biostudies-literatureQuinlan ZABlasker Environmental Grant of the San Diego FoundationNIEHS NIH HHSGordon and Betty Moore FoundationNational Science Foundation1275https://www.ebi.ac.uk/biostudies/studies/S-EPMC9786801biostudies-literatureUnknown12(12)Recent developments in molecular networking have expanded our ability to characterize the metabolome of diverse samples that contain a significant proportion of ion features with no mass spectral match to known compounds. Manual and tool-assisted natural annotation propagation is readily used to classify molecular networks; however, currently no annotation propagation tools leverage consensus confidence strategies enabled by hierarchical chemical ontologies or enable the use of new in silico tools without significant modification. Herein we present ConCISE (Consensus Classifications of In Silico Elucidations) which is the first tool to fuse molecular networking, spectral library matching and in silico class predictions to establish accurate putative classifications forMetabolitesConCISE: Consensus Annotation Propagation of Ion Features in Untargeted Tandem Mass Spectrometry Combining Molecular Networking and In Silico Metabolite Structure Prediction.PMC9786801MMI 6920P01-ES021921BLSK2016762722023298OCE-11552692019252845OCE-1313747Petras DAluwihare LIQuinlan ZANelson CEDorrestein PCKoester IWegley Kelly LAron ATfalseConCISE: Consensus Annotation Propagation of Ion Features in Untargeted Tandem Mass Spectrometry Combining Molecular Networking and In Silico Metabolite Structure Prediction.Recent developments in molecular networking have expanded our ability to characterize the metabolome of diverse samples that contain a significant proportion of ion features with no mass spectral match to known compounds. Manual and tool-assisted natural annotation propagation is readily used to classify molecular networks; however, currently no annotation propagation tools leverage consensus confidence strategies enabled by hierarchical chemical ontologies or enable the use of new in silico tools without significant modification. Herein we present ConCISE (Consensus Classifications of In Silico Elucidations) which is the first tool to fuse molecular networking, spectral library matching and in silico class predictions to establish accurate putative classifications for2022-01-01T00:00:00Z2022 Dec2025-04-04T07:59:52.212Z2025-04-04T07:59:52.212ZS-EPMC97868013655731310.3390/metabo12121275