Negative Mode and Charge Carriers

src/TopDownProteomics/MassSpectrometry/ChargedIsotopicDistribution.cs

@@ -18,18 +18,22 @@
         /// <param name="mz">The mz.</param>
         /// <param name="intensity">The intensity.</param>
         /// <param name="charge">The charge.</param>
-        public ChargedIsotopicDistribution(double[] mz, double[] intensity, int charge)
+        /// <param name="chargeCarrier">The charge carrier.</param>
+        public ChargedIsotopicDistribution(double[] mz, double[] intensity, int charge, double chargeCarrier)
         {
             _intensity = intensity;
             _mz = mz;
+
             this.Charge = charge;
+            this.ChargeCarrier = chargeCarrier;
         }
 
-        /// <summary>
-        /// Gets the charge.
-        /// </summary>
+        /// <summary>The charge.</summary>
         public int Charge { get; }
 
+        /// <summary>The mass of the charge carrier.</summary>
+        public double ChargeCarrier { get; }
+
         /// <summary>
         /// Gets the mz.
         /// </summary>
@@ -68,7 +72,7 @@
                 {
                     // 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);
+                        _intensity.SubSequence(i, i + numberOfPoints - 1).ToArray(), this.Charge, this.ChargeCarrier);
                 }
             }
 
@@ -89,7 +93,7 @@
                 mz[i] = _mz[i] + shiftMz;
             }
 
-            return new ChargedIsotopicDistribution(mz, (double[])_intensity.Clone(), this.Charge);
+            return new ChargedIsotopicDistribution(mz, (double[])_intensity.Clone(), this.Charge, this.ChargeCarrier);
         }
     }
 }

src/TopDownProteomics/MassSpectrometry/IChargedIsotopicDistribution.cs

@@ -5,11 +5,12 @@
     /// </summary>
     public interface IChargedIsotopicDistribution : IMzIntensityData
     {
-        /// <summary>
-        /// Gets the charge.
-        /// </summary>
+        /// <summary>The charge.</summary>
         int Charge { get; }
 
+        /// <summary>The mass of the charge carrier.</summary>
+        double ChargeCarrier { get; }
+
         /// <summary>
         /// Clones the distribution with a subset of the most intense points.
         /// </summary>
@@ -20,7 +21,7 @@ public interface IChargedIsotopicDistribution : IMzIntensityData
         /// <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>
+        /// <param name="shiftMz">The shift m/z in Thomsons (Th).</param>
         /// <returns></returns>
         IChargedIsotopicDistribution CloneAndShift(double shiftMz);
     }

src/TopDownProteomics/MassSpectrometry/IIsotopicDistribution.cs

@@ -1,40 +1,49 @@
-using System.Collections.Generic;
+using System;
+using System.Collections.Generic;
 
-namespace TopDownProteomics.MassSpectrometry
+namespace TopDownProteomics.MassSpectrometry;
+
+/// <summary>
+/// Neutral distribution of isotopes in a mass spectrometer.
+/// </summary>
+public interface IIsotopicDistribution
 {
     /// <summary>
-    /// Neutral distribution of isotopes in a mass spectrometer.
+    /// Gets the length.
+    /// </summary>
+    int Length { get; }
+
+    /// <summary>
+    /// Gets the masses.
     /// </summary>
-    public interface IIsotopicDistribution
-    {
-        /// <summary>
-        /// Gets the length.
-        /// </summary>
-        int Length { get; }
+    IList<double> Masses { get; }
 
-        /// <summary>
-        /// Gets the masses.
-        /// </summary>
-        IList<double> Masses { get; }
+    /// <summary>
+    /// Gets the intensities.
+    /// </summary>
+    IList<double> Intensities { get; }
 
-        /// <summary>
-        /// Gets the intensities.
-        /// </summary>
-        IList<double> Intensities { get; }
+    /// <summary>
+    /// Creates a charged isotopic distribution.
+    /// </summary>
+    /// <param name="charge">The charge.</param>
+    /// <param name="positiveCharge">if set to <c>true</c> [positive charge].</param>
+    /// <returns>A charged isotopic distribution with the same abundances.</returns>
+    [Obsolete("Use CreateChargedDistribution(int charge, double chargeCarrier) instead.")]
+    IChargedIsotopicDistribution CreateChargedDistribution(int charge, bool positiveCharge);
 
