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JUMPm: A Tool for Large-Scale Identification of Metabolites in Untargeted Metabolomics
| Content Provider | MDPI |
|---|---|
| Author | Wang, Xusheng Cho, Ji-Hoon Poudel, Suresh Li, Yuxin Jones, Drew R. Shaw, Timothy I. Tan, Haiyan Xie, Boer Peng, Junmin |
| Copyright Year | 2020 |
| Description | Metabolomics is increasingly important for biomedical research, but large-scale metabolite identification in untargeted metabolomics is still challenging. Here, we present Jumbo Mass spectrometry-based Program of Metabolomics (JUMPm) software, a streamlined software tool for identifying potential metabolite formulas and structures in mass spectrometry. During database search, the false discovery rate is evaluated by a target-decoy strategy, where the decoys are produced by breaking the octet rule of chemistry. We illustrated the utility of JUMPm by detecting metabolite formulas and structures from liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) analyses of unlabeled and stable-isotope labeled yeast samples. We also benchmarked the performance of JUMPm by analyzing a mixed sample from a commercially available metabolite library in both hydrophilic and hydrophobic LC-MS/MS. These analyses confirm that metabolite identification can be significantly improved by estimating the element composition in formulas using stable isotope labeling, or by introducing LC retention time during a spectral library search, which are incorporated into JUMPm functions. Finally, we compared the performance of JUMPm and two commonly used programs, Compound Discoverer 3.1 and MZmine 2, with respect to putative metabolite identifications. Our results indicate that JUMPm is an effective tool for metabolite identification of both unlabeled and labeled data in untargeted metabolomics. |
| Starting Page | 190 |
| e-ISSN | 22181989 |
| DOI | 10.3390/metabo10050190 |
| Journal | Metabolites |
| Issue Number | 5 |
| Volume Number | 10 |
| Language | English |
| Publisher | MDPI |
| Publisher Date | 2020-05-12 |
| Access Restriction | Open |
| Subject Keyword | Metabolites Biochemical Research Analytical Chemistry Metabolomics Metabolome Mass Spectrometry Metabolite Identification Database Search Metabolite Formula Metabolite Structure Software Algorithm Yeast |
| Content Type | Text |
| Resource Type | Article |
