Table 1.

Proteins identified by LTQ-Orbitrap mass spectrometry

A. Differentially expressed/localized proteins
									Normalized quantities a
Category	SSP	Gene Product/ Locus tag	gi accession number	Theoretical mass (kDa)	Unique peptides	PSM	Score (CID+ HCD)	Coverage (%)	N+	N−	Ratio (N−/N+)	Predicted localization	TM helices
TCA cycle	5110	SDH subunit D	83592539	13.5	2	7	269	15	ND	130.8	NA	CM	3
	5512	SDH Fe-S subunit beta	83592541	29.5	22	85	2142	45	348.7	2196.3	6.3	CMA	NA
	5811	SDH flavoprotein subunit alpha	83592540	64.7	24	91	2911	47	1228.4	4352.8	3.6	CMA	NA
	6614	Malate dehydrogenase	83592546	33.5	20	121	4335	68	ND	1420.7	NA	Cyt	NA
	7716	Succinyl-CoA synthetase beta subunit	83592547	42.6	20	51	1477	51	ND	92.9	NA	Cyt	NA
Amino acid metabolism	6901	O-acetylhomoserine/O-acetylserine sulfhydrylase	83593171	46.0	12	32	965	40	ND	105.5	NA	Cyt	NA
	7617	Cysteine synthase	83595123	35.4	17	49	1917	49	45.5	322.4	7.1	Cyt	NA
Transport	6615	TRAP dicarboxylate transporter-DctP subunit	83595007	36.1	23	96	2945	59	ND	1717.5	NA	Per	NA
Electron transport	7816	FixC like electron transfer flavoprotein dehydrogenase	83591605	59.5	19	54	1799	36	49.8	223.9	4.5	CMA	NA
	8501	FixB like electron transfer flavoprotein alpha	83594408	31.4	6	16	490	21	ND	66.2	NA	Cyt	NA
Proteolysis	6408	Clp protease subunit ClpP	83592885	23.9	9	22	800	34	ND	40.5	NA	Cyt	NA
Lipid synthesis	6711	Acetyl-CoA acetyltransferase	83591614	40.2	16	60	1702	38	ND	268.2	NA	Cyt	NA
	7310	50S ribosomal protein L6	83594005	19.4	6	8	371	27	38.1	124.1	3.2	Cyt	NA
Photosynthesis	3707	Uroporphyrinogen III synthase HEM4	83594896	74.9	20	53	2516	41	ND	283.4	NA	Cyt	NA
Unknown	3904	Alpha-2-macroglobulin-like protein	83591444	185.1	17	37	1543	10	ND	21.9	NA	Unk	NA
	3905	Alpha-2-macroglobulin-like protein	83591444	185.1	26	57	2147	16	ND	21.9	NA	Unk	NA
Transport	6608	Putative branched-chain amino acid periplasmic binding protein	83594835	44.2	10	36	886	25	121.7	ND	NA	Per	NA
	6613	TRAP dicarboxylate transporter- DctP subunit	83595007	36.1	33	151	4930	70	9255.9	59.38	0.01	Per	NA
	6817	Extracellular solute-binding protein	83593691	59.0	49	178	5720	64	25156.8	1173.6	0.05	Per	NA
	7601	Periplasmic ribose binding protein	83592701	33.2	30	144	5617	70	6207.6	273.3	0.04	Per	NA
	7603	Periplasmic phosphate binding protein	83591937	36.5	16	51	1637	50	926.7	14.9	0.02	Per	NA
	7606	Basic membrane lipoprotein	83593237	38.6	16	58	2167	45	4298.6	609.2	0.14	Per	NA
	7610	Branched-chain ligand-binding receptor	83593081	38.6	33	166	5161	61	4327.8	501.3	0.12	Per	NA
	7611	Thiosulphate-binding protein	83594729	38.5	16	53	1542	43	3215.9	396.2	0.12	Per	NA
	7614	Extracellular solute-binding protein	83592354	40.4	18	50	1685	38	3229.0	639.7	0.20	Per	NA
Porins	6505	OmpA/MotB (porin associated protein)	83594657	28.7	11	37	1509	40	219.5	ND	NA	OM	NA
	7501	OmpA family protein	83591777	35.6	23	83	3121	39	5394.9	444.0	0.08	OM	NA
Photosynthesis	2801	Uroporphyrinogen III synthase HEM4	83594896	74.9	30	82	2940	55	131.4	ND	NA	Cyt	NA
Unknown	4907	Alpha-2-macroglobulin-like protein	83591444	185.1	58	158	5686	34	1038.0	11.4	0.01	Unk	NA
	5901	Alpha-2-macroglobulin-like protein	83591444	185.1	39	89	3100	24	104.1	14.6	0.14	Unk	NA

