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

Example 6 with FragmentIon

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

the class PeptideUtils method calculatePrecursorIons.

/**
 * Returns precursor ions , minus 'NH3' and minus H2O.
 *
 * @return Vector<FragmentIon> precursorIons
 */
public static FragmentIon[] calculatePrecursorIons(double precursorMass, int charge, double hydrogenMass, double oxygenMass, 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]);
}

Example 7 with FragmentIon

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

the class PeptideUtils method calculateZHions.

/**
 * Return z-ions plus 'H' (zh-ions).
 *
 * @return Vector<FragmentIon> zhIons.
 */
public static Vector<FragmentIon> calculateZHions(FragmentIon[] zIons, double hydrogenMass) {
    Vector<FragmentIon> zhIons = new Vector<FragmentIon>();
    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;
}

Example 8 with FragmentIon

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

the class PeptideUtils method calculateZHHions.

/**
 * Return z-ions plus 'H2' (zhh-ions).
 *
 * @return Vector<FragmentIon> zhhIons.
 */
public static Vector<FragmentIon> calculateZHHions(FragmentIon[] zIons, double hydrogenMass) {
    Vector<FragmentIon> zhhIons = new Vector<FragmentIon>();
    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;
}

Example 9 with FragmentIon

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

the class PeptideUtils method calculateIonsLossH2O.

/**
 * Returns Ions minus 'H2O', single and double charge.
 *
 * @return Vector<FragmentIon> ions - H2O
 */
public static Vector<FragmentIon> calculateIonsLossH2O(FragmentIon[] bIons, double hydrogenMass, double oxygenMass, int indexFirstIonLossH2O, boolean doubleCharged, FragmentIonType ionType) {
    Vector<FragmentIon> bIonsLossH20 = new Vector<FragmentIon>();
    double lossMass;
    if (doubleCharged)
        lossMass = hydrogenMass + oxygenMass;
    else
        lossMass = (hydrogenMass * 2) + oxygenMass;
    double mass;
    // Verify position of fist aa who can loose H2O
    if (indexFirstIonLossH2O != bIons.length) {
        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;
}

Example 10 with FragmentIon

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

the class PeptideUtils method calculateDoubleChargedIons.

/**
 * Returns all double charged ions.
 *
 * @return Vector<FragmentIon> doubleChargedIons
 */
public static Vector<FragmentIon> calculateDoubleChargedIons(FragmentIon[] bIons, double hydrogenMass, FragmentIonType ionType) {
    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;
}