diff --git a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSHidePeptidesAndMolecules.java b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSHidePeptidesAndMolecules.java
index 2f5b826b2..a395d15f0 100644
--- a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSHidePeptidesAndMolecules.java
+++ b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSHidePeptidesAndMolecules.java
@@ -13,6 +13,10 @@
 
 import java.util.Arrays;
 
+/**
+ * Tests the ability to hide/show specific peptides and molecules in QC folders across multiple folder structure
+ * configurations.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 6)
 public class TargetedMSHidePeptidesAndMolecules extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSIsotopologueTest.java b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSIsotopologueTest.java
index 6dfbdff7d..7720306f3 100644
--- a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSIsotopologueTest.java
+++ b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSIsotopologueTest.java
@@ -13,6 +13,9 @@
 
 import static org.junit.Assert.assertTrue;
 
+/**
+ * Validates isotopologue metric display and calculation in the Panorama Dashboard QC metrics panel.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 3)
 public class TargetedMSIsotopologueTest extends TargetedMSPremiumTest
diff --git a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCFolderImportExport.java b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCFolderImportExport.java
index 466dbb664..d9fed84fd 100644
--- a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCFolderImportExport.java
+++ b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCFolderImportExport.java
@@ -17,6 +17,9 @@
 import java.util.LinkedHashMap;
 import java.util.Map;
 
+/**
+ * Tests import/export of QC folder configurations and data as a round-trip operation.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 6)
 public class TargetedMSQCFolderImportExport extends TargetedMSPremiumTest
diff --git a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCPremiumTest.java b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCPremiumTest.java
index 500b9551e..60414187f 100644
--- a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCPremiumTest.java
+++ b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCPremiumTest.java
@@ -37,6 +37,10 @@
 import static org.labkey.test.components.targetedms.QCPlotsWebPart.QCPlotType.CUSUMm;
 import static org.labkey.test.util.PermissionsHelper.READER_ROLE;
 
+/**
+ * Tests premium-tier QC functionality: guide sets, advanced QC metrics, CUSUM plots, and premium-specific permission
+ * checks.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 6)
 public class TargetedMSQCPremiumTest extends TargetedMSPremiumTest
diff --git a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSSampleManagerIntegrationTest.java b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSSampleManagerIntegrationTest.java
index a280d7580..117f714fb 100644
--- a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSSampleManagerIntegrationTest.java
+++ b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSSampleManagerIntegrationTest.java
@@ -20,6 +20,10 @@
 import java.util.List;
 import java.util.Map;
 
+/**
+ * Tests integration between TargetedMS and the Sample Manager module, including linked sample type data flowing into
+ * Skyline documents.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 3)
 public class TargetedMSSampleManagerIntegrationTest extends TargetedMSPremiumTest
diff --git a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSiRTMetricsTest.java b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSiRTMetricsTest.java
index 4cc9a7eea..24c74aaf8 100644
--- a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSiRTMetricsTest.java
+++ b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSiRTMetricsTest.java
@@ -18,6 +18,9 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+/**
+ * Tests iRT metrics calculations and their visualization specifically within the QC dashboard context.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class TargetedMSiRTMetricsTest extends TargetedMSPremiumTest
diff --git a/test/src/org/labkey/test/tests/targetedms/ClustergrammerTest.java b/test/src/org/labkey/test/tests/targetedms/ClustergrammerTest.java
index 6257464d4..73783a507 100644
--- a/test/src/org/labkey/test/tests/targetedms/ClustergrammerTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/ClustergrammerTest.java
@@ -27,6 +27,9 @@
 
 import java.util.Arrays;
 
+/**
+ * Tests the Clustergrammer heatmap visualization integration for peptide data.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class ClustergrammerTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/GetDataAPITest.java b/test/src/org/labkey/test/tests/targetedms/GetDataAPITest.java
index 65a860911..742c6e3b1 100644
--- a/test/src/org/labkey/test/tests/targetedms/GetDataAPITest.java
+++ b/test/src/org/labkey/test/tests/targetedms/GetDataAPITest.java
@@ -27,6 +27,9 @@
 import static org.hamcrest.CoreMatchers.containsString;
 import static org.junit.Assert.assertThat;
 