B. Constitutive proteins
Category	SSP	Gene Product/ Locus tag	gi accession number	Theoretical mass (kDa)	Unique peptides	PSM	Score (CID + HCD)	Coverage (%)	Predicted localization	TM helices
Energy metabolism	3312	ATP synthase delta subunit	83592559	19.6	14	30	929	51	CMA	NA
	3603	ATP synthase gamma subunit	83592561	32.4	7	20	553	23	CMA	NA
	3705	ATP synthase beta subunit	83592562	50.8	19	87	2973	52	CMA	NA
	3805	ATP synthase alpha subunit	83592560	55.2	30	109	3191	42	CMA	NA
	4207	ATP synthase b’ subunit	83594574	17.2	13	59	1889	66	CM	1
	4308	ATP synthase b subunit	83594573	19.6	15	60	2492	57	CM	1
	4309	ATP synthase epsilon subunit	83592563	14.3	7	60	1915	46	CMA	NA
	4603	ATP synthase gamma subunit	83592561	32.4	12	31	1194	39	CMA	NA
	5304	NADH dehydrogenase subunit B	83592891	20.2	5	15	594	29	CMA	NA
	5305	NADH dehydrogenase subunit I	83592898	18.6	5	10	197	20	CMA	NA
	5408	NADH dehydrogenase subunit C	83592892	24.8	18	56	1349	62	CMA	NA
	5411	Ubiquinol-cytochrome c reductase, ironsulfur subunit	83591704	19.6	4	14	184	18	CM	1
	5705	NADH dehydrogenase subunit D	83592893	44.3	10	23	666	28	CMA	NA
	6301	NADH dehydrogenase subunit I	83592898	18.6	8	18	390	22	CMA	NA
	6304	NADH dehydrogenase subunit B	83592891	20.2	6	21	765	32	CMA	NA
	6710	NADH dehydrogenase subunit D	83592893	44.3	14	38	715	32	CMA	NA
	7403	NADH dehydrogenase subunit C	83592892	24.8	28	100	2376	72	CMA	NA
Photosynthesis	2117	Light harvesting protein B870 (beta subunit)	83594307	7.7	4	15	550	30	CM	1
	2409	Photosynthetic reaction center M-chain	83594304	34.2	7	23	952	21	CM	5
	2504	Photosynthetic reaction center H-chain	83591956	27.9	21	67	2455	61	CM	1
	3121	Light harvesting protein B870 (beta subunit)	83594307	7.7	3	11	517	30	CM	1
	4407	Photosynthetic reaction center M-chain	83594304	34.2	8	37	861	21	CM	5
	4503	Photosynthetic reaction center. H-chain	83591956	27.9	17	49	1897	54	CM	1
	4504	Photosynthetic reaction center. H-chain	83591956	27.9	15	40	1439	45	CM	1
Transport	5609	Extracellular solute-binding protein	83593422	32.4	8	16	449	23	Per	NA
	6707	Extracellular solute-binding protein	83593691	59.0	41	223	7075	60	Per	NA
Unknown	2306	Putative membrane protein	83593120	14.5	4	28	729	22	CM	3

FDR – false discovery rate; SSP – standard spot number assigned by PDQuest 7.3.0; TM– transmembrane; ND – not detected; NA – non applicable; CM – integral chromatophore membrane protein; CMA – chromatophore membrane associated protein; Cyt – cytosolic protein; Per – periplasmic protein; OM – outer membrane protein; Unk – unknown; PSM – peptide-spectrum matches; Score – cumulative Mascot ion score; Coverage – all accounted peptides are from PSMs (peptide-spectra match) of <1% FDR (false discovery rate), as determined by Mascot search against the target-decoy database

^aQuantification using the “Total density in gel image” normalization method from PDQuest 7.3.0.

^bPredicted using the PSORTb 3.0.2 server (http://www.psort.org/psortb/index.html)

^cPredicted using the TMHMM 2.0 server (http://www.cbs.dtu.dk/services/TMHMM/)