Monoisotopic mass and m/z on isotopic envelopes

src/TopDownProteomics/MassSpectrometry/ChargedIsotopicDistribution.cs

@@ -1,99 +1,94 @@
 using System;
 using System.Linq;
 
-namespace TopDownProteomics.MassSpectrometry
-{
-    /// <summary>
-    /// Isotopic Distribution with a given charge.
-    /// </summary>
-    /// <seealso cref="IMzIntensityData" />
-    public class ChargedIsotopicDistribution : IMzIntensityData, IChargedIsotopicDistribution
-    {
-        private readonly double[] _intensity;
-        private readonly double[] _mz;
+namespace TopDownProteomics.MassSpectrometry;
 
-        /// <summary>
-        /// Initializes a new instance of the <see cref="ChargedIsotopicDistribution"/> class.
-        /// </summary>
-        /// <param name="mz">The mz.</param>
-        /// <param name="intensity">The intensity.</param>
-        /// <param name="charge">The charge.</param>
-        /// <param name="chargeCarrier">The charge carrier.</param>
-        public ChargedIsotopicDistribution(double[] mz, double[] intensity, int charge, double chargeCarrier)
-        {
-            _intensity = intensity;
-            _mz = mz;
+/// <summary>
+/// Isotopic Distribution with a given charge.
+/// </summary>
+/// <seealso cref="IMzIntensityData" />
+/// <remarks>
+/// Initializes a new instance of the <see cref="ChargedIsotopicDistribution"/> class.
+/// </remarks>
+/// <param name="monoMz">The mono m/z.</param>
+/// <param name="mz">The mz.</param>
+/// <param name="intensity">The intensity.</param>
+/// <param name="charge">The charge.</param>
+/// <param name="chargeCarrier">The charge carrier.</param>
+public class ChargedIsotopicDistribution(double monoMz, double[] mz, double[] intensity, int charge, double chargeCarrier) : IMzIntensityData, IChargedIsotopicDistribution
+{
+    private readonly double[] _intensity = intensity;
+    private readonly double[] _mz = mz;
 
-            this.Charge = charge;
-            this.ChargeCarrier = chargeCarrier;
-        }
+    /// <summary>The charge.</summary>
+    public int Charge { get; } = charge;
 
-        /// <summary>The charge.</summary>
-        public int Charge { get; }
+    /// <summary>The mass of the charge carrier.</summary>
+    public double ChargeCarrier { get; } = chargeCarrier;
 
-        /// <summary>The mass of the charge carrier.</summary>
-        public double ChargeCarrier { get; }
+    /// <summary>
+    /// Gets the mz.
+    /// </summary>
+    public double[] GetMz() => _mz;
 
-        /// <summary>
-        /// Gets the mz.
-        /// </summary>
-        public double[] GetMz() => _mz;
+    /// <summary>
+    /// Gets the first m/z.
+    /// </summary>
+    public double FirstMz => _mz[0];
 
-        /// <summary>
-        /// Gets the first m/z.
-        /// </summary>
-        public double FirstMz => _mz[0];
+    /// <summary>The monoisotopic m/z.</summary>
+    public double MonoisotopicMz { get; } = monoMz;
 
-        /// <summary>
-        /// Gets the last m/z.
-        /// </summary>
-        public double LastMz => _mz[_mz.Length - 1];
+    /// <summary>
+    /// Gets the last m/z.
+    /// </summary>
+    public double LastMz => _mz[_mz.Length - 1];
 
-        /// <summary>
-        /// Gets the intensity.
-        /// </summary>
-        public double[] GetIntensity() => _intensity;
+    /// <summary>
+    /// Gets the intensity.
+    /// </summary>
+    public double[] GetIntensity() => _intensity;
 
-        /// <summary>
-        /// Gets the length.
-        /// </summary>
-        public int Length => _mz.Length;
+    /// <summary>
+    /// Gets the length.
+    /// </summary>
+    public int Length => _mz.Length;
 
