Fix for Issue 967: Create matching small molecule versions of all sta…

…ndard peptide reports in Document Grid (#2693) Our change to remove peptide-only features in small molecule UI mode resulted in the loss of some useful reports. There is currently no equivalent to: "Peptide RT Results", which has headers: Peptide,Protein,Replicate,Predicted Retention Time,Peptide Retention Time,Peptide Peak Found Ratio and "Transition Results", which has headers: Peptide,Protein,Replicate,Precursor Mz,Precursor Charge,Product Mz,Product Charge,Fragment Ion,Retention Time,Area,Background,Peak Rank Reported by several users including Thomas Eichmann
ProteoWizard · Oct 3, 2023 · 362f4b6 · 362f4b6
1 parent 6055531
commit 362f4b6
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Showing 5 changed files with 107 additions and 7 deletions.
diff --git a/pwiz_tools/Skyline/Model/PersistedViews.cs b/pwiz_tools/Skyline/Model/PersistedViews.cs
@@ -130,7 +130,9 @@ private PersistedViews()
         }
 
         public int RevisionIndex { get; private set; }
-        public int RevisionIndexCurrent { get { return 12; } } // v12 adds small mol peak boundaries report
+        // v12 adds small mol peak boundaries report
+        // v13 adds small mol transitions report and small mol RT Results report
+        public int RevisionIndexCurrent { get { return 13; } } 
         public override void ReadXml(XmlReader reader)
         {
             RevisionIndex = reader.GetIntAttribute(Attr.revision);
@@ -194,6 +196,11 @@ public IEnumerable<KeyValuePair<ViewGroupId, ViewSpec>> GetDefaults(int revision
                 reportStrings.Add(REPORTS_V12); // Including molecule peak boundaries export
             }
 
+            if (revisionIndex >= 13)
+            {
+                reportStrings.Add(REPORTS_V13); // Including molecule RT results and molecule transitions result report
+            }
+
             var list = new List<KeyValuePair<ViewGroupId, ViewSpec>>();
             var xmlSerializer = new XmlSerializer(typeof(ViewSpecList));
             foreach (var reportString in reportStrings)
@@ -212,6 +219,8 @@ public IEnumerable<KeyValuePair<ViewGroupId, ViewSpec>> GetDefaults(int revision
                 {"Small Molecule Transition List", MainGroup.Id.ViewName(Resources.SkylineViewContext_GetTransitionListReportSpec_Small_Molecule_Transition_List)},
                 {"Molecule Quantification", MainGroup.Id.ViewName(Resources.PersistedViews_GetDefaults_Molecule_Quantification)},
                 {"Molecule Ratio Results", MainGroup.Id.ViewName(Resources.PersistedViews_GetDefaults_Molecule_Ratio_Results)},
+                {"Molecule RT Results", MainGroup.Id.ViewName(Resources.ReportSpecList_GetDefaults_Molecule_RT_Results)},
+                {"Molecule Transition Results", MainGroup.Id.ViewName(Resources.ReportSpecList_GetDefaults_Molecule_Transition_Results)},
                 {"SRM Collider Input", ExternalToolsGroup.Id.ViewName("SRM Collider Input")},
             };
             // ReSharper restore LocalizableElement
@@ -503,6 +512,37 @@ private List<KeyValuePair<ViewGroupId, ViewSpec>> RemoveDuplicates(
   </view>
 </views>";
 
+        private const string REPORTS_V13 = @"<views>
+  <view name='Molecule RT Results' rowsource='pwiz.Skyline.Model.Databinding.Entities.Peptide' sublist='Results!*' uimode='small_molecules'>
+    <column name='' />
+    <column name='Protein.Name' />
+    <column name='Results!*.Value.ResultFile.Replicate.Name' />
+    <column name='PredictedRetentionTime' />
+    <column name='Results!*.Value.PeptideRetentionTime' />
+    <column name='Results!*.Value.PeptidePeakFoundRatio' />
+    <filter column='Results!*.Value' opname='isnotnullorblank' />
+  </view>
+  <view name='Molecule Transition Results' rowsource='pwiz.Skyline.Model.Databinding.Entities.Transition' sublist='Results!*' uimode='small_molecules'>
+    <column name='Precursor.Peptide' />
+    <column name='Precursor.Peptide.Protein.Name' />
+    <column name='Results!*.Value.PrecursorResult.PeptideResult.ResultFile.Replicate.Name' />
+    <column name='Precursor.Mz' />
+    <column name='Precursor.Adduct' />
+    <column name='Precursor.Charge' />
+    <column name='FragmentIon' />
+    <column name='ProductMz' />
+    <column name='ProductAdduct' />
+    <column name='ProductCharge' />
+    <column name='Results!*.Value.RetentionTime' />
+    <column name='Results!*.Value.Area' />
+    <column name='Results!*.Value.Background' />
+    <column name='Results!*.Value.PeakRank' />
+    <filter column='Results!*.Value' opname='isnotnullorblank' />
+  </view>
+</views>";
+
+
+
         // ReSharper restore LocalizableElement
 
