PolycIMS: Polymers for Automated Cyclic Ion Mobility Spectrometry Calibration

The development and commercialization of cyclic ion mobility spectrometry (cIMS) instruments has considerably expanded the level of structural details that can be accessed for gaseous ions. Commercial cIMS instruments rely on travelling wave ion mobility spectrometry (TWIMS), a technique that requires calibration of the measured arrival times to enable the determination of collisional cross sections (CCS). Most calibration strategies use peptide mixtures that span a CCS range of approximately 100 – 400 Å2, which can introduce significant inaccuracies when extrapolating to larger ion structures. In addition, TWIMS calibration remains a tedious data processing step that would greatly benefit from automation. Here, we introduce polycIMS, a command-line tool that automates cIMS calibration and generates charge-independent calibration curves covering a broad CCS range from 100 – 1500 Ų, within just 3 minutes on a standard laptop. Calibrated CCS can be determined in He or N 2 ( TW CCS N2→He , TW CCS N2→N2 ) using inexpensive, commercially-available polymer standards and are validated against reported values for more than 50 reference ions. Furthermore, the derived calibration parameters are largely insensitive to collisional activation, making it possible to calibrate multistage cIMS workflows such as slice collision induced unfolding (CIU n ). We anticipate that the simplicity and accessibility of polycIMS will encourage its adoption as a new standard for cIMS calibration.