Examples with FragmentIon net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.FragmentIon used on opensource projects

Example 11 with FragmentIon

use of net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.FragmentIon in project mzmine2 by mzmine.

the class PeptideUtils method calculateAions.

/**
 * Return b-ions plus 'CO' minus 'H2' (a-ions).
 *
 * @return Vector<FragmentIon> aIons.
 */
public static Vector<FragmentIon> calculateAions(FragmentIon[] bIons, double carbonMass, double oxygenMass, double hydrogenMass) {
    Vector<FragmentIon> aIons = new Vector<FragmentIon>();
    double mass;
    double CO = carbonMass + oxygenMass;
    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;
}

Example 12 with FragmentIon

use of net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.FragmentIon in project mzmine2 by mzmine.

the class PeptideUtils method calculateXions.

/**
 * Return y-ion plus 'CO', minus 'H2' (x-ions).
 *
 * @return Vector<FragmentIon> zIons.
 */
public static Vector<FragmentIon> calculateXions(FragmentIon[] yIons, double carbonMass, double oxygenMass, double hydrogenMass) {
    Vector<FragmentIon> xIons = new Vector<FragmentIon>();
    double mass;
    double CO = carbonMass + oxygenMass;
    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;
}

Example 13 with FragmentIon

use of net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.FragmentIon in project mzmine2 by mzmine.

the class PeptideUtils method calculateZions.

/**
 * Return y-ions minus 'NH3' (z-ions).
 *
 * @return Vector<FragmentIon> zIons.
 */
public static Vector<FragmentIon> calculateZions(FragmentIon[] bIons, double nitrogenMass, double hydrogenMass) {
    Vector<FragmentIon> cIons = new Vector<FragmentIon>();
    double mass;
    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;
}