psmMap.resetDoubtfulMatchesFilters();
peptideMap.resetDoubtfulMatchesFilters();
proteinMap.resetDoubtfulMatchesFilters();
PeptideSpectrumAnnotator peptideSpectrumAnnotator = new PeptideSpectrumAnnotator();
HashMap<String, ArrayList<String>> spectrumKeysMap = identification.getSpectrumIdentificationMap();
if (metrics != null && metrics.getGroupedSpectrumKeys() != null) {
spectrumKeysMap = metrics.getGroupedSpectrumKeys();
}