Ion mobility collision cross-section atlas for known and unknown metabolite annotation in untargeted metabolomics

The metabolome includes not just known but also unknown metabolites; however, metabolite annotation remains the bottleneck in untargeted metabolomics. Ion mobility - mass spectrometry (IM-MS) has emerged as a promising technology by providing multi-dimensional characterizations of metabolites. Here, we curate an ion mobility CCS atlas, namely AIICCS, and develop an integrated strategy for metabolite annotation using known or unknown chemical structures. The AIICCS atlas covers vast chemical structures with >5000 experimental CCS records and -12 million calculated CCS values for >1.6 million small molecules. We demonstrate the high accuracy and wide applicability of AIICCS with medium relative errors of 0.5-2% for a broad spectrum of small molecules. AIICCS combined with in silico MS/MS spectra facilitates multi-dimensional match and substantially improves the accuracy and coverage of both known and unknown metabolite annotation from biological samples. Together, AIICCS is a versatile resource that enables confident metabolite annotation, revealing comprehensive chemical and metabolic insights towards biological processes.