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xtandem parser » de » proteinms » xtandemparser » xtandem » Masses.java
package de.proteinms.xtandemparser.xtandem;

/**
 * This class holds all the masses used for the calculation of theoretical masses.
 *
 * @author Thilo Muth
 */
public class Masses {

    // The masses for all the amino acids including empty values for non-amino acid letters
    // Update on 05/25/10: Using NEW mono isotopic reference masses due to wrong values. 

    //public static final double A = 71.037110;
    public static final double A = 71.037110;
    public static final double B = 114.534930;
    //public static final double C = 160.030649;
    public static final double C = 103.009185;
    //public static final double D = 115.026940;
    public static final double D = 115.026943;
    //public static final double E = 129.042590;
    public static final double E = 129.042593;
    //public static final double F = 147.068410;
    public static final double F = 147.068414;
    //public static final double G = 57.021460;
    public static final double G = 57.021464;
    //public static final double H = 137.058910;
    public static final double H = 137.058912;
    //public static final double I = 113.084060;
    public static final double I = 113.084064;    
    public static final double J = 0.000000;
    public static final double K = 128.094963;
    
    //public static final double L = 113.084060;
    public static final double L = 113.084064;
    //public static final double M = 131.040490;
    public static final double M = 131.040485;
    //public static final double N = 114.042930;
    public static final double N = 114.042927;
    public static final double O = 0.000000;
    //public static final double P = 97.052760;
    public static final double P = 97.052764;
    //public static final double Q = 128.058580;
    public static final double Q = 128.058578;
    //public static final double R = 156.101110;
    public static final double R = 156.101111;
    //public static final double S = 87.032030;
    public static final double S = 87.032028;
    //public static final double T = 101.047680;
    public static final double T = 101.047679;
    public static final double U = 0.000000;
    //public static final double V = 99.068410;
    public static final double V = 99.068414;
    //public static final double W = 186.079310;
    public static final double W = 186.079313;
    public static final double X = 111.000000;
    //public static final double Y = 163.063330;
    public static final double Y = 163.06332;
    public static final double Z = 128.550590;

    /**
     * The mass of Hydrogen
     */
    public static final double Hydrogen = 1.007825;
    /**
     * The mass of Carbon
     */
    public static final double Carbon = 12.000000;
    /**
     * The mass of Nitrogen
     */
    public static final double Nitrogen = 14.003070;
    /**
     * The mass of Oxygen
     */
    public static final double Oxygen = 15.994910;
    /**
     * The mass of an electron
     */
    public static final double Electron = 0.005490;
    /**
     * The mass of the C Terminus = Oxygen + Hydrogen
     */
    public static final double C_term = 17.002735;
    /**
     * The mass of the N Terminus = Hydrogen
     */
    public static final double N_term = 1.007825;
}
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