Histone proteins are subject to dynamic post-translational modifications (PTMs) that cooperatively modulate the chromatin structure and function. Nearly all functional PTMs are found on the N-terminal histone domains (tails) of ∼50 residues protruding from the nucleosome core. Using high-definition differential ion mobility spectrometry (FAIMS) with electron transfer dissociation, we demonstrate rapid baseline gas-phase separation and identification of tails involving monomethylation, trimethylation, acetylation, or phosphorylation in biologically relevant positions. These are by far the largest variant peptides resolved by any method, some with PTM contributing just 0.25% to the mass. This opens the door to similar separations for intact proteins and in top-down proteomics.

Nearly all molecules incorporate elements with stable isotopes. The resulting isotopologue envelopes in mass spectra tell the exact stoichiometry but nothing about the geometry. Chromatography and electrophoresis at high resolution also can distinguish isotopologues, again without revealing structural information. In high-definition differential ion mobility (FAIMS) spectra, these envelopes universally split in a structure-specific manner, providing a new general approach to isomer delineation. Here, we show that the peak shifts from instances of the same isotope are equal and can be averaged into characteristic elemental shifts, namely C andCl for dichloroanilines (DCA). Matrices of these shifts, including the gas composition dimension, are unique to the structure. Hence, all six DCA isomers (with four making two unresolved pairs) are readily delineated in the C/Cl maps with He/CO buffer gases. Mixtures of coeluting isomers are also distinguished from pure components.

Nearly all compounds comprise numerous isotopologues ensuing from stable natural isotopes for constituent elements. The consequent isotopic envelopes in mass spectra can reveal the ion stoichiometry but not geometry. We found those envelopes to split in differential ion mobility (FAIMS) spectra in a manner dependent on the ion geometry and buffer gas composition. The resulting multidimensional matrix of isotopic shifts is specific to isomers, providing a fundamentally new approach to the characterization of chemical structure. The physical origins of the effect remain to be clarified but likely ensue from the transposition of center of mass of the ion within its geometry frame affecting the partition of energy in above-thermal collisions between the translational and rotational degrees of freedom. The additivity of shifts, holding with no exception so far, may be the key to unraveling the foundations of observed behavior.

Nearly all molecules incorporate at least one element with stable isotopes, yielding ubiquitous isotopologic envelopes in mass spectra. Those envelopes split in differential or field asymmetric waveform ion mobility (FAIMS) spectra depending on the ion geometry, enabling a new general approach to isomer delineation as we demonstrated for chloroanilines. Here, we report that analogous bromoanilines exhibit qualitatively distinct isotopic shifts under identical conditions, some changing signs depending on the gas. This dramatic elemental specificity conveys the breadth and diversity of structural isotopic effect in FAIMS, suggesting unique information-rich patterns for compounds involving various elements and feasibility of enhancing the structural elucidation by atom substitution. We also introduce the capability to make or ensure structural assignments employing major isomer-specific peak broadening due to unresolved isotopomer mixtures.

Despite often minute concentrations in vivo, D-amino acid containing peptides (DAACPs) are crucial to many life processes. Standard proteomics protocols fail to detect them as D/L substitutions do not affect the peptide parent and fragment masses. The differences in fragment yields are often limited, obstructing the investigations of important but low abundance epimers in isomeric mixtures. Separation of D/L-peptides using ion mobility spectrometry (IMS) was impeded by small collision cross section differences (commonly ~1%). Here, broad baseline separation of DAACPs with up to ~30 residues employing trapped IMS with resolving power up to ~340, followed by time-of-flight mass spectrometry is demonstrated. The D/L-pairs co-eluting in one charge state were resolved in another, and epimers merged as protonated species were resolved upon metalation, effectively turning the charge state and cationization mode into extra separation dimensions. Linear quantification down to 0.25% proved the utility of high resolution IMS-MS for real samples with large inter-isomeric dynamic range. Very close relative mobilities found for DAACP pairs using traveling-wave IMS (TWIMS) with different ion sources and faster IMS separations showed the transferability of results across IMS platforms. Fragmentation of epimers can enhance their identification and further improve detection and quantification limits, and we demonstrate the advantages of online mobility separated collision-induced dissociation (CID) followed by high resolution mass spectrometry (TIMS-CID-MS) for epimer analysis.