Development of Diagnostic Biomarkers for Detecting Diabetic Retinopathy at Early Stages Using Quantitative Proteomics

Table 1

Experimental MRM conditions for 15 selected proteins.

	Protein	Accession number	Gene	Peptide sequence		Peptide		Charge stage		Ions^c	DP^d	CE^e (V)	RT^f (min)
				(light^a and heavy^b)		Q1	Q3	Q1	Q3
1	Amyloid-like protein 2	Q06481	APLP2	Light	WEPDPTGTK	515.74	503.28	2	1	y5, y6, y8	123	28	20.8
				Heavy	WEPDPTGT[13C-15N-K]	519.75	511.29	2	1
2	Apolipoprotein A-IV	P06727	APOA4	Light	LAPLAEDVR	492.28	589.29	2	1	y5, y6, y7	123	27	25.1
				Heavy	LAPLAEDV[13C-15N-R]	497.28	599.30	2	1
3	Beta-2-glycoprotein 1	P02749	APOH	Light	ATVVYQGER	511.80	652.30	2	1	y5, y6, y7	123	30.52	16
				Heavy	ATVVYQGE[13C-15N-R]	516.77	662.31	2	1
4	N-Acetyllactosaminide beta-1,3-N-Acetylglucosaminyltransferase	O43505	B3GNT1	Light	QYGFNR	392.69	656.31	2	1	y3, y4, y5	123	22	18.4
				Heavy	QYGFN[13C-15N-R]	397.69	666.32	2	1
5	Complement C4-B	P0C0l5	C4B	Light	VDFTLSSER	527.26	839.43	2	1	y5, y6, y7	69.6	25.8	29
				Heavy	VDFTLSSE[13C-15N-R]	532.27	849.43	2	1
6	Complement C5	P01031	C5	Light	TDAPDLPEENQAR	728.34	843.39	2	1	y7, y9, y10	84.2	37.3	22.1
				Heavy	TDAPDLPEENQA[13C-15N-R]	733.34	853.40	2	1
7	Complement component C7	P10643	C7	Light	AASGTQNNVLR	565.79	743.41	2	1	y5, y6, y9	72.4	28	13.9
				Heavy	AASGTQNNVL[13C-15N-R]	570.80	753.42	2	1
8	Monocyte differentiation antigen CD14	P08571	CD14	Light	FPAIQNLALR	571.83	714.42	2	1	y6, y7, y8	72.8	28.3	41.3
				Heavy	FPAIQNLAL[13C-15N-R]	576.84	724.43	2	1
9	Clusterin	P10909	CLU	Light	ASSIIDELFQDR	697.35	1035.51	2	1	y6, y7, y8	123	38.69	46.3
				Heavy	ASSIIDELFQD[13C-15N-R]	702.35	1045.52	2	1
10	Fibronectin	P02751	FN1	Light	FLATTPNSLLVSWQPPR	964.02	1393.75	2	1	y3, y8, y12	101.4	50.7	45.8
				Heavy	FLATTPNSLLVSWQPP[13C-15N-R]	969.02	1403.77	2	1
11	Gelsolin	P06396	GSN	Light	GGVASGFK	361.70	509.27	2	1	y4, y5, y6	123	21	15.4
				Heavy	GGVASGF[13C-15N-K]	365.70	517.29	2	1
12	Inter-alpha-trypsin inhibitor heavy chain H2	P19823	ITIH2	Light	VQSTITSR	446.24	664.36	2	1	y4, y5, y6	63.6	21.2	9.41
				Heavy	VQSTITS[13C-15N-R]	451.25	674.37	2	1
13	Keratin, type II cytoskeletal 1	P04264	KRT1	Light	AQYEDIAQK	533.26	866.42	2	1	y5, y6, y7	123	28	19.6
				Heavy	AQYEDIAQ[13C-15N-K]	537.27	874.44	2	1
14	Pigment epithelium-derived factor	P36955	SERPINF1	Light	LSYEGEVTK	513.26	662.35	2	1	y5, y6, y7	123	28	20.2
				Heavy	LSYEGEVT[13C-15N-K]	517.27	670.35	2	1
15	Vitronectin	P04004	VTN	Light	DVWGIEGPIDAAFTR	823.91	947.49	2	1	y8, y9, y13	123	41	46.4
				Heavy	DVWGIEGPIDAAFT[13C-15N-R]	828.91	957.50	2	1

Light peptides represent endogenous peptides in plasma. ^bheavy peptides represent SIS peptides (>95% purity). ^cIons represent the top 3 ions, where bold type indicates the ions used in quantitation. ^dDP, ^eCE, and ^fRT represent declustering potential, collisional energy, and average retention time, respectively.