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%