Skyline: Add TMTpro reporter ions up to 18-plex (#2768)

ProteoWizard · Nov 2, 2023 · 614b6d4 · 614b6d4
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Showing 2 changed files with 47 additions and 7 deletions.
diff --git a/pwiz_tools/Skyline/Properties/Settings.cs b/pwiz_tools/Skyline/Properties/Settings.cs
@@ -2553,25 +2553,50 @@ public sealed class MeasuredIonList : SettingsList<MeasuredIon>
         public static readonly MeasuredIon TMT_130_L = CreateMeasuredIon(@"TMT-130L", @"C5C'3H16N'");
         public static readonly MeasuredIon TMT_130_H = CreateMeasuredIon(@"TMT-130H", @"C4C'4H16N");
         public static readonly MeasuredIon TMT_131 = CreateMeasuredIon(@"TMT-131", @"C4C'4H16N'");
+        // TMTpro reporter ion chemical formulas from Phil Remes and the following papers
+        // https://pubs.acs.org/doi/full/10.1021/acs.analchem.9b04474
+        // https://www.nature.com/articles/s41592-020-0781-4
+        public static readonly MeasuredIon TMT_131_L = CreateMeasuredIon(@"TMT-131L", @"C4C'4H16N'");
+        public static readonly MeasuredIon TMT_131_H = CreateMeasuredIon(@"TMT-131H", @"C3C'5H16N");
+        public static readonly MeasuredIon TMT_132_L = CreateMeasuredIon(@"TMT-132L", @"C3C'5H16N'");
+        public static readonly MeasuredIon TMT_132_H = CreateMeasuredIon(@"TMT-132H", @"C2C'6H16N");
+        public static readonly MeasuredIon TMT_133_L = CreateMeasuredIon(@"TMT-133L", @"C2C'6H16N'");
+        public static readonly MeasuredIon TMT_133_H = CreateMeasuredIon(@"TMT-133H", @"C1C'7H16N");
+        public static readonly MeasuredIon TMT_134_L = CreateMeasuredIon(@"TMT-134L", @"C1C'7H16N'");
+        // https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8210943/
+        public static readonly MeasuredIon TMT_134_H = CreateMeasuredIon(@"TMT-134H", @"C'8H16N");
+        public static readonly MeasuredIon TMT_135 = CreateMeasuredIon(@"TMT-135", @"C'8H16N'");
 
         private static MeasuredIon CreateMeasuredIon(string name, string formula)
         {
             return new MeasuredIon(name, formula, null, null, Adduct.M_PLUS);
         }
 
-        public override int RevisionIndexCurrent { get { return 1; } }
+        public override int RevisionIndexCurrent { get { return 2; } }
 
         public override IEnumerable<MeasuredIon> GetDefaults(int revisionIndex)
         {
             var listDefaults = new List<MeasuredIon>(new[] {NTERM_PROLINE, CTERM_GLU_ASP});
             if (revisionIndex < 1)
                 return listDefaults;
-
-            listDefaults.AddRange(new[]
+            if (revisionIndex == 1)
             {
-                ITRAQ_114, ITRAQ_115, ITRAQ_116, ITRAQ_117,
-                TMT_126, TMT_127_L, TMT_127_H, TMT_128_L, TMT_128_H, TMT_129_L, TMT_129_H, TMT_130_L, TMT_130_H, TMT_131
-            });
+                listDefaults.AddRange(new[]
+                {
+                    ITRAQ_114, ITRAQ_115, ITRAQ_116, ITRAQ_117,
+                    TMT_126, TMT_127_L, TMT_127_H, TMT_128_L, TMT_128_H, TMT_129_L, TMT_129_H, TMT_130_L, TMT_130_H, TMT_131
+                });
+            }
+            else
+            {
+                listDefaults.AddRange(new[]
+                {
+                    ITRAQ_114, ITRAQ_115, ITRAQ_116, ITRAQ_117,
+                    TMT_126, TMT_127_L, TMT_127_H, TMT_128_L, TMT_128_H, TMT_129_L, TMT_129_H, TMT_130_L, TMT_130_H,
+                    TMT_131_L, TMT_131_H, TMT_132_L, TMT_132_H, TMT_133_L, TMT_133_H, TMT_134_L, TMT_134_H, TMT_135
+                });
+
+            }
             return listDefaults;
         }
 

diff --git a/pwiz_tools/Skyline/Test/MeasuredIonTest.cs b/pwiz_tools/Skyline/Test/MeasuredIonTest.cs
@@ -39,7 +39,7 @@ public void TestMeasuredIonRoundTrip()
 
             // Verify that the masses of the TMT ions are the same as published in:
             // https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0015866_2162600_TMT_MassTagging_UG.pdf
-            const double delta = .000001;
+            double delta = .000001;
             Assert.AreEqual(126.127726, MeasuredIonList.TMT_126.SettingsCustomIon.MonoisotopicMassMz, delta);
             Assert.AreEqual(127.124761, MeasuredIonList.TMT_127_L.SettingsCustomIon.MonoisotopicMassMz, delta);
             Assert.AreEqual(127.131081, MeasuredIonList.TMT_127_H.SettingsCustomIon.MonoisotopicMassMz, delta);
@@ -50,6 +50,21 @@ public void TestMeasuredIonRoundTrip()
             Assert.AreEqual(130.134825, MeasuredIonList.TMT_130_L.SettingsCustomIon.MonoisotopicMassMz, delta);
             Assert.AreEqual(130.141145, MeasuredIonList.TMT_130_H.SettingsCustomIon.MonoisotopicMassMz, delta);
             Assert.AreEqual(131.138180, MeasuredIonList.TMT_131.SettingsCustomIon.MonoisotopicMassMz, delta);
+            // Verify TMT pro masses the same as publications
+            // https://pubs.acs.org/doi/full/10.1021/acs.analchem.9b04474
+            // https://www.nature.com/articles/s41592-020-0781-4
+            Assert.AreEqual(131.138180, MeasuredIonList.TMT_131_L.SettingsCustomIon.MonoisotopicMassMz, delta);
+            delta *= 100; // Published m/z's don't agree with Skyline until 4th decimal place rounding
+            Assert.AreEqual(131.14450, MeasuredIonList.TMT_131_H.SettingsCustomIon.MonoisotopicMassMz, delta);
+            Assert.AreEqual(132.14150, MeasuredIonList.TMT_132_L.SettingsCustomIon.MonoisotopicMassMz, delta);
+            Assert.AreEqual(132.14785, MeasuredIonList.TMT_132_H.SettingsCustomIon.MonoisotopicMassMz, delta);
+            Assert.AreEqual(133.14488, MeasuredIonList.TMT_133_L.SettingsCustomIon.MonoisotopicMassMz, delta);
+            Assert.AreEqual(133.15120, MeasuredIonList.TMT_133_H.SettingsCustomIon.MonoisotopicMassMz, delta);
+            Assert.AreEqual(134.14824, MeasuredIonList.TMT_134_L.SettingsCustomIon.MonoisotopicMassMz, delta);
+            // https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8210943/
+            delta /= 10; // Agree at 5th decimal place for 18-plex ions
+            Assert.AreEqual(134.154557, MeasuredIonList.TMT_134_H.SettingsCustomIon.MonoisotopicMassMz, delta);
+            Assert.AreEqual(135.151592, MeasuredIonList.TMT_135.SettingsCustomIon.MonoisotopicMassMz, delta);
         }
     }
 }