treating "scan start time" and "retention time" equivalently for PSMs

medbioinf · Jul 16, 2024 · 6838dd6 · 6838dd6
1 parent d7b183a
commit 6838dd6
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Showing 2 changed files with 25 additions and 2 deletions.
diff --git a/src/main/java/de/mpc/pia/intermediate/compiler/parser/MzIdentMLFileParser.java b/src/main/java/de/mpc/pia/intermediate/compiler/parser/MzIdentMLFileParser.java
@@ -520,11 +520,33 @@ private static Double parseRetentionTime(SpectrumIdentificationResult specIdResu
         Double rt = null;
 
         // get the "scan start time" cvParams
-        List<CvParam> scanStartCvParams = specIdResult.getCvParam().stream()
+        List<CvParam> rtCvParams = specIdResult.getCvParam().stream()
             .filter(cvParam -> cvParam.getAccession().equals(OntologyConstants.SCAN_START_TIME.getPsiAccession()))
             .toList();
+        rt = extractRTfromCVs(rtCvParams);
+
+        if (rt == null) {
+            // did not find the RT with this param, try "retention time"
+            rtCvParams = specIdResult.getCvParam().stream()
+                .filter(cvParam -> cvParam.getAccession().equals(OntologyConstants.RETENTION_TIME.getPsiAccession()))
+                .toList();
+                rt = extractRTfromCVs(rtCvParams);
+        }
+
+        return rt;
+    }
+
+
+    /**
+     * Extract scan time in seconds from the the retention time / scan start time CV params.
+     * 
+     * @param scanTimeCvParams
+     * @return
+     */
+    private static Double extractRTfromCVs(List<CvParam> scanTimeCvParams) {
+        Double rt = null;
 
-        for (CvParam cvParam : scanStartCvParams) {
+        for (CvParam cvParam : scanTimeCvParams) {
             try {
                 rt = Double.parseDouble(cvParam.getValue());
 

diff --git a/src/main/java/de/mpc/pia/tools/OntologyConstants.java b/src/main/java/de/mpc/pia/tools/OntologyConstants.java
@@ -27,6 +27,7 @@ public enum OntologyConstants {
     SEARCH_ENGINE_PSM_SCORE("search engine specific score for PSMs", "MS:1001143"),
     SPECTRUM_TITLE("spectrum title", "MS:1000796"),
     SCAN_START_TIME("scan start time", "MS:1000016"),
+    RETENTION_TIME("retention time", "MS:1000894"),
     SCAN_NUMBERS("scan number(s)", "MS:1001115"),
     DELTA_MZ("delta m/z", "MS:1001975"),
     CLEAVAGE_AGENT_NAME("cleavage agent name", "MS:1001045"),