-        /// <summary>
-        /// Clones the distribution with a subset of the most intense points.
-        /// </summary>
-        /// <param name="numberOfPoints">The number of points to keep.</param>
-        /// <returns></returns>
-        public IChargedIsotopicDistribution CloneWithMostIntensePoints(int numberOfPoints)
+    /// <summary>
+    /// Clones the distribution with a subset of the most intense points.
+    /// </summary>
+    /// <param name="numberOfPoints">The number of points to keep.</param>
+    /// <returns></returns>
+    public IChargedIsotopicDistribution CloneWithMostIntensePoints(int numberOfPoints)
+    {
+        for (int i = 0; i < _mz.Length - numberOfPoints; i++)
         {
-            for (int i = 0; i < _mz.Length - numberOfPoints; i++)
+            if (_intensity[i] > _intensity[i + numberOfPoints])
             {
-                if (_intensity[i] > _intensity[i + numberOfPoints])
-                {
-                    // Moving any more would only make things less intense ... stop
-                    return new ChargedIsotopicDistribution(_mz.SubSequence(i, i + numberOfPoints - 1).ToArray(),
-                        _intensity.SubSequence(i, i + numberOfPoints - 1).ToArray(), this.Charge, this.ChargeCarrier);
-                }
+                // Moving any more would only make things less intense ... stop
+                return new ChargedIsotopicDistribution(this.MonoisotopicMz, _mz.SubSequence(i, i + numberOfPoints - 1).ToArray(),
+                    _intensity.SubSequence(i, i + numberOfPoints - 1).ToArray(), this.Charge, this.ChargeCarrier);
             }
-
-            throw new Exception($"Cannot find most {numberOfPoints} intense points.");
         }
 
-        /// <summary>
-        /// Clones the distribution and shifts it by an m/z (Th) value.
-        /// </summary>
-        /// <param name="shiftMz">The shift m/z in thomsons (Th).</param>
-        /// <returns></returns>
-        public IChargedIsotopicDistribution CloneAndShift(double shiftMz)
-        {
-            double[] mz = new double[this.Length];
+        throw new Exception($"Cannot find most {numberOfPoints} intense points.");
+    }
 
-            for (int i = 0; i < this.Length; i++)
-            {
-                mz[i] = _mz[i] + shiftMz;
-            }
+    /// <summary>
+    /// Clones the distribution and shifts it by an m/z (Th) value.
+    /// </summary>
+    /// <param name="shiftMz">The shift m/z in Thomsons (Th).</param>
+    /// <returns></returns>
+    public IChargedIsotopicDistribution CloneAndShift(double shiftMz)
+    {
+        double[] mz = new double[this.Length];
+        double monoMz = this.MonoisotopicMz + shiftMz;
 
-            return new ChargedIsotopicDistribution(mz, (double[])_intensity.Clone(), this.Charge, this.ChargeCarrier);
+        for (int i = 0; i < this.Length; i++)
+        {
+            mz[i] = _mz[i] + shiftMz;
         }
+
+        return new ChargedIsotopicDistribution(monoMz, mz, (double[])_intensity.Clone(), this.Charge, this.ChargeCarrier);
     }
 }

src/TopDownProteomics/MassSpectrometry/IChargedIsotopicDistribution.cs

@@ -11,6 +11,9 @@ public interface IChargedIsotopicDistribution : IMzIntensityData
         /// <summary>The mass of the charge carrier.</summary>
         double ChargeCarrier { get; }
 
+        /// <summary>Gets the monoisotopic m/z.</summary>
+        double MonoisotopicMz { get; }
+
         /// <summary>
         /// Clones the distribution with a subset of the most intense points.
         /// </summary>

src/TopDownProteomics/MassSpectrometry/IIsotopicDistribution.cs

@@ -13,6 +13,9 @@ public interface IIsotopicDistribution
     /// </summary>
     int Length { get; }
 
+    /// <summary>The monoisotopic mass.</summary>
+    double MonoisotopicMass { get; }
+
     /// <summary>
     /// Gets the masses.
     /// </summary>