-        /// <summary>
-        /// Creates a charged isotopic distribution.
-        /// </summary>
-        /// <param name="charge">The charge.</param>
-        /// <param name="positiveCharge">if set to <c>true</c> [positive charge].</param>
-        /// <returns>A charged isotopic distribution with the same abundances.</returns>
-        IChargedIsotopicDistribution CreateChargedDistribution(int charge, bool positiveCharge = true);
+    /// <summary>
+    /// Creates a charged isotopic distribution.
+    /// </summary>
+    /// <param name="charge">The charge.</param>
+    /// <param name="chargeCarrier">The charge carrier.</param>
+    /// <returns>A charged isotopic distribution with the same abundances.</returns>
+    IChargedIsotopicDistribution CreateChargedDistribution(int charge, double chargeCarrier = Utility.Proton);
 
-        /// <summary>
-        /// Clones the distribution and shifts it by a mass (Da) value.
-        /// </summary>
-        /// <param name="shift">The shift mass in daltons (Da).</param>
-        /// <returns></returns>
-        IIsotopicDistribution CloneAndShift(double shift);
-    }
+    /// <summary>
+    /// Clones the distribution and shifts it by a mass (Da) value.
+    /// </summary>
+    /// <param name="shift">The shift mass in daltons (Da).</param>
+    /// <returns>The cloned distribution shifted by the specified mass.</returns>
+    IIsotopicDistribution CloneAndShift(double shift);
 }

src/TopDownProteomics/MassSpectrometry/IsotopicDistribution.cs

@@ -1,4 +1,5 @@
 using System.Collections.Generic;
+using System.Diagnostics;
 using System.Linq;
 
 namespace TopDownProteomics.MassSpectrometry
@@ -55,7 +56,19 @@
             double[] mz = new double[this.Length];
 
             for (int i = 0; i < this.Length; i++)
+#pragma warning disable CS0618 // Type or member is obsolete
                 mz[i] = Utility.ConvertMassToMz(_masses[i], charge, positiveCharge);
+#pragma warning restore CS0618 // Type or member is obsolete
+
+            return mz;
+        }
+
+        private double[] GetMz(int charge, double chargeCarrier)
+        {
+            double[] mz = new double[this.Length];
+
+            for (int i = 0; i < this.Length; i++)
+                mz[i] = Utility.ConvertMassToMz(_masses[i], charge, chargeCarrier);
 
             return mz;
         }
@@ -66,9 +79,26 @@
         /// <param name="charge">The charge.</param>
         /// <param name="positiveCharge">if set to <c>true</c> [positive charge].</param>
         /// <returns></returns>
-        public IChargedIsotopicDistribution CreateChargedDistribution(int charge, bool positiveCharge = true)
+        public IChargedIsotopicDistribution CreateChargedDistribution(int charge, bool positiveCharge)
         {
-            return new ChargedIsotopicDistribution(this.GetMz(charge, positiveCharge), _abundances, charge);
+            Debug.Assert(charge > 0, "Charge must be greater than 0.");
+
+            return new ChargedIsotopicDistribution(this.GetMz(charge, positiveCharge), _abundances, charge, Utility.Proton);
+        }
+
+        /// <summary>
+        /// Creates a charged isotopic distribution.
+        /// </summary>
+        /// <param name="charge">The charge.</param>
+        /// <param name="chargeCarrier">The charge carrier.</param>
+        /// <returns>
+        /// A charged isotopic distribution with the same abundances.
+        /// </returns>
+        public IChargedIsotopicDistribution CreateChargedDistribution(int charge, double chargeCarrier = Utility.Proton)
+        {
+            Debug.Assert(chargeCarrier > 0, "Charge carrier must be greater than 0.");
+
+            return new ChargedIsotopicDistribution(this.GetMz(charge, chargeCarrier), _abundances, charge, chargeCarrier);
         }
 
         /// <summary>