Table I. A comparison of recent mitochondria mass spectrometry-based crosslinking studies.
| Reference | This work | Schweppe et al. “Mitochondrial protein interactome elucidated by chemical crosslinking mass spectrometry.” Proceedings of the National Academy of Sciences 114.7 (2017): 1732–1737. | Liu et al. “The interactome of intact mitochondria by crosslinking mass spectrometry provides evidence for coexisting respiratory supercomplexes.” Molecular & Cellular Proteomics 17.2 (2018): 216–232. |
|---|---|---|---|
| Organism | Yeast | Mouse | Mouse |
| Material | Isolated mitochondria | Isolated mitochondria | Isolated mitochondria |
| Crosslinker | CBDPS | BDP-NHP | DSSO |
| Number of LC-MS runs | 55 LC-MS runs | 72 LC-MS runs | 42 LC-MS runs for native condition crosslinking data |
| 11 biological replicates run in technical duplicate | 21 SCX fractions for 2 biological replicates | ||
| Soluble-protein/membrane-protein fractionation | Yes | No | No |
| SCX fractionation | Yes | Yes | Yes |
| Affinity enrichment | Yes | Yes | No |
| Isotope labelling | Yes | No | No |
| Acquisition method types | TopN | ReACT (PMID:23413883) | TopN |
| Platform MS | Orbitrap Q Exactive HF | Velos-FTICR (custom-build) | Orbitrap Fusion |
| Non-redundant CL pairs | Inter:751 | inter+intra: 2427 | inter+intra: 3322 |
| Intra:9521 | |||
| Proteins Involved | Inter:251 (unambiguous) | inter+intra: 327 | inter+intra: 359 |
| Intra:784 (unambiguous) | |||
| Total:811 (unambiguous) | |||
| PPI's | Inter:338 (unambiguous) | 459 | Total: 885 |
| Intra:784 (unambiguous) | Intra: 276 | ||
| Inter:609 | |||
| (Not reported in manuscript, counted from supplementary materials) | |||
| FDR | 2% | 1.91% | 2% |