         #region XML Serialization

diff --git a/pwiz_tools/Skyline/Properties/Resources.Designer.cs b/pwiz_tools/Skyline/Properties/Resources.Designer.cs
diff --git a/pwiz_tools/Skyline/Properties/Resources.resx b/pwiz_tools/Skyline/Properties/Resources.resx
@@ -2568,6 +2568,12 @@ Are you sure you want to continue?</value>
   <data name="ReportSpecList_GetDefaults_Peptide_RT_Results" xml:space="preserve">
     <value>Peptide RT Results</value>
   </data>
+  <data name="ReportSpecList_GetDefaults_Molecule_RT_Results" xml:space="preserve">
+    <value>Molecule RT Results</value>
+  </data>
+  <data name="ReportSpecList_GetDefaults_Molecule_Transition_Results" xml:space="preserve">
+    <value>Molecule Transition Results</value>
+  </data>
   <data name="MessageBoxHelper_ValidateNameTextBox__0__cannot_be_empty" xml:space="preserve">
     <value>{0} cannot be empty.</value>
   </data>

diff --git a/pwiz_tools/Skyline/TestFunctional/SmallMoleculesDocumentGridTest.cs b/pwiz_tools/Skyline/TestFunctional/SmallMoleculesDocumentGridTest.cs
@@ -33,7 +33,7 @@ public class SmallMoleculesDocumentGridTest : AbstractFunctionalTestEx
         [TestMethod]
         public void TestSmallMoleculesDocumentGrid()
         {
-            TestFilesZip = @"TestFunctional\SmallMoleculesDocumentGrid.zip";
+            TestFilesZipPaths = new [] { @"TestFunctional\SmallMoleculesDocumentGrid.zip", @"TestFunctional\SmallMoleculeIrtTest.zip"} ;
             RunFunctionalTest();
         }
 
@@ -42,6 +42,7 @@ public void TestSmallMoleculesDocumentGrid()
         /// </summary>
         protected override void DoTest()
         {
+            TestSmallMoleculeResultsDoc();
             TestMixedDoc();
             TestPeptideOnlyDoc();
             TestSmallMoleculeOnlyDoc();
@@ -82,7 +83,21 @@ private void TestSmallMoleculeOnlyDoc()
             CheckDocumentGridAndColumns(smallMoleculeSky,
                 Resources.SkylineViewContext_GetDocumentGridRowSources_Molecules,
                 1, 10, SrmDocument.DOCUMENT_TYPE.small_molecules);
+        }
 
+        private void TestSmallMoleculeResultsDoc() 
+        {
+            const string smallMoleculeSky = "DextranLadder.sky";
+            CheckDocumentGridAndColumns(smallMoleculeSky,
+                Resources.ReportSpecList_GetDefaults_Molecule_RT_Results,
+                113, 6, SrmDocument.DOCUMENT_TYPE.small_molecules, 
+                null, null, null, null, null, 
+                14.64);
+            CheckDocumentGridAndColumns(smallMoleculeSky,
+                Resources.ReportSpecList_GetDefaults_Molecule_Transition_Results,
+                113, 14, SrmDocument.DOCUMENT_TYPE.small_molecules,
+                null, null, null, null, null,
+                14.64);
         }
 
