QueryToPeptideMap queryPeptideMap = mdf.getQueryToPeptideMap();
int numberOfQueries = mdf.getNumberOfQueries();
for (int i = 1; i <= numberOfQueries; i++) {
PeptideHit pepHit = queryPeptideMap.getPeptideHitOfOneQuery(i);
if (pepHit != null) {
Query q = mdf.getQuery(i);
String title = q.getTitle();
String[] tokens = title.split(" ");
int rowId = Integer.parseInt(tokens[1]);