A validated analysis pipeline for mass spectrometry-based vitreous proteomics: new insights into proliferative diabetic retinopathy

Weber, Sarah R.; Zhao, Yuanjun; Ma, Jingqun; Gates, Christopher; da Veiga Leprevost, Felipe; Basrur, Venkatesha; Nesvizhskii, Alexey I.; Gardner, Thomas W.; Sundstrom, Jeffrey M.

doi:10.1186/s12014-021-09328-8

Clinical Proteomics

Table 2 Experiment 2 vitrectomy patient demographics

From: A validated analysis pipeline for mass spectrometry-based vitreous proteomics: new insights into proliferative diabetic retinopathy

Plex	Study ID	Subphenotype	Exp 2: used in pool 2	Surgical indication	Sex	Age	Lens status	Past ocular history			Intravitreal anti-VEGF prior to surgery	Weeks between last injection and sample collection	Prior PRP	Weeks between last laser and sample collection	Hemoglobin Conc. (g/dL)	Bilirubin Conc. (mg/dL)
Plex	Study ID	Subphenotype	Exp 2: used in pool 2	Surgical indication	Sex	Age	Lens status	PVD	Cataract	Other	Intravitreal anti-VEGF prior to surgery	Weeks between last injection and sample collection	Prior PRP	Weeks between last laser and sample collection	Hemoglobin Conc. (g/dL)	Bilirubin Conc. (mg/dL)
2.1	193	CTL	Yes	MH/VMT OS	F	62	Pseudophakic	Yes	Yes	None	No	–	No	–	–	–
2.1	229	CTL	Yes	ERM/MH OD	M	71	Phakic	Yes	Yes	None	No	–	No	–	–	–
2.1	232	CTL	No	ERM/MH OD	F	49	Phakic	Yes	Yes	None	No	–	No	–	–	–
2.1	423	PDR-L	No	PDR: NCVH OD	M	49	Phakic	Yes	Yes	None	Yes	4	Yes	Unknown	0	0.00225
2.1	503	PDR-L	Yes	PDR: NCVH OS	F	71	Pseudophakic	Yes	Yes	ERM	No	–	Yes	13	0	0.00235
2.1	508	PDR-L	No	PDR: NCVH OS	M	49	Phakic	Yes	Yes	None	No	–	Yes	11	0.00010	0.00319
2.1	516	PDR-M	Yes	PDR: NCVH OD	M	56	Pseudophakic	Yes	Yes	None	Yes	2	Yes	Unknown	0.00050	0.00262
2.1	526	PDR-M	Yes	PDR: NCVH OS	F	27	Phakic	Yes	No	None	Yes	6	Yes	7	0.00020	0.00271
2.1	–	Pool 1.6
2.1	–	Pool 2.1
2.2	242	CTL	Yes	ERM/MH OD	F	68	Phakic	Yes	Yes	None	No	–	No	–	–	–
2.2	334	CTL	No	ERM OS	M	77	Phakic	Yes	Yes	Hyperopia	No	–	No	–	–	–
2.2	377	CTL	Yes	MH OS	F	59	Phakic	Yes	Yes	None	No	–	No	–	–	–
2.2	554	PDR-L	Yes	PDR: NCVH OS	M	37	Phakic	Yes	Yes	None	No	–	Yes	63	0	0.00231
2.2	715	PDR-L	No	PDR: NCVH OS	M	42	Phakic	No	Yes	None	Yes	33	Yes	40	0	0.00205
2.2	728	PDR-L	Yes	PDR: NCVH OD	F	34	Phakic	No	Yes	None	Yes	1	Yes	24	0	0.00332
2.2	661	PDR-M	Yes	PDR: NCVH OS	F	64	Pseudophakic	Yes	Yes	None	Yes	20	Yes	Unknown	0.00080	0.00281
2.2	808	PDR-M	Yes	PDR: NCVH OD	F	56	Pseudophakic	Yes	Yes	None	Yes	6	Yes	Unknown	0.00030	0.00912
2.2	–	Pool 1.7
2.2	–	Pool 2.2
2.3	519	CTL	Yes	MH OS	F	76	Pseudophakic	Yes	Yes	None	No	–	No	–	–	–
2.3	546	CTL	Yes	MH OD	F	74	Phakic	Yes	Yes	None	No	–	No	–	–	–
2.3	780	PDR-L	Yes	PDR: NCVH OD	M	53	Phakic	Yes	Yes	None	Yes	62	Yes	Unknown	0	0.00276
2.3	842	PDR-L	Yes	PDR:NCVH OD	F	58	Phakic	Yes	Yes	None	Yes	2	Yes	Unknown	0	0.00252
2.3	856	PDR-L	Yes	PDR: NCVH OS	F	55	Phakic	Yes	Yes	ERM	Yes	30	Yes	Unknown	0	0.00247
2.3	942	PDR-L	Yes	PDR: NCVH OD	F	45	Phakic	Yes	Yes	ERM	No	–	Yes	13	0	0.00246
2.3	890	PDR-M	Yes	PDR: NCVH OS	F	73	Pseudophakic	Yes	Yes	None	Yes	5	Yes	Unknown	0.00170	0.00280
2.3	934	PDR-M	Yes	PDR: NCVH OD	M	52	Phakic	Yes	Yes	None	No	–	Yes	Unknown	0.00140	0.00244
2.3	-	Pool 1.8
2.3	-	Pool 2.3
2.4	875	CTL	Yes	MH OS	F	69	Pseudophakic	Yes	Yes	None	No	–	No	–	–	–
2.4	988	CTL	Yes	MH OD	F	56	Phakic	Yes	Yes	None	No	–	No	–	–	–
2.4	315	PDR-H	No	PDR: NCVH OS	M	54	Phakic	Yes	Yes	None	No	–	Yes	Unknown	0.00660	0.00366
2.4	414	PDR-H	No	PDR: NCVH OD	F	45	Phakic	Yes	Yes	None	Yes	33	Yes	108	0.00520	0.00317
2.4	449	PDR-H	No	PDR: NCVH OS	M	54	Phakic	Yes	Yes	None	Yes	26	Yes	Unknown	0.00840	0.00286
2.4	523	PDR-H	No	PDR: NCVH OS	M	44	Phakic	Yes	No	None	No	–	Yes	Unknown	0.00510	0.00327
2.4	632	PDR-H	No	PDR: NCVH OS	F	78	Pseudophakic	Yes	Yes	None	No	–	Yes	Unknown	0.00490	0.00342
2.4	682	PDR-H	No	PDR: NCVH OS	F	58	Phakic	Yes	Yes	None	Yes	10	Yes	Unknown	0.00500	0.00316
2.4	–	Pool 1.9
2.4	–	Pool 2.4
–	951	PDR-L	Yes	PDR: NCVH OD	M	47	Phakic	N	Yes		N	–	Yes	6	0.00000	0.00245

Clinical information for patients from whom individual control and PDR samples and Pool2 aliquots were obtained
OS oculus sinister (left eye), OD oculus dexter (right eye), MH/VMT macular hole/vitreomacular traction, ERM epiretinal membrane, PDR: NCVH proliferative diabetic retinopathy: non-clearing vitreous haemorrhage, PVD posterior vitreous detachment, VEGF vascular endothelial growth factor, PRP pan-retinal photocoagulation

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