}
}
if (idFilter.validateModifications(peptide, sequenceMatchingPreferences, searchParameters.getModificationProfile())) {
// Estimate the theoretic mass with the new modifications
peptide.estimateTheoreticMass();
if (!idFilter.validatePrecursor(peptideAssumption, spectrumKey, spectrumFactory)) {
spectrumMatch.removeAssumption(assumption);
precursorIssue++;
} else if (!idFilter.validateProteins(peptideAssumption.getPeptide(), sequenceMatchingPreferences)) {
// Check whether there is a potential first hit which does not belong to both the target and the decoy database