diff --git a/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.html b/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.html
index 276a348e..42772416 100644
--- a/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.html
+++ b/src/app/features/genes/components/gene-comparison-tool/gene-comparison-tool.component.html
@@ -403,7 +403,7 @@ <h1 class="gct-heading h2">Gene Comparison Tool</h1>
                 <div *ngIf="genesTable.filteredValue?.length">
                   <button
                     class="pin-all-button"
-                    [disabled]="pinnedItems.length >= maxPinnedGenes"
+                    [disabled]="getPinDisabledStatus()"
                     [ngClass]="{
                       disabled: getPinDisabledStatus()
                     }"
@@ -472,7 +472,7 @@ <h1 class="gct-heading h2">Gene Comparison Tool</h1>
                       <div>
                         <button
                           (click)="onPinGeneClick(gene)"
-                          [disabled]="pinnedItems.length >= maxPinnedGenes"
+                          [disabled]="getPinDisabledStatus()"
                           [ngClass]="{
                             disabled: getPinDisabledStatus()
                           }"
diff --git a/tests/gene-comparison-tool-pinning-cache.spec.ts b/tests/gene-comparison-tool-pinning-cache.spec.ts
index 26a5ed0f..6fc0b530 100644
--- a/tests/gene-comparison-tool-pinning-cache.spec.ts
+++ b/tests/gene-comparison-tool-pinning-cache.spec.ts
@@ -130,7 +130,7 @@ test.describe('GCT: Caching pinned genes', () => {
     });
   });
 
-  test.fail(
+  test(
     'Pinned proteins are maintained when switching between Protein subcategories',
     async ({ page }) => {
       const gene1 = geneWithMultipleProteinsTMT.name;
@@ -154,9 +154,7 @@ test.describe('GCT: Caching pinned genes', () => {
       }
 
       await test.step('confirm # genes and proteins pinned on Protein page', async () => {
-        // FIXME - will fail until gene count is separated from protein count (AG-1425)
         await expectPinnedGenesCountText(page, nGenes);
-        // FIXME - will fail until protein count is displayed (AG-1425)
         await expectPinnedProteinsCountText(page, nProteins);
         await confirmPinnedItemsCount(page, nProteins);
       });
@@ -184,9 +182,7 @@ test.describe('GCT: Caching pinned genes', () => {
       );
 
       await test.step('confirm same genes and proteins pinned on Protein page', async () => {
-        // FIXME - will fail until gene count is separated from protein count (AG-1425)
         await expectPinnedGenesCountText(page, nGenes);
-        // FIXME - will fail until protein count is displayed (AG-1425)
         await expectPinnedProteinsCountText(page, nProteins);
         await confirmPinnedItemsCount(page, nProteins);
 
@@ -196,7 +192,7 @@ test.describe('GCT: Caching pinned genes', () => {
     }
   );
 
-  test.fail(
+  test(
     'Pinned proteins are maintained when switching categories: Protein -> RNA -> Protein',
     async ({ page }) => {
       const gene1 = geneWithMultipleProteinsTMT.name;
@@ -220,9 +216,7 @@ test.describe('GCT: Caching pinned genes', () => {
       }
 
       await test.step('confirm # genes and proteins pinned on Protein page', async () => {
-        // FIXME - will fail until gene count is separated from protein count (AG-1425)
         await expectPinnedGenesCountText(page, nGenes);
-        // FIXME - will fail until protein count is displayed (AG-1425)
         await expectPinnedProteinsCountText(page, nProteins);
         await confirmPinnedItemsCount(page, nProteins);
       });
@@ -248,13 +242,9 @@ test.describe('GCT: Caching pinned genes', () => {
       );
 
       await test.step('confirm same genes and proteins pinned on Protein page', async () => {
-        // FIXME - will fail until gene count is separated from protein count (AG-1425)
         await expectPinnedGenesCountText(page, nGenes);
-        // FIXME - will fail until protein count is displayed (AG-1425)
         await expectPinnedProteinsCountText(page, nProteins);
 
-        // FIXME - the following steps will fail until the protein cache is maintained
-        // ...when switching from Protein -> RNA -> Protein (AG-1425)
         await confirmPinnedItemsCount(page, nProteins);
         await confirmPinnedProteins(page, gene1, proteins1);
         await confirmPinnedProteins(page, gene2, proteins2);
@@ -262,7 +252,7 @@ test.describe('GCT: Caching pinned genes', () => {
     }
   );
 
