patRoon 3.0: enhanced non-target analysis workflows with ion mobility separation and other major improvements

Abstract Non-target analysis (NTA) is used to identify or annotate many chemicals in complex samples, with applications in environmental analysis, metabolomics, exposomics and others. Chemical analysis is predominantly performed with chromatography coupled to high resolution mass spectrometry (HRMS). Although this technique can screen numerous chemicals simultaneously in complex sample material, the retention time and mass data obtained is often insufficient to completely separate and unequivocally identify chemicals of interest. Ion mobility separation (IMS) is increasingly used as an additional separation technique, providing complementary collision cross section (CCS) data to aid annotation. This work introduces the third major release of patRoon , an established open source platform to perform comprehensive NTA, which was upgraded to support the data complexity of IMS-HRMS instruments and integrate the benefits of this technique throughout the complete data processing workflow. This is implemented through msdata , a raw data interface optimized for complex IMS-HRMS data, and the simple, flexible and fast piek and greedy algorithms to obtain IMS-HRMS resolved features. These are combined with new functionality and existing algorithms in patRoon to obtain features and assign mobility and CCS data via two mobility assignment workflows. The IMS data assigned to features can be used throughout patRoon to enhance annotation by matching empirical or predicted CCS data and improve prioritization and interpretation of NTA data. Evaluation of this work demonstrated ease of use combined with optimized runtime performance, while the two mobility assignment workflows were complementary in terms of complexity, algorithm compatibility and performance, with each revealing unique data. Nevertheless, when applied to samples of different complexities and acquired with different instruments, both workflows resulted in CCS data that was comparable to vendor software. Thus, patRoon 3.0 brings comprehensive and vendor agnostic workflows for IMS-HRMS based NTA. Since most of the upgrades are not limited to IMS data, patRoon 3.0 (available at https://rickhelmus.github.io/patRoon/ ) has the potential to enhance data processing and outcomes in a wide variety of NTA studies. Scientific contribution The complete patRoon workflow was upgraded to make it compatible with ion mobility separation, extending the analytical strengths of ion mobility separation to a wide variety of non-target analysis studies. A highly optimized raw data interface and data processing algorithms were developed to effectively process complex ion mobility resolved data, which also improved the non-target analysis workflows without ion mobility data. Since the workflows developed here yield similar results to vendor software, patRoon 3.0 can act as unifying, vendor agnostic platform to improve the processing, consistency and comparability of ion mobility resolved data.