From c1d0c107bf3962b623616b3feecee1c7037c8771 Mon Sep 17 00:00:00 2001
From: "DESKTOP-382ETUR\\Hiroshi Tsugawa" <htsugawa@go.tuat.ac.jp>
Date: Wed, 11 Mar 2026 15:26:24 +0900
Subject: [PATCH 1/2] added quant mass property to masscenter

---
 src/MSDIAL5/MsdialCore/Utility/DataObjConverter.cs            | 4 ++++
 .../MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs       | 4 +++-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/MSDIAL5/MsdialCore/Utility/DataObjConverter.cs b/src/MSDIAL5/MsdialCore/Utility/DataObjConverter.cs
index eee695a80..45fe3a9ea 100644
--- a/src/MSDIAL5/MsdialCore/Utility/DataObjConverter.cs
+++ b/src/MSDIAL5/MsdialCore/Utility/DataObjConverter.cs
@@ -174,6 +174,10 @@ public static void SetRepresentativeProperty(AlignmentSpotProperty spot) {
                 Mz = new MzValue(spot.MassCenter, representative.ChromXsTop.Mz.Unit),
                 Drift = new DriftTime(alignedPeaks.Average(peak => peak.ChromXsTop.Drift.Value), representative.ChromXsTop.Drift.Unit),
             };
+
+            if (spot.QuantMass > 0) {
+                spot.MassCenter = spot.QuantMass;
+            }
         }
 
         public static AlignmentChromPeakFeature? GetRepresentativePeak(IReadOnlyList<AlignmentChromPeakFeature> alignment) {
diff --git a/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs b/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs
index 19fe95205..1e42d82d4 100644
--- a/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs
+++ b/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs
@@ -76,6 +76,7 @@ private List<AlignmentSpotProperty> ResetQuantMasses(List<AlignmentSpotProperty>
                 var reference = _refer.Refer(spot.MatchResults.Representative);
                 if (reference is not null && _parameter.PeakPickBaseParam.IsInMassRange(reference.QuantMass)) {
                     spot.MassCenter = reference.QuantMass;
+                    spot.QuantMass = reference.QuantMass;
                     results.Add(spot);
                     continue;
                 }
@@ -90,6 +91,7 @@ private List<AlignmentSpotProperty> ResetQuantMasses(List<AlignmentSpotProperty>
 
             if (_parameter.IsRepresentativeQuantMassBasedOnBasePeakMz) {
                 spot.QuantMass = msdec.Spectrum.Argmax(s => s.Intensity).Mass;
+                spot.MassCenter = spot.QuantMass;
                 results.Add(spot);
                 continue;
             }
@@ -110,7 +112,7 @@ private List<AlignmentSpotProperty> ResetQuantMasses(List<AlignmentSpotProperty>
             else {
                 spot.QuantMass = msdec.Spectrum.Argmax(s => s.Intensity).Mass;
             }
-
+            spot.MassCenter = spot.QuantMass;
             results.Add(spot);
         }
         var counter = 0;

From 58a153fe632f322f1963d8e6ffbc2c2b8392f7a5 Mon Sep 17 00:00:00 2001
From: YukiMatsuzawa <122433968+YukiMatsuzawa@users.noreply.github.com>
Date: Wed, 11 Mar 2026 15:51:21 +0900
Subject: [PATCH 2/2] Add ContinueOnError to DownloadFile task

---
 src/MSDIAL4/MsDial/MSDIAL.csproj | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/MSDIAL4/MsDial/MSDIAL.csproj b/src/MSDIAL4/MsDial/MSDIAL.csproj
index f8b047bbd..a3396ad56 100644
--- a/src/MSDIAL4/MsDial/MSDIAL.csproj
+++ b/src/MSDIAL4/MsDial/MSDIAL.csproj
@@ -258,7 +258,7 @@
     <ItemGroup>
       <_DeployToItem Include="$(TargetDir)\*.lbm*" />
     </ItemGroup>
-    <DownloadFile SourceUrl="$(Lbm2Url)" DestinationFolder="$(TargetDir)" Condition="!Exists('%(_DeployToItem.FullPath)')" />
+    <DownloadFile SourceUrl="$(Lbm2Url)" DestinationFolder="$(TargetDir)" Condition="!Exists('%(_DeployToItem.FullPath)')" ContinueOnError="true"/>
     <Exec Command="xcopy &quot;$(ProjectDir)CytoscapeLocalBrowser&quot; &quot;$(TargetDir)CytoscapeLocalBrowser&quot; /D/E/C/I/H/Y" />
   </Target>
-</Project>
\ No newline at end of file
+</Project>