private synchronized void verifyXTandemPtms() {
if (!xTandemPtmsCheck) {
ModificationProfile modificationProfile = searchParameters.getModificationProfile();
IdentificationAlgorithmParameter algorithmParameter = searchParameters.getIdentificationAlgorithmParameter(Advocate.xtandem.getIndex());
if (algorithmParameter != null) {
XtandemParameters xtandemParameters = (XtandemParameters) algorithmParameter;
if (xtandemParameters.isProteinQuickAcetyl() && !modificationProfile.contains("acetylation of protein n-term")) {
PTM ptm = PTMFactory.getInstance().getPTM("acetylation of protein n-term");
modificationProfile.addVariableModification(ptm);
}
String[] pyroMods = {"pyro-cmc", "pyro-glu from n-term e", "pyro-glu from n-term q"};
if (xtandemParameters.isQuickPyrolidone()) {
for (String ptmName : pyroMods) {
if (!modificationProfile.getVariableModifications().contains(ptmName)) {
PTM ptm = PTMFactory.getInstance().getPTM(ptmName);
modificationProfile.addVariableModification(ptm);
}