From 50cd4b1d3a6a8b890cae76050912810c4cd9c5eb Mon Sep 17 00:00:00 2001 From: Yuki Matsuzawa Date: Mon, 23 Mar 2026 14:45:18 +0900 Subject: [PATCH 1/2] Revert "changed alignment mass tolearnce to 0.5 Da (#710)" This reverts commit 3b62d50f5ccab168b1f0c49fd607fb96aba2643b. --- src/MSDIAL5/MsdialCore/Parameter/ParameterBase.cs | 2 +- src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/MSDIAL5/MsdialCore/Parameter/ParameterBase.cs b/src/MSDIAL5/MsdialCore/Parameter/ParameterBase.cs index b0b1c0f39..7f40291f2 100644 --- a/src/MSDIAL5/MsdialCore/Parameter/ParameterBase.cs +++ b/src/MSDIAL5/MsdialCore/Parameter/ParameterBase.cs @@ -1148,7 +1148,7 @@ public class AlignmentBaseParameter { [Key(3)] public float SpectrumSimilarityAlignmentFactor { get; set; } = 0.5F; [Key(4)] - public float Ms1AlignmentTolerance { get; set; } = 0.5F; + public float Ms1AlignmentTolerance { get; set; } = 0.015F; [Key(5)] public float RetentionTimeAlignmentTolerance { get; set; } = 0.10F; [Key(6)] diff --git a/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs b/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs index 1e42d82d4..11017b5a4 100644 --- a/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs +++ b/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs @@ -45,7 +45,7 @@ protected GcmsPeakJoiner(AlignmentIndexType indextype, RiCompoundType riCompound _comparer = comparer; _alignmentParameter = parameter.AlignmentBaseParam; _riCompoundType = riCompoundType; - _msMatchParam = new MsRefSearchParameterBase() { Ms1Tolerance = 0.5F, Ms2Tolerance = 0.5F, MassRangeBegin = 0, MassRangeEnd = 2000 }; + _msMatchParam = msMatchParam; _parameter = parameter; _evaluator = evaluator; _refer = refer; From 9a6cce0cc73eab9f3fc4f31408edb3f26b97252c Mon Sep 17 00:00:00 2001 From: Yuki Matsuzawa Date: Mon, 23 Mar 2026 14:48:59 +0900 Subject: [PATCH 2/2] Set default MS tolerances for GCMS alignment and matching GcmsPeakJoiner now always initializes _msMatchParam with default tolerances for MS1 and MS2, and MsdialGcmsParameter sets AlignmentBaseParam.Ms1AlignmentTolerance to 0.5f by default. This ensures consistent and appropriate default values for GCMS alignment and spectral matching. --- .../MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs | 2 +- src/MSDIAL5/MsdialGcMsApi/Parameter/MsdialGcmsParameter.cs | 5 ++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs b/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs index 11017b5a4..f52f84e61 100644 --- a/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs +++ b/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs @@ -45,7 +45,7 @@ protected GcmsPeakJoiner(AlignmentIndexType indextype, RiCompoundType riCompound _comparer = comparer; _alignmentParameter = parameter.AlignmentBaseParam; _riCompoundType = riCompoundType; - _msMatchParam = msMatchParam; + _msMatchParam = new MsRefSearchParameterBase { Ms1Tolerance = .5f, Ms2Tolerance = .5f, MassRangeBegin = 0, MassRangeEnd = 2000, }; _parameter = parameter; _evaluator = evaluator; _refer = refer; diff --git a/src/MSDIAL5/MsdialGcMsApi/Parameter/MsdialGcmsParameter.cs b/src/MSDIAL5/MsdialGcMsApi/Parameter/MsdialGcmsParameter.cs index 61dad1435..fcfc130f2 100644 --- a/src/MSDIAL5/MsdialGcMsApi/Parameter/MsdialGcmsParameter.cs +++ b/src/MSDIAL5/MsdialGcMsApi/Parameter/MsdialGcmsParameter.cs @@ -10,7 +10,10 @@ namespace CompMs.MsdialGcMsApi.Parameter { [MessagePackObject] public class MsdialGcmsParameter : ParameterBase { - public MsdialGcmsParameter(bool isLabUseOnly) : base(isLabUseOnly) { this.MachineCategory = MachineCategory.GCMS; } + public MsdialGcmsParameter(bool isLabUseOnly) : base(isLabUseOnly) { + this.MachineCategory = MachineCategory.GCMS; + AlignmentBaseParam.Ms1AlignmentTolerance = .5f; + } [SerializationConstructor] public MsdialGcmsParameter() : this(isLabUseOnly: false) { }