMass * 2;


    for (int i = 0; i < yIons.length; i++) {
      // y-ion minus 'NH3' plus 'H2'
      mass = yIons[i].getMass() + CO - H2;
      xIons.add(new FragmentIon(mass, FragmentIonType.X_ION, (i + 1)));
    }
    return xIons;
  }

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    double NH3 = nitrogenMass + (hydrogenMass * 3);


    for (int i = 0; i < bIons.length; i++) {
      // y-ion minus 'NH3'
      mass = bIons[i].getMass() - NH3;
      cIons.add(new FragmentIon(mass, FragmentIonType.Z_ION, (i + 1)));
    }
    return cIons;
  }

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    double mass;


    for (int i = 0; i < zIons.length; i++) {
      // b-ion minus 'CO' plus 'H2'
      mass = zIons[i].getMass() + hydrogenMass;
      zhIons.add(new FragmentIon(mass, FragmentIonType.ZH_ION, (i + 1)));
    }
    return zhIons;
  }

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    double mass;


    for (int i = 0; i < zIons.length; i++) {
      // z-ion plus 'H2'
      mass = zIons[i].getMass() + (hydrogenMass * 2);
      zhhIons.add(new FragmentIon(mass, FragmentIonType.ZHH_ION, (i + 1)));
    }
    return zhhIons;
  }

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    Vector<FragmentIon> bDoubleIons = new Vector<FragmentIon>();
    double mass;
    for (int i = 0; i < bIons.length; i++) {
      // b-ion plus 'H' over a double charge
      mass = (bIons[i].getMass() + hydrogenMass) / 2.0;
      bDoubleIons.add(new FragmentIon(mass, ionType, i + 1));
    }
    return bDoubleIons;
  }

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      for (int i = indexFirstIonLossH2O; i < bIons.length; i++) {
        // b-ion minus 'H2O'
        mass = bIons[i].getMass() - lossMass;
        if (doubleCharged)
          mass /= 2.0;
        bIonsLossH20.add(new FragmentIon(mass, ionType, i + 1));
      }
    }
    return bIonsLossH20;
  }

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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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