-  test.fail(
+  test(
     'Last pinned genes are maintained even if proteins were pinned initially',
     async ({ page }) => {
       const rnaCategoryGene = geneWithMultipleProteinsTMT.name;
@@ -312,11 +302,8 @@ test.describe('GCT: Caching pinned genes', () => {
           GCT_PROTEIN_SUBCATEGORIES.SRM,
           GCT_PROTEIN_SUBCATEGORIES.TMT
         );
-        // FIXME - will fail until gene count is separated from protein count (AG-1425)
         await expectPinnedGenesCountText(page, 1);
-        // FIXME - will fail until protein count is displayed (AG-1425)
         await expectPinnedProteinsCountText(page, rnaCategoryProteins.length);
-        // FIXME - will fail until all proteins for a gene are pinned (AG-1425)
         await confirmPinnedProteins(page, rnaCategoryGene, rnaCategoryProteins);
       });
 
@@ -335,7 +322,7 @@ test.describe('GCT: Caching pinned genes', () => {
     }
   );
 
-  test.fail(
+  test(
     'Last pinned proteins are maintained even if genes were pinned initially',
     async ({ page }) => {
       const rnaCategoryGene = geneWithMultipleProteinsTMT.name;
@@ -375,9 +362,7 @@ test.describe('GCT: Caching pinned genes', () => {
         await pinAllItemsViaSearchByGene(page, proteinCategoryGene);
 
         await test.step('confirm pinned items', async () => {
-          // FIXME - will fail until gene count is separated from protein count (AG-1425)
           await expectPinnedGenesCountText(page, 1);
-          // FIXME - will fail until protein count is displayed (AG-1425)
           await expectPinnedProteinsCountText(
             page,
             proteinCategoryProteins.length
@@ -414,9 +399,7 @@ test.describe('GCT: Caching pinned genes', () => {
         );
 
         await test.step('confirm pinned items', async () => {
-          // FIXME - will fail until gene count is separated from protein count (AG-1425)
           await expectPinnedGenesCountText(page, 1);
-          // FIXME - will fail until protein count is displayed (AG-1425)
           await expectPinnedProteinsCountText(
             page,
             proteinCategoryProteins.length
diff --git a/tests/gene-comparison-tool-pinning-ui.spc.ts b/tests/gene-comparison-tool-pinning-ui.spec.ts
similarity index 100%
rename from tests/gene-comparison-tool-pinning-ui.spc.ts
rename to tests/gene-comparison-tool-pinning-ui.spec.ts
diff --git a/tests/gene-comparison-tool-pinning-url.spec.ts b/tests/gene-comparison-tool-pinning-url.spec.ts
index aed0d92b..82732fcc 100644
--- a/tests/gene-comparison-tool-pinning-url.spec.ts
+++ b/tests/gene-comparison-tool-pinning-url.spec.ts
@@ -15,7 +15,6 @@ import {
 } from './helpers/data';
 import { expectGctPageLoaded, getGeneRowButtons } from './helpers/gct';
 import {
-  closePinnedGeneWarningModal,
   confirmPinnedItemsByGeneName,
   confirmPinnedItemsCount,
   expectPinnedGenesCountText,
@@ -141,7 +140,13 @@ test.describe('GCT: Pinning Genes from URL', () => {
     });
   });
 
-  test('when RNA url includes proteins, the related gene is pinned', async ({
+  test.fail('when RNA url includes proteins, the related gene is pinned', {
+    annotation: {
+      type: 'fail', 
+      description: 'Since AG-1425, only genes will be pinned from RNA url'
+    }
+  },
+  async ({
     page,
   }) => {
     const geneProteins = geneWithMultipleProteinsTMT.uniProtIds.map(
@@ -166,7 +171,12 @@ test.describe('GCT: Pinning Genes from URL', () => {
   });
 
   test.fail(
-    'when Protein url includes a gene, all related proteins are pinned',
+    'when Protein url includes a gene, all related proteins are pinned', {
+      annotation: {
+        type: 'fail', 
+        description: 'Since AG-1425, only proteins will be pinned from Protein url'
+      }
+    },
     async ({ page }) => {
       const url = `${URL_GCT_PROTEIN_TMT}&${formatPinnedGenesQueryParam([
         geneWithMultipleProteinsTMT.ensemblId,
@@ -184,7 +194,6 @@ test.describe('GCT: Pinning Genes from URL', () => {
         geneWithMultipleProteinsTMT.uniProtIds.length
       );
 
-      // FIXME - will fail until protein counts are separated from gene counts (AG-1425)
       await test.step('confirm counts', async () => {
         await confirmPinnedItemsCount(page, 5);
         await expectPinnedGenesCountText(page, 1);
@@ -193,7 +202,7 @@ test.describe('GCT: Pinning Genes from URL', () => {
     }
   );
 
-  test.fail(
+  test(
     'when Protein url includes 50 proteins from 50 unique genes, all proteins are pinned',
     async ({ page }) => {
       const url = `${URL_GCT_PROTEIN_TMT}&${formatPinnedGenesQueryParam(
@@ -209,13 +218,12 @@ test.describe('GCT: Pinning Genes from URL', () => {
       await test.step('confirm counts', async () => {
         await confirmPinnedItemsCount(page, 50);
         await expectPinnedGenesCountText(page, 50);
-        // FIXME - will fail until protein counts are separated from gene counts (AG-1425)
         await expectPinnedProteinsCountText(page, 50);
       });
     }
   );
 
