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

Example 1 with FragmentIon

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

the class PeptideUtils method calculateBions.

/**
 * This method calculates fragment ions b.
 */
public static Vector<FragmentIon> calculateBions(double[] peptideMasses, double hydrogenMass) {
    Vector<FragmentIon> bIons = new Vector<FragmentIon>();
    for (int i = 1; i < peptideMasses.length; i++) {
        double bMass = 0.0;
        /*
       * Sum all the peptides from left until the current position. Finally add 1 extra hydrogen on
       * the N-terminal AA if there is no fixed N-terminal modification. A B-ion has no new
       * components at its C-terminal end.
       */
        for (int j = 0; j < i; j++) {
            bMass += peptideMasses[j];
        }
        bMass = bMass + hydrogenMass;
        bIons.add(new FragmentIon(bMass, FragmentIonType.B_ION, i));
    }
    return bIons;
}

Example 2 with FragmentIon

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

the class PeptideUtils method calculateYions.

/**
 * This method calculates fragment ions y.
 */
public static Vector<FragmentIon> calculateYions(double[] peptideMasses, double hydrogenMass, double oxygenMass) {
    Vector<FragmentIon> yIons = new Vector<FragmentIon>();
    double ctermMass = hydrogenMass + oxygenMass;
    for (int i = 1; i < peptideMasses.length; i++) {
        double yMass = 0.0;
        /*
       * Sum all the peptides from right until the current position. Finally add 1 extra hydroxyl on
       * the C-terminal AA. A Y-ion also has 2 extra Hydrogens on its N-terminal end (NH in peptide
       * bond, NH3+ when its free).
       */
        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;
}

Example 3 with FragmentIon

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

the class PeptideUtils method getIonCoverage.

/**
 * Returns the coverage of the ion series.
 *
 * @param dataPoints
 * @param peptide
 * @param ionType
 * @param intensityThreshold
 * @return
 */
public static double getIonCoverage(DataPoint[] dataPoints, Peptide peptide, SerieIonType ionType, double intensityThreshold) {
    PeptideFragmentation fragmentation = peptide.getFragmentation();
    FragmentIon[] fragmentIons = fragmentation.getFragmentIons(ionType);
    PeptideIdentityDataFile peptideDataFile = peptide.getScan().getPeptideDataFile();
    double fragmentIonMassErrorTol = peptideDataFile.getFragmentIonMassErrorTolerance();
    DataPoint[] matchedDataPoints = getMatchedIons(dataPoints, fragmentIons, fragmentIonMassErrorTol, intensityThreshold);
    double ionCoverage = calculateSerieCoverage(matchedDataPoints, fragmentIons);
    return ionCoverage;
}

Example 4 with FragmentIon

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

the class PeptideUtils method calculateIonsLossNH3.

/**
 * Returns Ions minus 'NH3', single and double charge.
 *
 * @return Vector<FragmentIon> ions - NH3
 */
public static Vector<FragmentIon> calculateIonsLossNH3(FragmentIon[] bIons, double hydrogenMass, double nitrogenMass, int indexFirstIonLossNH3, boolean doubleCharged, FragmentIonType ionType) {
    Vector<FragmentIon> bIonsLossH20 = new Vector<FragmentIon>();
    double lossMass;
    if (doubleCharged)
        lossMass = nitrogenMass + (hydrogenMass * 2);
    else
        lossMass = nitrogenMass + (hydrogenMass * 3);
    double mass;
    // losses NH3
    if (indexFirstIonLossNH3 != bIons.length) {
        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;
}

Example 5 with FragmentIon

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

the class PeptideUtils method calculateCions.

/**
 * Return b-ions plus 'NH3' (c-ions).
 *
 * @return Vector<FragmentIon> cIons.
 */
public static Vector<FragmentIon> calculateCions(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++) {
        // b-ion plus 'NH3'
        mass = bIons[i].getMass() + NH3;
        cIons.add(new FragmentIon(mass, FragmentIonType.C_ION, (i + 1)));
    }
    return cIons;
}