After the compounds are separated then they pass through the mass spectrometer, or the MS part of the test.  During this part of the test the materials are destroyed in by a strong magnetic field.  The various fragments of the material are then analyzed by their molecular weight.  The molecular weight of the fragments is then compared to databases which represent the statistical likelihood of certain compounds to separate into fragments in specific ways.  No direct analysis of the material is ever done and the accuracy of the results depends upon the precision of the database being used.  This is where many false positive results are reported.  For example, a false positive for opiates can be given if the individual is taking certain antibiotics because the fragmentation patterns of the antibiotics that the person was taking were cot recorded in the database that was used in the test so the software that the testing equipment was using automatically defaulted to the next likely match.  Most drug testing labs are operated by chemists who lack the experience to analyze compounds outside of the database being used.  Unknown compounds are not grouped in with the compounds found in the database.  In order to correctly identify unknown compounds it requires the chemist to study four years at the graduate level of analytical chemistry and another two years of medical school training in toxicology to discern unknown compounds through the gas chromatography/mass spectrometry drug testing method.  Most drug testing labs are staffed by highly trained and experienced technicians supervised by a chemist or engineer but false positives should still be questioned because no lab is infallible.