change RT tolerance for MS2 pairing
@@ -561,9 +561,13 @@ public class BatchWizardController {
groupParam.setParameter(GroupMS2SubParameters.mzTol,
msParameters.getValue(BatchWizardMassSpectrometerParameters.scanToScanMzTolerance));
groupParam.setParameter(GroupMS2SubParameters.combineTimsMsMs, false);
- groupParam.setParameter(GroupMS2SubParameters.limitRTByFeature, minDP > 4);
+ boolean limitByRTEdges = minDP >= 4;
+ groupParam.setParameter(GroupMS2SubParameters.limitRTByFeature, limitByRTEdges);
groupParam.setParameter(GroupMS2SubParameters.lockMS2ToFeatureMobilityRange, true);
- groupParam.setParameter(GroupMS2SubParameters.rtTol, new RTTolerance(fwhm * 3, Unit.MINUTES));
+ // rt tolerance is +- while FWHM is the width. still the MS2 might be triggered very early
+ // change rt tol depending on number of datapoints
+ groupParam.setParameter(GroupMS2SubParameters.rtTol,
+ new RTTolerance(limitByRTEdges ? fwhm * 3 : fwhm, Unit.MINUTES));
groupParam.setParameter(GroupMS2SubParameters.outputNoiseLevel, hasIMS);
groupParam.getParameter(GroupMS2SubParameters.outputNoiseLevel).getEmbeddedParameter().setValue(
msParameters.getParameter(BatchWizardMassSpectrometerParameters.ms2NoiseLevel).getValue()
