Adjust peptide map report to only show tryptic matches (#1122)

Author: labkey-jeckels

resources/views/scheduleInstrument.html

@@ -175,7 +175,7 @@ <h3>Time Scheduled</h3>
         instrument = instrument ? parseInt(instrument) || null : null;
 
         if (!project) {
-            alert('No project selected');
+            document.getElementById('calendar').innerText = 'Invalid or no project specified';
             return;
         }
 

src/org/labkey/targetedms/view/CrossLinkedPeptideInfo.java

@@ -189,12 +189,13 @@ public List<Match> findMatches(List<Protein> proteins)
                     do
                     {
                         index = proteinSequence.indexOf(getUnmodified(), index + 1);
-                        if (index >= 0)
+                        if (index != -1 &&
+                                (index == 0 || proteinSequence.charAt(index - 1) == 'K' || proteinSequence.charAt(index - 1) == 'R'))
                         {
                             result.add(new Match(protein, index));
                         }
                     }
-                    while (index > 0);
+                    while (index >= 0);
                 }
             }
             return result;
@@ -255,6 +256,37 @@ public void testOmittedIndices()
             Assert.assertEquals("Link location", Set.of(9), i.getExtraSequences().get(0).getLinkIndices());
             Assert.assertEquals("Link location", Set.of(4, 7, 0, 1), i.getExtraSequences().get(4).getLinkIndices());
         }
+
+        @Test
+        public void testTrypticMatches()
+        {
+            CrossLinkedPeptideInfo info = new CrossLinkedPeptideInfo("PEPTIDE");
+            PeptideSequence seq = info.getBaseSequence();
+
+            // Single protein containing multiple occurrences of PEPTIDE:
+            // - at start (allowed)
+            // - preceded by A (disallowed)
+            // - preceded by K (allowed)
+            // - preceded by R (allowed)
+            Protein protein = new Protein();
+            String proteinSeq = "PEPTIDE" + "APEPTIDE" + "KPEPTIDE" + "RPEPTIDE";
+            protein.setSequence(proteinSeq);
+
+            List<Protein> proteins = Arrays.asList(protein);
+            List<Match> matches = seq.findMatches(proteins);
+
+            // Expect three valid matches: indices 0 (start), 16 (after K), 24 (after R)
+            Assert.assertEquals("Should find three valid matches within a single protein sequence", 3, matches.size());
+
+            Assert.assertSame("First match should be at start (index 0)", protein, matches.get(0).protein());
+            Assert.assertEquals(0, matches.get(0).index());
+
+            Assert.assertSame("Second match should be after K at index 16", protein, matches.get(1).protein());
+            Assert.assertEquals(16, matches.get(1).index());
+
+            Assert.assertSame("Third match should be after R at index 24", protein, matches.get(2).protein());
+            Assert.assertEquals(24, matches.get(2).index());
+        }
     }
 
     public class Linker

test/sampledata/TargetedMS/CrosslinkPeptideMapTest.sky.zip

@@ -19,6 +19,8 @@
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 import org.labkey.test.Locator;
+import org.labkey.test.util.DataRegion;
+import org.labkey.test.util.DataRegionTable;
 
 import static org.junit.Assert.assertTrue;
 
@@ -56,10 +58,13 @@ public void testSteps()
         assertTextPresent("Chromatograms");
 
         clickAndWait(Locator.linkContainingText("Peptide Map"));
+        DataRegionTable table = new DataRegionTable("PeptideIds", getDriver());
+        table.setPageSize(250);
         assertTextPresentInThisOrder("11.3", "14.1", "14.8");
         assertTextPresentInThisOrder("1501.75", "1078.50", "1547.71");
-        assertTextPresentInThisOrder("NU205", "NU205", "1433Z", "UCRI; RL35");
-        assertTextPresentInThisOrder("70-84", "325-333", "28-41", "190-196; 26-32");
+        assertTextPresentInThisOrder("NU205", "1433Z", "RL35", "HSP72; HSP7C");
+        assertTextNotPresent("UCRI; RL35"); // Ensure we don't have non-tryptic matches anymore
+        assertTextPresentInThisOrder("70-84", "325-333", "28-41", "305-314; 302-311");
         assertTextPresentInThisOrder("(K)ASTEGVAIQGQQGTR(L)", "(K)AQYEDIANR(S)", "(K)SVTEQGAELSNEER(N)");
         assertTextPresentInThisOrder("Carbamidomethyl Cysteine @ C157", "Carbamidomethyl Cysteine @ C245", "Carbamidomethyl Cysteine @ C94");
 
@@ -75,15 +80,15 @@ public void testCrossLinkedPeptideMap()
         clickAndWait(Locator.linkContainingText("Panorama Dashboard"));
         clickAndWait(Locator.linkContainingText(CROSS_LINKED_SKY_FILE));
 
-        verifyRunSummaryCountsPep(2,3,0, 3,3, 1, 0, 0);
+        verifyRunSummaryCountsPep(2,2,0, 2,2, 1, 0, 0);
 
         clickAndWait(Locator.linkContainingText("Peptide Map"));
-        assertTextPresentInThisOrder("364-366", "367-369", "364-367");
+        assertTextPresentInThisOrder("121-124", "342-345", "142-145");
         // Disulfide bonds
-        assertTextPresentInThisOrder("Q364-T369-D364/\nN366-T369-D364", "V121-S345-Q142/\nQ124-S345-Q142");
-        assertTextPresentInThisOrder("(A)LKPLALV(D)", "(G)AVVQDPA(Y)", "(F)YGEATSR(E)");
+        assertTextPresentInThisOrder("V121-S345-Q142/\nQ124-S345-Q142", "L11-A137-Y271/\nL11-A137-Y271/\nV17-A137-Y271/");
+        assertTextPresentInThisOrder("(K)LKPLALV(D)", "(K)AVVQDPA(Y)", "(R)YGEATSR(E)");
 
         // Ensure that the highlighting is as expected for both crosslinking and modification
-        assertTrue(getHtmlSource().contains("(Y)<span style=\"font-weight:bold;color:green;text-decoration:underline;\">Q</span><span style=\"font-weight:bold;text-decoration:underline;\">M</span><span style=\"font-weight:bold;color:green;\">N</span>(D)"));
+        assertTrue(getHtmlSource().contains("(R)<span style=\"font-weight:bold;color:green;text-decoration:underline;\">V</span>SS<span style=\"font-weight:bold;color:green;\">Q</span>(Q)"));
     }
 }