if (experiment.getUrParam(experimentSettings) instanceof PSSettings) {
// convert old settings files using utilities version 3.10.68 or older
// convert the old ProcessingPreferences object
PSSettings tempSettings = (PSSettings) experiment.getUrParam(experimentSettings);
ProcessingPreferences tempProcessingPreferences = new ProcessingPreferences();
tempProcessingPreferences.setProteinFDR(tempSettings.getProcessingPreferences().getProteinFDR());
tempProcessingPreferences.setPeptideFDR(tempSettings.getProcessingPreferences().getPeptideFDR());
tempProcessingPreferences.setPsmFDR(tempSettings.getProcessingPreferences().getPsmFDR());
// convert the old PTMScoringPreferences object
PTMScoringPreferences tempPTMScoringPreferences = new PTMScoringPreferences();
tempPTMScoringPreferences.setaScoreCalculation(tempSettings.getPTMScoringPreferences().aScoreCalculation());
tempPTMScoringPreferences.setaScoreNeutralLosses(tempSettings.getPTMScoringPreferences().isaScoreNeutralLosses());
tempPTMScoringPreferences.setFlrThreshold(tempSettings.getPTMScoringPreferences().getFlrThreshold());
experimentSettings = new PeptideShakerSettings(tempSettings.getSearchParameters(), tempSettings.getAnnotationPreferences(),
tempSettings.getSpectrumCountingPreferences(), tempSettings.getProjectDetails(), tempSettings.getFilterPreferences(),
tempSettings.getDisplayPreferences(),
tempSettings.getMetrics(), tempProcessingPreferences, tempSettings.getIdentificationFeaturesCache(),
tempPTMScoringPreferences, new GenePreferences(), new IdFilter(), SequenceMatchingPreferences.getDefaultSequenceMatching(tempSettings.getSearchParameters()));
} else {
experimentSettings = (PeptideShakerSettings) experiment.getUrParam(experimentSettings);
}