Table 2.

List of proteins detected by nano-LC-MS/MS from spots with relative abundance fold change ≥ 1.5 (ANOVA, p ≤ 0.05) from PPA and WBM media during stationary growth phase.

Spot no.a	Fold change	Mwb	pIb	LC-MS/MS score	No of match. pept.c	Seq. cov. (%)c	Locus in reference organismd	Name	Annotation
PPA
29	1.6	137,778	5.2	2689	40	33	PFREUD_01840	NifJ1	Pyruvate synthase/pyruvate-flavodoxin oxidoreductase
30	1.9	137778	5.2	2525	59	34	PFREUD_01840	NifJ1	Pyruvate synthase/pyruvate-flavodoxin oxidoreductase
31	1.7	137,778	5.2	3124	71	42	PFREUD_01840	NifJ1	Pyruvate synthase/pyruvate-flavodoxin oxidoreductase
36	1.7	96,275	4.8	2351	50	39	PFREUD_03230	PPDK	Pyruvate phosphate dikinase
37	2.3	94,317	5.3	2756	48	44	PFREUD_17920	ClpB2	ATP-dependent Clp protease B2
39	2.4	75,276	6.0	1488	36	36	PFREUD_14311	SdhA3	Succinate dehydrogenase flavoprotein subunit
42	1.9	60,757	5.5	1966	67	62	PFREUD_01830	GLS	FAD-dependent pyridine nucleotide-disulfide oxidoreductase
43e	3.6	53,385	5.1	825	62	25	PFREUD_16320	AspA1	Aspartate ammonia-lyase
43e	3.6	53,526	5.1	748	48	26	PFREUD_16330	AspA2	Aspartate ammonia-lyase
46	2	47,518	5.0	270	4	11	PFREUD_01350	SerRS1	Seryl-tRNA synthetase
47	1.5	47,953	5.7	678	11	27	PFREUD_05140	GGR	Electron transfer oxidoreductase (Geranylgeranyl reductase superfamily)
57	1.6	24,018	5.2	352	21	33	PFREUD_22440	SDR_c	Short subunit dehydrogenase (classical)
WBM
59	2	93,458	5.1	2766	46	50	PFREUD_19250	ClpB1	ATP-dependent Clp protease B1
60	1.5	93,458	5.1	2527	49	46	PFREUD_19250	ClpB1	ATP-dependent Clp protease B1
70	2	49,226	5.5	1290	20	51	PFREUD_17610	GDH	glutamate dehydrogenase
75	3	34,225	4.9	661	15	31	PFREUD_12840	L-LDH	L-lactate dehydrogenase
78	1.6	35,532	5.2	609	8	27	PFREUD_15130	GAPDH	Glyceraldehyde-3-phosphate dehydrogenase
81	2	32,368	5.0	582	8	34	PFREUD_23890	FBA2	Fructose-bisphosphate aldolase class I
85	3.7	33,620	5.1	431	6	28	PFREUD_16420	Cys2	Cysteine synthase A
86	2.2	33,620	5.1	826	47	54	PFREUD_16420	Cys2	Cysteine synthase A
91	1.8	23,335	5.0	476	6	46	PFREUD_23970	SDR	Oxidoreductase
92	1.5	22,619	5.3	314	6	18	PFREUD_06110	SodA	Superoxide dismutase
93	5.2	16,830	4.9	575	8	58	PFREUD_09500	IbpA	Molecular chaperone (small heat shock protein)

Only spots with single identification are presented.

^aSpot numbers refer to those shown in Figure 5A.

^bTheoretical molecular weight (Mw) and pI values were obtained.

^cNo. match. pept., number of matched peptides; Seq. cov., sequence coverage.

^dP.freudenreichii CIRM-BIA1^T GenBank: FN806773.1.

^eIn the spot 43 two proteins were identified; both were isoforms of aspartate ammonia-lyase and are therefore included in the table.