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Item AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry-mass spectrometry(Oxford University Press, 2021) Lee, Joon-Yong; Bilbao, Aivett; Conant, Christopher R.; Bloodsworth, Kent J.; Orton, Daniel J.; Zhou, Mowei; Wilson, Jesse W.; Zheng, Xueyun; Webb, Ian K.; Li, Ailin; Hixson, Kim K.; Fjeldsted, John C.; Ibrahim, Yehia M.; Payne, Samuel H.; Jansson, Christer; Smith, Richard D.; Metz, Thomas O.; Chemistry and Chemical Biology, School of ScienceMotivation: Ion mobility spectrometry (IMS) separations are increasingly used in conjunction with mass spectrometry (MS) for separation and characterization of ionized molecular species. Information obtained from IMS measurements includes the ion's collision cross section (CCS), which reflects its size and structure and constitutes a descriptor for distinguishing similar species in mixtures that cannot be separated using conventional approaches. Incorporating CCS into MS-based workflows can improve the specificity and confidence of molecular identification. At present, there is no automated, open-source pipeline for determining CCS of analyte ions in both targeted and untargeted fashion, and intensive user-assisted processing with vendor software and manual evaluation is often required. Results: We present AutoCCS, an open-source software to rapidly determine CCS values from IMS-MS measurements. We conducted various IMS experiments in different formats to demonstrate the flexibility of AutoCCS for automated CCS calculation: (i) stepped-field methods for drift tube-based IMS (DTIMS), (ii) single-field methods for DTIMS (supporting two calibration methods: a standard and a new enhanced method) and (iii) linear calibration for Bruker timsTOF and non-linear calibration methods for traveling wave based-IMS in Waters Synapt and Structures for Lossless Ion Manipulations. We demonstrated that AutoCCS offers an accurate and reproducible determination of CCS for both standard and unknown analyte ions in various IMS-MS platforms, IMS-field methods, ionization modes and collision gases, without requiring manual processing. Availability and implementation: https://github.com/PNNL-Comp-Mass-Spec/AutoCCS. Supplementary information: Supplementary data are available at Bioinformatics online. Demo datasets are publicly available at MassIVE (Dataset ID: MSV000085979).Item Experimental Trapped-ion Quantum Simulation of the Kibble-Zurek dynamics in momentum space(SpringerNature, 2016-09-16) Cui, Jin-Ming; Huang, Yun-Feng; Wang, Zhao; Cao, Dong-Yang; Wang, Jian; Lv, Wei-Min; Luo, Le; del Campo, Adolfo; Han, Yong-Jian; Li, Chuan-Feng; Guo, Guang-Can; Department of Physics, School of ScienceThe Kibble-Zurek mechanism is the paradigm to account for the nonadiabatic dynamics of a system across a continuous phase transition. Its study in the quantum regime is hindered by the requisite of ground state cooling. We report the experimental quantum simulation of critical dynamics in the transverse-field Ising model by a set of Landau-Zener crossings in pseudo-momentum space, that can be probed with high accuracy using a single trapped ion. We test the Kibble-Zurek mechanism in the quantum regime in the momentum space and find the measured scaling of excitations is in accordance with the theoretical prediction.