Table 2. FDR-based compound searching of human metabolome DDA datasets.
| Dataset 1 | Dataset 2 | Dataset 3 | Dataset 4 | |
|---|---|---|---|---|
| Repository | Metabolomics Workbench |
Metabolomics Workbench |
Metabolomics Workbench |
MetaboLights |
| ID | ST001171 | ST002338 | ST002338 | MTBLS417 |
| Title | Metabolomics of World Trade Center Exposed New York City Firefighters31) | Interplay Between Cruciferous Vegetables and the Gut Microbiome: A Multi-Omic Approach30) | Interplay Between Cruciferous Vegetables and the Gut Microbiome: A Multi-Omic Approach30) | Customized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow32) |
| Author | Anna Nolan, Laboratory at NYU/Bellevue | Bouranis John, Oregon State University | Bouranis John, Oregon State University | Zhou Lei, Hyungwon Choi, National University of Singapore |
| Sample | Human, serum | Human, Feces | Human, Feces | Human, serum |
| Mass Spectrometer | Q Exactive HF-X Orbitrap, Thermo Scientific |
TripleTOF 5600, AB Sciex |
TripleTOF 5600, AB Sciex |
TripleTOF 5600+, AB Sciex |
| HPLC | Reverse phase ODS | Reverse phase ODS | Reverse phase ODS | Reverse phase ODS |
| Polarity | Positive | Positive | Negative | Positive |
| Number of data files | 248 | 40 | 40 | 60 |
| The number of raw spectra in the dataset | 3,242,674 | 256,580 | 220,008 | 548,663 |
| The number of averaged spectra (with more than 3 fragment ion signal) | 21,403 (8104) | 3062 (1789) | 2317 (1170) | 3077 (1450) |
| The number of hits at FDR = 5% | ||||
| Polarity-switching (FDRc) | 709 | 247 | 57 | 166 |
| Mirroring (FDRc) | 512 | 250 | 12 | 82 |
| Spectral-sampling (FDRc) | 355 | 186 | 11 | 42 |
| Second-rank (FDRrank2) | 642 | 182 | 41 | 100 |
| The number of hits without HMDB ID in the second-rank results | 56 | 24 | 1 | 12 |
FDR, false discovery rate; HMDB, human metabolome database.