-  test.fail(
+  test(
     'when Protein url includes >50 proteins from 50 unique genes, all proteins are pinned',
     async ({ page }) => {
       const fortyNineProteinsToUniqueGenes =
@@ -234,10 +242,6 @@ test.describe('GCT: Pinning Genes from URL', () => {
 
       await page.goto(url);
 
-      // FIXME - remove this step once pinning is fixed so that modal does not
-      // appear when >50 proteins are pinned for 50 unique genes (AG-1425)
-      await closePinnedGeneWarningModal(page);
-
       await expectGctPageLoaded(
         page,
         GCT_CATEGORIES.PROTEIN,
@@ -246,9 +250,7 @@ test.describe('GCT: Pinning Genes from URL', () => {
 
       await test.step('confirm counts', async () => {
         await expectPinnedGenesCountText(page, 50);
-        // FIXME - will fail until >50 proteins can be pinned for 50 unique genes (AG-1425)
         await confirmPinnedItemsCount(page, allProteins.length);
-        // FIXME - will fail until protein counts are separated from gene counts (AG-1425)
         await expectPinnedProteinsCountText(page, allProteins.length);
       });
 
@@ -260,7 +262,7 @@ test.describe('GCT: Pinning Genes from URL', () => {
     }
   );
 
-  test.fail(
+  test(
     'when Protein url includes proteins from 51 unique genes, only proteins from 50 genes are pinned',
     async ({ page }) => {
       const oneGeneWithManyProteins =
@@ -282,8 +284,6 @@ test.describe('GCT: Pinning Genes from URL', () => {
 
       await page.goto(url);
 
-      await closePinnedGeneWarningModal(page);
-
       await expectGctPageLoaded(
         page,
         GCT_CATEGORIES.PROTEIN,
@@ -292,9 +292,7 @@ test.describe('GCT: Pinning Genes from URL', () => {
 
       await test.step('confirm counts', async () => {
         await expectPinnedGenesCountText(page, 50);
-        // FIXME - will fail until >50 proteins can be pinned for 50 unique genes (AG-1425)
         await confirmPinnedItemsCount(page, expectedPinnedProteins.length);
-        // FIXME - will fail until protein counts are separated from gene counts (AG-1425)
         await expectPinnedProteinsCountText(
           page,
           expectedPinnedProteins.length
@@ -303,7 +301,7 @@ test.describe('GCT: Pinning Genes from URL', () => {
     }
   );
 
-  test.fail(
+  test(
     'when Protein url includes invalid protein, that protein is dropped from the url',
     async ({ page }) => {
       const validGeneProtein = fiftyProteinsToFiftyUniqueGenesTMT[1];
@@ -326,7 +324,6 @@ test.describe('GCT: Pinning Genes from URL', () => {
       await test.step('confirm only pinned 1 protein', async () => {
         await expectPinnedGenesCountText(page, 1);
         await confirmPinnedItemsCount(page, 1);
-        // FIXME - will fail until pinned protein text is added (AG-1425)
         await expectPinnedProteinsCountText(page, 1);
       });
 
diff --git a/tests/helpers/gct-pinning.ts b/tests/helpers/gct-pinning.ts
index b05bb5c1..87023f49 100644
--- a/tests/helpers/gct-pinning.ts
+++ b/tests/helpers/gct-pinning.ts
@@ -28,13 +28,15 @@ export const expectPinnedProteinsCountText = async (
   page: Page,
   nProteins: number
 ) => {
-  await expect(page.getByText(`Pinned Proteins (${nProteins})`)).toBeVisible();
+  await expect(
+    page.getByText(`${nProteins} Protein${nProteins > 1 ? 's' : ''}`)
+  ).toBeVisible();
 };
 
 export const expectTooManyPinnedGenesToast = async (page: Page) => {
   const alert = page.getByRole('alert');
   await expect(alert).toHaveText(
-    'Only 50 genes were added, because you reached the maxium of 50 pinned genes. '
+    'Only 50 rows were added, because you reached the maximum of 50 pinned Ensembl identifiers.'
   );
 };
 
diff --git a/tests/helpers/gct.ts b/tests/helpers/gct.ts
index 7e30922d..03927b54 100644
--- a/tests/helpers/gct.ts
+++ b/tests/helpers/gct.ts
@@ -87,7 +87,7 @@ const changeGctDropdown = async (
     await test.step('wait for page to redirect', async () => {
       await expect(() => {
         expect(page.url()).not.toEqual(url);
-      }).toPass({ timeout: 45_000 });
+      }).toPass({ timeout: 60_000 });
     });
 
     // Handle case where listbox doesn't close after page redirects