A mass spectrometer is an expensive instrument which can't distinguish between optical or geometrical isomers. It is used to analyze the mass, formula and structure of a compound, measuring charge to mass ratios of fragments.
A mass spectrometer cannot distinguish between geometric isomers of a compound. Geometric isomers are compounds having the same molecular formula but different structural formula; these are termed as cis and trans isomers. For example, consider the organic compound 1,2-dichloroethene. A mass spectrometer cannot distinguish and identify the two geometrical isomers of this compound, namely, trans-1,2-dichloroethene and cis-1,2-dichloroethene.
Mass spectrometers cannot distinguish between optical isomers. Optical isomers are non-superimposible mirror images of each other and are termed as enantiomers. For example, alanine is an amino acid that is composed of (+) and (–) forms. Enantiomers react differently to plane polarized light.
Mass spectrometers cannot distinguish between ortho(o-), meta(m-), and para(p-) substituents of aromatic compounds. Disubstitution can occur in three different orientations in an aromatic compound. 1,2-disubstituted is termed as ortho aromatic ring, while 1,4-disubstituted is termed as para aromatic ring. 1,3-disubstituted is termed as meta aromatic ring.
Mass spectrometers fail to identify similar fragmented ions in hydrocarbons. The ionization process sometimes produces too much fragmentation, so we cannot determine whether highest mass ion is a molecular ion of hydrocarbons.