+/**
+ * Tests the GetData API with query transformations, filtering, and pivot operations on TargetedMS data.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class GetDataAPITest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/InstrumentSchedulingTest.java b/test/src/org/labkey/test/tests/targetedms/InstrumentSchedulingTest.java
index 50fdd277a..3718b04d3 100644
--- a/test/src/org/labkey/test/tests/targetedms/InstrumentSchedulingTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/InstrumentSchedulingTest.java
@@ -48,6 +48,9 @@
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
+/**
+ * Tests instrument scheduling workflows including date/time handling and permissions across QC folders.
+ */
 @Category({})
 @FixMethodOrder(MethodSorters.NAME_ASCENDING) // Don't insert additional projects until after testSchedule() has run
 public class InstrumentSchedulingTest extends TargetedMSTest implements PostgresOnlyTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSAuditLogTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSAuditLogTest.java
index 871d2d0ea..d63cc6fb6 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSAuditLogTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSAuditLogTest.java
@@ -10,6 +10,9 @@
 
 import static org.junit.Assert.assertEquals;
 
+/**
+ * Verifies that audit log entries from Skyline documents are correctly imported and displayed as an audit trail.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class TargetedMSAuditLogTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSChromatogramOptimizationTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSChromatogramOptimizationTest.java
index 2cbc35bbe..ae44b6ea8 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSChromatogramOptimizationTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSChromatogramOptimizationTest.java
@@ -20,6 +20,9 @@
 import java.util.LinkedList;
 import java.util.List;
 
+/**
+ * Tests chromatogram optimization workflows and library file generation from imported Skyline documents.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 3)
 public class TargetedMSChromatogramOptimizationTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSDocumentFormatsTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSDocumentFormatsTest.java
index bba9d6919..fc7b8c7be 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSDocumentFormatsTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSDocumentFormatsTest.java
@@ -31,6 +31,9 @@
 import java.util.Collections;
 import java.util.List;
 
+/**
+ * Tests backward compatibility by importing Skyline documents across multiple historical format versions.
+ */
 @Category({})
 public class TargetedMSDocumentFormatsTest extends TargetedMSTest
 {
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSEarlyStagePTMReportTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSEarlyStagePTMReportTest.java
index c0b5907b1..8b9b4d703 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSEarlyStagePTMReportTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSEarlyStagePTMReportTest.java
@@ -12,6 +12,10 @@
 
 import static org.junit.Assert.assertEquals;
 
+/**
+ * Tests the PTM (post-translational modification) peptide report feature, including data pre-pivoting for
+ * early-stage PTM analysis.
+ */
 @Category({})
 public class TargetedMSEarlyStagePTMReportTest extends TargetedMSTest
 {
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentIrtTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentIrtTest.java
index 7a4c0c798..f0cb08f44 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentIrtTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentIrtTest.java
@@ -21,6 +21,9 @@
 
 import static org.junit.Assert.assertEquals;
 
+/**
+ * Tests iRT (indexed Retention Time) scale import in experiment folders, validating the standard peptide set.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class TargetedMSExperimentIrtTest extends TargetedMSIrtTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentTest.java
index 5e3f7d79c..2f70382b3 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentTest.java
@@ -56,6 +56,9 @@
 import static org.labkey.test.util.DataRegionTable.DataRegion;
 import static org.labkey.test.util.PermissionsHelper.READER_ROLE;
 
+/**
+ * Broad coverage of experiment folder behavior: file uploads, shared file access, and folder-level permissions.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 8)
 public class TargetedMSExperimentTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentalQCLinkTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentalQCLinkTest.java
index 93c7c2f0d..5719f123c 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentalQCLinkTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentalQCLinkTest.java
@@ -17,6 +17,9 @@
 import java.util.Arrays;
 import java.util.List;
 
