combine tims msms by default
@@ -381,7 +381,7 @@ public class BatchWizardController {
msParameters.getParameter(BatchWizardMassSpectrometerParameters.scanToScanMzTolerance)
.getValue());
param.getParameter(MinimumSearchFeatureResolverParameters.groupMS2Parameters)
- .getEmbeddedParameters().setParameter(GroupMS2SubParameters.combineTimsMsMs, false);
+ .getEmbeddedParameters().setParameter(GroupMS2SubParameters.combineTimsMsMs, true);
param.getParameter(MinimumSearchFeatureResolverParameters.groupMS2Parameters)
.getEmbeddedParameters().setParameter(GroupMS2SubParameters.limitRTByFeature, true);
param.getParameter(MinimumSearchFeatureResolverParameters.groupMS2Parameters)
@@ -396,7 +396,7 @@ public class BatchWizardController {
.getEmbeddedParameters().getParameter(GroupMS2SubParameters.outputNoiseLevel)
.getEmbeddedParameter().setValue(
msParameters.getParameter(BatchWizardMassSpectrometerParameters.ms2NoiseLevel).getValue()
- * 3);
+ * 2);
param.setParameter(MinimumSearchFeatureResolverParameters.dimension,
ResolvingDimension.RETENTION_TIME);
@@ -434,7 +434,7 @@ public class BatchWizardController {
msParameters.getParameter(BatchWizardMassSpectrometerParameters.scanToScanMzTolerance)
.getValue());
param.getParameter(MinimumSearchFeatureResolverParameters.groupMS2Parameters)
- .getEmbeddedParameters().setParameter(GroupMS2SubParameters.combineTimsMsMs, false);
+ .getEmbeddedParameters().setParameter(GroupMS2SubParameters.combineTimsMsMs, true);
param.getParameter(MinimumSearchFeatureResolverParameters.groupMS2Parameters)
.getEmbeddedParameters().setParameter(GroupMS2SubParameters.limitRTByFeature, true);
param.getParameter(MinimumSearchFeatureResolverParameters.groupMS2Parameters)
@@ -449,7 +449,7 @@ public class BatchWizardController {
.getEmbeddedParameters().getParameter(GroupMS2SubParameters.outputNoiseLevel)
.getEmbeddedParameter().setValue(
msParameters.getParameter(BatchWizardMassSpectrometerParameters.ms2NoiseLevel).getValue()
- * 3);
+ * 2);
param.setParameter(MinimumSearchFeatureResolverParameters.dimension,
ResolvingDimension.MOBILITY);
