Table 1. Subunits of complex I from Y. lipolytica indicating proteins missing in subcomplex nb8mΔ (bold and underlined) according to combined data from dSDS-PAGE, LILBID-MS, and ESI-MS.

	Subunit	Ortholog B. taurus	Mr Mature, Da	Module	Identified in Subcomplex nb8mΔ by ESI-MSa
1	NUAM	75-kDa	75,199	Q/N	yes
2	NUBM	51-kDa	51,660	Q/N	yes
3	NUCM	49-kDa	49,945	Q/N	yes
4	NUGM	30-kDa	30,476b	Q/N	yes
5	NUHM	24-kDa	24,069	Q/N	yes
6	NUIM	TYKY	22,321	Q/N	yes
7	NUKM	PSST	20,426	Q/N	yes
8	NU1M	ND1	38,348	PP	yes
9	NU2M	ND2	53,332	PP	n.d.c
10	NU3M	ND3	14,471	PP	yes
11	NU4M	ND4	54,481	PD	no
12	NU5M	ND5	73,705	PD	no
13	NU6M	ND6	20,758	PP	n.d.
14	NULM	ND4L	9,811	PP	n.d.
15d	NUEM	39-kDa	40,434	Q/N	yes
16	ST1	—	34,490	unknown	n.d.
17	NESM	ESSS	23,438	PD	no
18	NUJM	B14.7	20,696	PD	no
19	NUZM	B14.5a	19,750	Q/N	yes
20	NUPM	PGIV	19,196	PP	yes
21	NUXM	—	18,565	PP	yes
22	N7BM	B17.2	16,153	Q/N	yes
23	NUYM	AQDQ	15,940	Q/N	yes
24	NUFM	B13	15,573	Q/N	yes
25	NIAM	ASHI	14,642	PD	no
26	NB4M	B14	14,627	PP	yes
27	NB6M	B16.6	13,960	PP	yes
28	NUNM	—	13,301	PD	no
29	NUMM	13-kDa	13,117	Q/N	yes
30	NI2M	B22	12,749	PD	no
31	NB8M	B18	11,068	PD	no
32	NIDM	PDSW	10,890	PD	no
33	NB5M	B15	10,348	PD	no
34	ACPM2	—	10,092e	PD	no
35	NIPM	PFFD	9,887	PD	no
36	NIMM	MWFE	9,662	PP	yes
37	NUUM f	—	9,652	PD	no
38	ACPM1	SDAP	9,636e	PP	yes
39	NI8M	B8	9,473	Q/N	yes
40	NI9M	B9	8,981	PP	yes
41	NEBMg	—	7,917	PP	yes
42	NB2M	B12	6,805	PD	no

^aUnpublished data. Purified subcomplex nb8mΔ was run on BN-PAGE, subjected to tryptic in-gel digestion and analysed by nano liquid chromatography ESI-MS.

^bMolecular mass includes 1,267.3 Da for the hexa-histidine tag and hexa-alanine spacer [18].

^cNot determined; the hydrophobic subunits ND2, ND6, and ND4L are not reliably identified by ESI-MS and subunit ST1 is known to dissociate from the complex during BN-PAGE [13].

^dAccessory subunits are numbered according to their molecular mass. Not that this numbering is not identical to Morgner et al. [13].

^eMolecular mass includes 564.7 Da for covalently bound phosphopantetheine-hydroxy-tetradecanoate.

^fSubunit NUUM was recently found in Y. lipolytica complex I [35], but we found an intron near the N-terminus resulting in a larger protein that lacked the N-terminal methionine. This was confirmed by peptide identification with LC/ESI-MS analysis at 100% sequence coverage (not shown).

^gSubunit NEBM was identified and characterized recently in another study from our laboratory (E. Nübel et al., in preparation).