biostudies-literatureKong DNIA NIH HHSNIDA NIH HHSNIDDK NIH HHSNINDS NIH HHS103https://www.ebi.ac.uk/biostudies/studies/S-EPMC11751189biostudies-literatureUnknown8(1)Enzymes play a pivotal role in orchestrating complex cellular responses to external stimuli and environmental changes through signal transduction pathways. Despite their crucial roles, measuring enzyme activities is typically indirect and performed on a smaller scale, unlike protein abundance measured by high-throughput proteomics. Moreover, it is challenging to derive the activity of enzymes from proteome-wide post-translational modification (PTM) profiling data. To address this challenge, we introduce enzyme activity inference with structural equation modeling under the JUMP umbrella (JUMPsem), a novel computational tool designed to infer enzyme activity using PTM profiling data. We demonstrate that the JUMPsem program enables estimating kinase activities using phosphoproteome data, ubiqCommunications biologyA computational tool to infer enzyme activity using post-translational modification profiling data.PMC11751189RF1 AG064909RF1 AG072703R01 DA056523RF1 AG068581R01 DK130913R01 NS123456Wu LMishra AHigh AAYuan ZFFu YKong DWang XLi LZhang APeng JfalseA computational tool to infer enzyme activity using post-translational modification profiling data.Enzymes play a pivotal role in orchestrating complex cellular responses to external stimuli and environmental changes through signal transduction pathways. Despite their crucial roles, measuring enzyme activities is typically indirect and performed on a smaller scale, unlike protein abundance measured by high-throughput proteomics. Moreover, it is challenging to derive the activity of enzymes from proteome-wide post-translational modification (PTM) profiling data. To address this challenge, we introduce enzyme activity inference with structural equation modeling under the JUMP umbrella (JUMPsem), a novel computational tool designed to infer enzyme activity using PTM profiling data. We demonstrate that the JUMPsem program enables estimating kinase activities using phosphoproteome data, ubiq2025-01-01T00:00:00Z2025 Jan2025-04-22T05:26:59.383Z2025-04-05T21:20:17.952ZS-EPMC117511893983808310.1038/s42003-025-07548-4