+/**
+ * Tests linking of experiment folders to QC folders, then validates guide sets and metrics flow across the link.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 4)
 public class TargetedMSExperimentalQCLinkTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSInstrumentNicknameTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSInstrumentNicknameTest.java
index a29837308..aa06df71c 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSInstrumentNicknameTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSInstrumentNicknameTest.java
@@ -35,6 +35,9 @@
 import static org.labkey.test.util.PermissionsHelper.EDITOR_ROLE;
 import static org.labkey.test.util.PermissionsHelper.READER_ROLE;
 
+/**
+ * Tests creation, inheritance, and permission-gating of instrument nicknames across folder hierarchies.
+ */
 @Category({})
 public class TargetedMSInstrumentNicknameTest extends TargetedMSTest
 {
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSLibraryIrtTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSLibraryIrtTest.java
index 35b90c0d0..590750f1e 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSLibraryIrtTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSLibraryIrtTest.java
@@ -23,6 +23,9 @@
 
 import static org.junit.Assert.assertEquals;
 
+/**
+ * Tests iRT scale updates in library folders, specifically the weighted-average recalculation logic.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 10)
 public class TargetedMSLibraryIrtTest extends TargetedMSIrtTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSLibraryTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSLibraryTest.java
index 9f6b3dacf..ea4057fe6 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSLibraryTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSLibraryTest.java
@@ -36,6 +36,9 @@
 import static org.junit.Assert.assertTrue;
 import static org.labkey.test.util.PermissionsHelper.READER_ROLE;
 
+/**
+ * Tests protein library folders, library revisions, and conflict resolution when uploaded documents contain the same targets as the existing library (parallel to the peptide and small molecule library tests).
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class TargetedMSLibraryTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSLightHeavyRatioTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSLightHeavyRatioTest.java
index 2229b33ae..ec6d31ae6 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSLightHeavyRatioTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSLightHeavyRatioTest.java
@@ -15,6 +15,9 @@
 import static org.junit.Assert.assertTrue;
 import static org.labkey.test.Locator.tag;
 
+/**
+ * Validates light/heavy peptide ratio calculations and reproducibility report output.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 3)
 public class TargetedMSLightHeavyRatioTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSLinkVersionsTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSLinkVersionsTest.java
index 326a9a95c..51dab04f4 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSLinkVersionsTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSLinkVersionsTest.java
@@ -28,6 +28,9 @@
 
 import static org.junit.Assert.assertEquals;
 
+/**
+ * Tests the version-linking feature for multiple documents within experiment folders.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 25)
 public class TargetedMSLinkVersionsTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSListTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSListTest.java
index bb4dfbce0..8ef5ee315 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSListTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSListTest.java
@@ -35,6 +35,9 @@
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
 
+/**
+ * Tests list query functionality with document imports and property handling specific to TargetedMS.
+ */
 @Category({})
 public class TargetedMSListTest extends TargetedMSTest
 {
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSMAMTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSMAMTest.java
index c7f393179..4b9beb6b1 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSMAMTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSMAMTest.java
@@ -24,6 +24,9 @@
 
 import static org.junit.Assert.assertTrue;
 
+/**
+ * Tests MAM (Multi-Attribute Monitoring) experiment folders, including cross-linked peptides and iRT data.
+ */
 @Category({})
 public class TargetedMSMAMTest extends TargetedMSTest
 {
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSMovingSKYDocAcrossFoldersTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSMovingSKYDocAcrossFoldersTest.java
index d2b6abfdd..456c4deff 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSMovingSKYDocAcrossFoldersTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSMovingSKYDocAcrossFoldersTest.java
@@ -11,6 +11,9 @@
 import org.labkey.test.util.APIContainerHelper;
 import org.labkey.test.util.DataRegionTable;
 
+/**
+ * Verifies that Skyline documents can be moved between different folder types (experiment and MAM).
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 4)
 public class TargetedMSMovingSKYDocAcrossFoldersTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSMultiplePeptidePlotTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSMultiplePeptidePlotTest.java
index 7d485b215..6c62045c9 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSMultiplePeptidePlotTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSMultiplePeptidePlotTest.java
@@ -14,6 +14,9 @@
 import java.io.File;
 import java.util.List;
 
