Table 2. Results of the label-free quantification of differentially glycated proteins and the corresponding AGE sites in the proteome of bean nodule bacteroids.

The search was performed by the SEQUEST engine against a sequence database of Rhizobium leguminosarum bv phaseoli. As far as possible, for each glycated site, the corresponding unique protein-specific nonglycated peptide was used for relative label-free quantification. Unmodified peptides for Arg biosynthesis bifunctional protein ArgJ, 30S ribosomal proteins S2 and S10, peptidyl-dipeptidase, and monophenol monooxygenase are shown. For all peptides, the statistical significance of differential expression and glycation (P < 0.05) was confirmed by the Mann-Whitney U test. CEA, N^ε-(carboxyethyl)arginine. Other abbreviations as in Table 1.

No.	Protein Annotation		Peptide Sequence	Sites	m/z	z	tR	Quantification
	Protein Name	Accession No.						Maturea	Senescentb
								fold change
1	Arg biosynthesis bifunctional protein ArgJ	A0A072C5E0	35 NRTDVLMMVFD[CML]PAAVAGVFTR 56	K46	624.82	4	137.91	40.53	182.82
			331 IVMAVGK 337		359.22	2	52.50	1.68	0.21
			155 AIMTTDTYPK 164		570.78	2	65.13	0.02	0.02
2	30S ribosomal protein S2	A0A072C5T7	116 LR[CML]LDEILGGEAQGFTKK 133	K118	516.04	4	90.41	3.52	0.56
			108 TISNSIQR 115		459.75	2	40.72	5.76	0.30
			55 ALQVVSDTVAR 65		579.82	2	73.25	–	0.19
3	30S ribosomal protein S10	A0A072C6R8	10 L[CEL]AFDHR 16	K11	320.17	3	67.85	18.75	44.64
			17 ILDASTREIVSTAKR 31		553.98	3	73.49	1.46	1.02
4	Peptidyl-dipeptidase	A0A072BWW2	248 AWVA[CMA]GENGGETDNRAVIR 266	R252	533.01	4	69.75	8.43	9.34
			248 AWVA[MG-H]GENGGETDNRAVIR 266 75	R252	482.76	2	108.18	0.20	5.31
			75 VSALFWNK 82
			227 SIIEPFLTFSER 238		719.88	2	138.27	6.67	14.72
5	Monophenol monooxygenase	A0A072BUN7	462 VYGGRGQTDGEAIDLQLIPVGSGAG[CML]PGAVAPAKLEIAIVSA 503	K487	1,368.74	3	138.16	∞	–
			462VYGGRGQTDGEAIDLQLIPVGSGAGKPGAVAPA[CML]LEIAIVSA 503	K495	530.29	2	113.58	0.19	3.65
			248 IWATWNLR 255
6	Uncharacterized protein	A0A072C7M7	186 NVQDSV[Glarg]ALLSGVVR 200	R192	413.98	4	109.24	5.92	193.92
7	Anti-sigma factor transcriptional activator protein	A0A072C686	42 LVSSLELLAGEALE[CMA]SPEAAIADR 65	R56	642.84	4	63.078	3.59	0.36
8	Type VI secretion system baseplate subunit TssK	A0A072BS04	50 LN[Argpyr]ELLGLGK 59	R52	398.24	3	97.12	–	∞
9	ABC transporter substrate-binding protein	A0A072BSX7	213 LMSGDVALVEDPRMIEALEML[Argpyr][Argpyr]LSNYAEPLEK 245	R234, R235	1,322.34	3	142.63	–	∞
10	Integrase	A0A072BY45	68 LDRLA[Glarg]SVADLMGITE[Glarg]LR 86	R73, R84	571.05	4	118.65	13.03	0.79
11	GntR family transcriptional regulator	A0A072C3K4	24 IVGMIADGTFPVNE[Glarg]LPSETR 44	R38	586.30	4	105.32	3.72	0.09
12	ABC transporter ATP-binding protein	A0A072BVM6	41 HPWQAGFAIGATLVASTFQLMIP[Glarg] 64	R64	712.17	5	110.60	0.30	1.94
13	α/β-Hydrolase fold protein	A0A072CKM0	82 GL[CML]AVNVFAMSWGGTVAGAYAAR 104	K84	791.06	3	139.83	3.11	23.70
14	Cytochrome bc biosynthesis ABC transporter ATP-binding protein	A0A072BTW6	307 GALDLG[Argpyr]TLLAAR 319	R313	352.45	4	77.35	69.96	27.83
15	Uncharacterized protein	A0A072C8Y3	24 IGELL[TH-Argpyr] 29	R29	422.74	2	56.70	2.88	0.13
16	Molecular chaperone protein DnaJ	A0A072BWF0	7 YFD[TH-Argpyr] IR 12	R10	338.50	3	63.58	0.08	53.40
17	NADPH quinone reductase	A0A072BTA3	22 LA[CML]ALVRFAPPELEMSEISFK 42	K24	812.10	3	133.53	2.36	24.76
18	FAD-dependent l-sorbose dehydrogenase	A0A072C6X7	207 KNLTV[CEA]TGA[CEA] 216	R212, R216	420.57	3	34.45	9.31	0.01

^aFold change observed in mature plants relative to young plants.

^bFold change observed in senescent plants relative to young plants.