         private void TestPeptideOnlyDoc()
@@ -111,7 +126,8 @@ private void CheckDocumentGridAndColumns(string docName,
             string expectedFragmentIon = null,
             string expectedMolecularFormula = null,
             string expectedPrecursorNeutralFormula = null,
-            string expectedPrecursorIonFormula = null)
+            string expectedPrecursorIonFormula = null,
+            double? expectedRT = null)
         {
             var oldDoc = SkylineWindow.Document;
             OpenDocument(docName);
@@ -133,6 +149,7 @@ private void CheckDocumentGridAndColumns(string docName,
             var colProductIonFormula = documentGrid.FindColumn(PropertyPath.Parse("ProductIonFormula"));
             var colProductNeutralFormula = documentGrid.FindColumn(PropertyPath.Parse("ProductNeutralFormula"));
             var colProductAdduct = documentGrid.FindColumn(PropertyPath.Parse("ProductAdduct"));
+            var colProductCharge = documentGrid.FindColumn(PropertyPath.Parse("ProductCharge"));
             var colFragmentIon = documentGrid.FindColumn(PropertyPath.Parse("FragmentIonType"));
             var colMoleculeFormula = documentGrid.FindColumn(PropertyPath.Parse("Precursor.Peptide.MoleculeFormula"));
             var colPrecursorNeutralFormula = documentGrid.FindColumn(PropertyPath.Parse("Precursor.NeutralFormula"));
@@ -141,15 +158,16 @@ private void CheckDocumentGridAndColumns(string docName,
             {
                 Assert.IsNull(colProductIonFormula);
                 Assert.IsNull(colProductNeutralFormula);
-                Assert.IsNull(colProductAdduct);
             }
             else RunUI(() =>
             {
                 var formula = documentGrid.DataGridView.Rows[0].Cells[colProductIonFormula.Index].Value.ToString();
+                var adduct = documentGrid.DataGridView.Rows[0].Cells[colProductAdduct.Index].Value.ToString();
+                var z = documentGrid.DataGridView.Rows[0].Cells[colProductCharge.Index].Value;
+                Assert.AreEqual(z, Adduct.FromString(adduct, Adduct.ADDUCT_TYPE.non_proteomic, null).AdductCharge);
                 if (expectedProductIonFormula.Contains("["))
                 {
                     var formulaNeutral = documentGrid.DataGridView.Rows[0].Cells[colProductNeutralFormula.Index].Value.ToString();
-                    var adduct = documentGrid.DataGridView.Rows[0].Cells[colProductAdduct.Index].Value.ToString();
                     Assert.AreEqual(expectedProductIonFormula, formulaNeutral+adduct);
                 }
                 else
@@ -170,6 +188,16 @@ private void CheckDocumentGridAndColumns(string docName,
                 var frag = documentGrid.DataGridView.Rows[0].Cells[colFragmentIon.Index].Value.ToString();
                 Assert.AreEqual(expectedFragmentIon, frag);
             });
+            if (expectedRT.HasValue)
+            {
+                var colRT = documentGrid.FindColumn(PropertyPath.Parse("Results!*.Value.PeptideRetentionTime")) ??
+                            documentGrid.FindColumn(PropertyPath.Parse("Results!*.Value.RetentionTime"));
+                RunUI(() =>
+                {
+                    Assert.AreEqual(expectedRT.Value,
+                        (double)documentGrid.DataGridView.Rows[0].Cells[colRT.Index].Value, .001);
+                });
+            }
             RunUI(() => documentGrid.Close());
         }
 

diff --git a/pwiz_tools/Skyline/TestUtil/AbstractFunctionalTestEx.cs b/pwiz_tools/Skyline/TestUtil/AbstractFunctionalTestEx.cs
@@ -71,8 +71,16 @@ public void Run(string zipFile = null)
         /// <param name="documentPath">File path of document</param>
         public void OpenDocument(string documentPath)
         {
-            var documentFile = TestFilesDir.GetTestPath(documentPath);
-            WaitForCondition(() => File.Exists(documentFile));
+            string documentFile = null;
+            foreach (var testFileDir in TestFilesDirs)
+            {
+                documentFile = testFileDir.GetTestPath(documentPath);
+                if (File.Exists(documentFile))
+                {
+                    break;
+                }
+            }
+
             if (documentPath.EndsWith(@".zip", true, CultureInfo.InvariantCulture))
             {
                 RunUI(() => SkylineWindow.OpenSharedFile(documentFile));