diff --git a/src/org/labkey/targetedms/TargetedMSManager.java b/src/org/labkey/targetedms/TargetedMSManager.java
index af1013ca9..9807db0a2 100644
--- a/src/org/labkey/targetedms/TargetedMSManager.java
+++ b/src/org/labkey/targetedms/TargetedMSManager.java
@@ -55,6 +55,7 @@
 import org.labkey.api.exp.api.ExpProtocol;
 import org.labkey.api.exp.api.ExpRun;
 import org.labkey.api.exp.api.ExperimentService;
+import org.labkey.api.files.FileContentService;
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.module.ModuleProperty;
@@ -692,12 +693,11 @@ private static ExpRun wrapRun(TargetedMSRun run, User user, PipeRoot pipeRoot, I
             }
 
             ExpData expData = ExperimentService.get().getExpData(run.getDataId());
-            Path skylineFile = pipeRoot.resolveToNioPathFromUrl(expData.getDataFileUrl());
 
             ExpRun expRun = ExperimentService.get().createExperimentRun(container, run.getDescription());
             expRun.setProtocol(protocol);
             expRun.setJobId(jobId);
-            expRun.setFilePathRootPath(null != skylineFile ? skylineFile.getParent() : null);
+            expRun.setFilePathRootPath(FileContentService.get().getFileRootPath(container, FileContentService.ContentType.files));
             ViewBackgroundInfo info = new ViewBackgroundInfo(container, user, null);
 
             Map<ExpData, String> inputDatas = new HashMap<>();