try {
PSMaps pSMaps = new PSMaps();
pSMaps = (PSMaps) peptideShakerGUI.getIdentification().getUrParam(pSMaps);
PeptideShaker miniShaker = new PeptideShaker(peptideShakerGUI.getExperiment(), peptideShakerGUI.getSample(), peptideShakerGUI.getReplicateNumber(), pSMaps);
miniShaker.proteinMapChanged(progressDialog, peptideShakerGUI.getProcessingPreferences());
modifiedMaps.put(0, false);
} catch (Exception e) {
peptideShakerGUI.catchException(e);
}