PNNL

Abstract

Motivation: 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: 1) stepped field methods for drift tube-based IMS (DTIMS), 2) single field methods for DTIMS (supporting two calibration methods: a standard and a new ‘enhanced’ method) and 3) non-linear calibration methods for traveling wave based-IMS (TWIMS) in Structures for Lossless Ion Manipulations (SLIM). 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: Demo data in ftp://MSV000085979:CCS3644@massive.ucsd.edu/ (Username: MSV000085979 and Password: CCS3644).