+/**
+ * Tests rendering of multiple peptides on the same chromatogram visualization panel.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 2)
 public class TargetedMSMultiplePeptidePlotTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSMxNReproducibilityReportTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSMxNReproducibilityReportTest.java
index 126cf0c67..180dd6665 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSMxNReproducibilityReportTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSMxNReproducibilityReportTest.java
@@ -23,6 +23,9 @@
 
 import static org.labkey.test.Locator.tag;
 
+/**
+ * Tests M×N reproducibility reports with both single and multiple replicate configurations.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 6)
 public class TargetedMSMxNReproducibilityReportTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSPeptideLibraryTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSPeptideLibraryTest.java
index f6e19088c..307e41d37 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSPeptideLibraryTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSPeptideLibraryTest.java
@@ -35,6 +35,9 @@
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
 
+/**
+ * Tests peptide library folder revisions and conflict resolution when multiple documents define the same library entries.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class TargetedMSPeptideLibraryTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSPeptideSummaryHeatmapTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSPeptideSummaryHeatmapTest.java
index 64c3c0a9c..8e62262d8 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSPeptideSummaryHeatmapTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSPeptideSummaryHeatmapTest.java
@@ -17,6 +17,9 @@
 
 import static org.junit.Assert.assertEquals;
 
+/**
+ * Tests the peptide/molecule summary heatmap visualization in QC dashboards.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class TargetedMSPeptideSummaryHeatmapTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSPrecursorLevelDataTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSPrecursorLevelDataTest.java
index eb9e83520..1cc8f111a 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSPrecursorLevelDataTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSPrecursorLevelDataTest.java
@@ -18,6 +18,9 @@
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 
+/**
+ * Validates precursor-level quantification data and figures-of-merit calculations.
+ */
 @Category({})
 public class TargetedMSPrecursorLevelDataTest extends AbstractQuantificationTest
 {
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinGroupingTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinGroupingTest.java
index b8ad5dff4..dd285d028 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinGroupingTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinGroupingTest.java
@@ -8,6 +8,9 @@
 import org.labkey.test.components.CustomizeView;
 import org.labkey.test.util.DataRegionTable;
 
+/**
+ * Tests protein grouping logic and the protein match visualization UI.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 2)
 public class TargetedMSProteinGroupingTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinSequenceViewTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinSequenceViewTest.java
index 3f83fda4b..b961c283d 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinSequenceViewTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinSequenceViewTest.java
@@ -10,6 +10,9 @@
 
 import java.util.Arrays;
 
+/**
+ * Tests protein sequence views including confidence score display and rendering of modified peptides.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 12)
 public class TargetedMSProteinSequenceViewTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java
index 89e8708df..e34b17b0f 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java
@@ -19,6 +19,9 @@
 import java.util.Map;
 import java.util.regex.Pattern;
 
+/**
+ * Tests the QC metric configuration UI and verifies settings propagate consistently across folder hierarchies.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class TargetedMSQCConfigureMetricTest extends TargetedMSPremiumTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCGuideSetTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCGuideSetTest.java
index f911a0c2f..476a0467d 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCGuideSetTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCGuideSetTest.java
@@ -51,6 +51,9 @@
 
 import static org.junit.Assert.assertEquals;
 
+/**
+ * Tests guide set management, statistics computation, and Pareto plot generation in QC folders.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 25)
 public class TargetedMSQCGuideSetTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCSummaryTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCSummaryTest.java
index f3f87ee71..e9bb5f67e 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCSummaryTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCSummaryTest.java
@@ -56,6 +56,9 @@
 import static org.junit.Assert.fail;
 import static org.labkey.test.util.PermissionsHelper.READER_ROLE;
 
+/**
+ * Tests the QC summary dashboard including guide sets, annotations, permissions, and trailing statistic calculations.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 12)
 public class TargetedMSQCSummaryTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCTest.java
index 141bc3e7c..b51926618 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCTest.java
@@ -69,6 +69,9 @@
 import static org.labkey.test.components.targetedms.QCPlotsWebPart.QCPlotType.TrailingCV;
 import static org.labkey.test.util.PermissionsHelper.READER_ROLE;
 
