Structural characterization of small molecular ions by ion mobility mass spectrometry in nitrogen drift gas: improving the accuracy of trajectory method calculations.

The investigation of ion structures based on a combination of ion mobility mass spectrometry (IM-MS) experiments and theoretical collision cross section (CCS) calculations has become important to many fields of research. However, the accuracy of current CCS calculations for ions in nitrogen drift gas limits the information content of many experiments. In particular, few studies have evaluated and attempted to improve the theoretical tools for CCS calculation in nitrogen drift gas. In this study, based on high-quality experimental measurements and theoretical modeling, a comprehensive evaluation of various aspects of CCS calculations in nitrogen drift gas is performed. It is shown that the modification of the ion-nitrogen van der Waals (vdW) interaction potential enables accurate CCS predictions of 29 small ions with ca. 3% maximum relative error. The present method exhibits no apparent systematic bias with respect to ion CCS (size) and dipole moment, suggesting that the method adequately describes the long-range interactions between the ions and the buffer gas. However, the method shows limitations in reproducing experimental CCS at low temperatures (<150 K) and for macromolecular ions, and calculations for these cases should be complemented by CCS calculation methods in helium drift gas. This study presents an accurate and well-characterized CCS calculation method for ions in nitrogen drift gas that is expected to become an important tool for ion structural characterization and molecular identification. The experimental values reported here also provide a foundation for future studies aiming at developing more efficient computational tools.

Collision cross sections and ion structures: development of a general calculation method via high-quality ion mobility measurements and theoretical modeling.

Ion mobility mass spectrometry (IM-MS) has become an important tool for the structural investigation of ions in the gas phase. Accurate theoretical evaluation of ion collision cross sections (CCSs) is essential for the effective application of IM-MS in structural studies. However, current theoretical tools have limitations in accurately describing a broad range of ions from small molecules to macromolecules. Significant difficulties in developing theoretical tools for CCS calculations are associated with obtaining high-quality experimental data and molecular models. In this study, we present a general CCS calculation method by employing two drift-tube IM-MS (DTIM-MS) instruments and thorough molecular modeling procedures. It is demonstrated that an appropriate description of the van der Waals (vdW) interactions is important for accurate CCS calculations in helium drift gas. By utilizing the vdW potentials from molecular mechanics force fields, it is shown that both the appropriate vdW potential-forms and their parameters are necessary for the highly reliable CCS predictions of small molecules. We further show that specific characteristics of the vdW interaction potential become less influential on the calculated CCS with increasing ion size, and that the calculated CCS values for the macromolecules converge to the values at the hard-sphere limit. Based on these results, a general CCS calculation method is presented that can be applied to ions of various sizes and compositions for the gas-phase structural studies.

Large-Scale Structural Characterization of Drug and Drug-Like Compounds by High-Throughput Ion Mobility-Mass Spectrometry.

Ion mobility-mass spectrometry (IM-MS) can provide orthogonal information, i.e., m/z and collision cross section (CCS), for the identification of drugs and drug metabolites. However, only a small number of CCS values are available for drugs, which limits the use of CCS as an identification parameter and the assessment of structure-function relationships of drugs using IM-MS. Here, we report the development of a rapid workflow for the measurement of CCS values of a large number of drug or drug-like molecules in nitrogen on the widely available traveling wave IM-MS (TWIM-MS) platform. Using a combination of small molecule and polypeptide CCS calibrants, we successfully determined the nitrogen CCS values of 1425 drug or drug-like molecules in the MicroSource Discovery Systems' Spectrum Collection using flow injection analysis of 384-well plates. Software was developed to streamline data extraction, processing, and calibration. We found that the overall drug collection covers a wide CCS range for the same mass, suggesting a large structural diversity of these drugs. However, individual drug classes appear to occupy a narrow and unique space in the CCS-mass 2D spectrum, suggesting a tight structure-function relationship for each class of drugs with a specific target. We observed bimodal distributions for several antibiotic species due to multiple protomers, including the known fluoroquinolone protomers and the new finding of cephalosporin protomers. Lastly, we demonstrated the utility of the high-throughput method and drug CCS database by quickly and confidently confirming the active component in a pharmaceutical product.

Effects of Drift Gas Selection on the Ambient-Temperature, Ion Mobility Mass Spectrometry Analysis of Amino Acids.

Ion mobility (IM) separates ions based on their response to an electric field in the presence of a drift gas. Because of its speed and sensitivity, the integration of IM and mass spectrometry (MS) offers many potential advantages for the analysis of small molecules. To determine the effects that drift gas selection has on the information content of IM separations, absolute collision cross sections (Ω) with He, N2, Ar, CO2, and N2O were measured for the 20 common amino acids using low-pressure, ambient-temperature ion mobility experiments performed in a radio frequency-confining drift cell. The drift gases were selected to span a range of masses, geometries, and polarizabilities. The information content of each separation was quantified using its peak capacity, which depended on factors contributing to widths of peaks as well as the range of Ω relative to the average Ω for the analytes. The selectivity of each separation was quantified by calculating the peak-to-peak resolution for each pairwise combination of amino acid ions. The number of pairs that were resolved depended strongly on the peak capacity, but the identities of the pairs resolved also depended on the drift gas. Therefore, results using different drift gases are partially orthogonal and provide complementary chemical information. The temperatures and pressures used for these experiments are similar to those used in many IM-MS instruments, therefore, the outcomes of this research are applicable to optimizing the information content of a wide range of contemporary and future IM-MS experiments.