Ion Mobility Mass Spectrometry (IMS) is a powerful tool that has been utilized to disentangle components out of a complex mixture, distinguish isomers and elucidate geometries. Linear IMS is based on the absolute mobility K at a moderate normalized electric field E/N while the field asymmetric waveform IMS (FAIMS) relies on the difference in mobilities at high E/N. FAIMS has previously been demonstrated for isomer differentiation and separation of PTMs of histone tails. Characterizing isomers (like glycoforms) and obtaining dipole moment and directional collision cross section of proteins has been a challenge for IMS, MS, and other techniques, that require extensive chemistry or a lot of time. FAIMS has been utilized to study isomer separation and dipole alignment. The superior abilities of FAIMS studied here are to distinguish and characterize isomers based on their isotopic shifts, separation of isomeric glycoforms with variations on the peptide and glycan level and extraction of dipole moment and directional collision cross section of aligned macromolecules. Various halogenated aniline isomers are delineated by the structurally specific splitting of isotopologues in FAIMS. and shifts are powerful in differentiating molecules containing them at the structural level and show the specificity of the approach. A new tool, low-field differential IMS (LODIMS), is introduced here, which operates at low field and ambient pressure, and the weak heating favors the locking of the permanent macromolecular ion dipoles. This locking facilitates the production of novel separations based solely on their alignment and provides the directional collision cross section that is more relevant to the structure. This powerful approach will facilitate structural biology, forensics, and drug development.