+/**
+ * Broad QC folder test covering plots, metric types, annotations, guide sets, and permissions together in one suite.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 35)
 public class TargetedMSQCTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSSampleFileChromInfoTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSSampleFileChromInfoTest.java
index 0fd519ca6..2367e2c33 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSSampleFileChromInfoTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSSampleFileChromInfoTest.java
@@ -27,6 +27,9 @@
 
 import java.util.Arrays;
 
+/**
+ * Tests sample file-scoped chromatograms (e.g., pressure traces) parsed from Skyline documents.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 6)
 public class TargetedMSSampleFileChromInfoTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSSkydTextIdTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSSkydTextIdTest.java
index 96db4eaed..a3fab4d9f 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSSkydTextIdTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSSkydTextIdTest.java
@@ -27,6 +27,9 @@
 import java.util.List;
 import java.util.stream.Collectors;
 
+/**
+ * Tests upload and parsing of small molecule SKYD text-format files.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 6)
 public class TargetedMSSkydTextIdTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSSmallMoleculeLibraryTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSSmallMoleculeLibraryTest.java
index a08cd843d..542f6c683 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSSmallMoleculeLibraryTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSSmallMoleculeLibraryTest.java
@@ -32,6 +32,10 @@
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
 
+/**
+ * Tests small molecule library folders, document revisions, and conflict resolution (parallel to the peptide library
+ * test but for small molecules).
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class TargetedMSSmallMoleculeLibraryTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSSmallMoleculeLightHeavyRatioTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSSmallMoleculeLightHeavyRatioTest.java
index 1d266316e..1f4fdcc1c 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSSmallMoleculeLightHeavyRatioTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSSmallMoleculeLightHeavyRatioTest.java
@@ -15,6 +15,9 @@
 
 import static org.junit.Assert.assertEquals;
 
+/**
+ * Validates light/heavy ratio metrics specifically for small molecule data in QC dashboards.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 3)
 public class TargetedMSSmallMoleculeLightHeavyRatioTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSTrailingMeanAndCVTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSTrailingMeanAndCVTest.java
index b0897a054..c492bb9af 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSTrailingMeanAndCVTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSTrailingMeanAndCVTest.java
@@ -13,6 +13,9 @@
 import org.labkey.test.util.PortalHelper;
 import org.openqa.selenium.support.ui.ExpectedConditions;
 
+/**
+ * Tests trailing mean and coefficient-of-variation metric calculations in the QC system.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class TargetedMSTrailingMeanAndCVTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSTransitionChromInfoLimitTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSTransitionChromInfoLimitTest.java
index 1d1717f6a..f41f7dbf4 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSTransitionChromInfoLimitTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSTransitionChromInfoLimitTest.java
@@ -10,6 +10,10 @@
 
 import java.util.List;
 
+/**
+ * Validates behavior at chromatogram data storage limits for transitions and precursors, with custom configuration
+ * overrides.
+ */
 @Category({})
 public class TargetedMSTransitionChromInfoLimitTest extends TargetedMSTest
 {
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSUtilizationCalendarTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSUtilizationCalendarTest.java
index 05ed29770..77898b1d7 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSUtilizationCalendarTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSUtilizationCalendarTest.java
@@ -16,6 +16,9 @@
 
 import static org.labkey.test.util.PermissionsHelper.READER_ROLE;
 
+/**
+ * Tests the instrument utilization calendar: display options, date ranges, and permission-gating.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class TargetedMSUtilizationCalendarTest extends TargetedMSTest
diff --git a/test/src/org/labkey/test/tests/targetedms/passport/PassportTest.java b/test/src/org/labkey/test/tests/targetedms/passport/PassportTest.java
index 76554c4d2..5857064b3 100644
--- a/test/src/org/labkey/test/tests/targetedms/passport/PassportTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/passport/PassportTest.java
@@ -24,6 +24,10 @@
 
 import java.util.List;
 
+/**
+ * Tests Panorama Passport integration end-to-end, covering user management, permission setup, and project
+ * configuration for both normal and admin users.
+ */
 @Category({})
 public class PassportTest extends PassportTestPart
 {