Table 3. Proteins in the albumin-depleted aqueous humor fraction of patients with cataracts identified with high confidence using LC-MS/MS.

Swiss-Prot number	Protein common name	Plasma protein	MW (kDa)	Distinct sequences	Minimum peptide q-value	Peptide sequence with minimum q-value
229479	740525A lipoprotein Gln I	NF	28	8	3.42E-06	VSFLSALEEYTK
P43652	Afamin	Yes	69	3	2.01E-07	DADPDTFFAK
P02763	Alpha-1-acid glycoprotein 1 [1]	Yes	24	4	0.00E+00	EQLGEFYEALDCLR
P19652	Alpha-1-acid glycoprotein 2	Yes	24	3	1.42E-07	TLMFGSYLDDEK
P01011	Alpha-1-antichymotrypsin, Isoform 1	Yes	48	7	1.85E-10	AVLDVFEEGTEASAATAVK
P01011	Alpha-1-antichymotrypsin, Isoform 2	Yes	48	3	1.44E-08	LYGSEAFATDFQDSAAAK
P01009	Alpha-1-antitrypsin [1,15]	Yes	47	16	0.00E+00	DTEEEDFHVDQVTTVK
P04217	Alpha-1B-glycoprotein	Yes	54	2	7.26E-05	CEGPIPDVTFELLR
P25311	Alpha-2-glycoprotein 1, zinc	Yes	34	4	3.42E-06	AYLEEECPATLR
P02765	Alpha-2-HS-glycoprotein	Yes	39	4	3.93E-06	EHAVEGDCDFQLLK
P01023	Alpha-2-macroglobulin [1]	Yes	163	5	1.06E-07	NEDSLVFVQTDK
Q06481	Amyloid-like protein 2, Isoform 1	NF	87	2	1.65E-05	VPYVAQEIQEEIDELLQEQR
Q7KZ97	Antithrombin III variant [1]	Yes	53	8	4.50E-06	DDLYVSDAFHK
P02647	Apolipoprotein A-I [1,5]	Yes	31	14	6.42E-09	DYVSQFEGSALGK
Q76EI7	Apolipoprotein A-II	Yes	3	3	5.70E-08	EPCVESLVSQYFQTVTDYGK
P06727	Apolipoprotein A-IV [1]	Yes	45	3	4.82E-06	SLAPYAQDTQEK
P05090	Apolipoprotein D [1]	Yes	21	2	3.17E-08	CPNPPVQENFDVNK
P02649	Apolipoprotein E [1]	Yes	36	5	4.38E-07	VQAAVGTSAAPVPSDNH
P02749	Beta-2-glycoprotein 1	Yes	38	4	3.37E-06	CSYTEDAQCIDGTIEVPK
P61769	Beta-2-microglobulin [5]	Yes	14	3	5.63E-04	VNHVTLSQPK
O94985	Calsyntenin 1 isoform 2	NF	110	2	3.07E-08	AASEFESSEGVFLFPELR
P00450	Ceruloplasmin [1]	Yes	122	20	7.16E-08	HYYIGIIETTWDYASDHGEK
P10909	Clusterin [15]	Yes	52	13	0.00E+00	EILSVDCSTNNPSQAK
P01024	Complement C3	Yes	187	14	2.12E-07	SGSDEVQVGQQR
P02462	Collagen alpha-1(IV) chain [1]	Yes	161	2	0.00E+00	GDPGLKGDK
P0C0L4	Complement C4-A [1]	Yes	193	8	1.24E-08	VLSLAQEQVGGSPEK
P00751	Complement factor B, Isoform 1	Yes	86	3	4.68E-06	EAGIPEFYDYDVALIK
P01034	Cystatin C [1,5]	Yes	16	4	7.15E-08	ALDFAVGEYNK
Q9UBP4	Dickkopf-related protein 3	NF	38	7	4.75E-11	SAVEEMEAEEAAAK
Q12805	EGF-containing fibulin-like extracellular matrix protein 1	Yes	55	2	4.05E-05	IQCAAGYEQSEHNVCQDIDECTAGTHNCR
P06396	Gelsolin, Isoform 1	Yes	86	7	5.52E-07	PALPAGTEDTAK
P22352	Glutathione peroxidase 3	Yes	26	4	2.10E-06	NSCPPTSELLGTSDR
P00739	Haptoglobin-related protein, Isoform 1	Yes	39	4	5.42E-06	AVGDKLPECEAVCGKPK
Q8IZI0	Hemoglobin beta chain variant Hb-I Toulouse	NF	12	7	3.31E-08	VNVDEVGGEALGR
P69905	Hemoglobin subunit alpha [5]	Yes	15	5	4.97E-11	VGAHAGEYGAEALER
P68871	Hemoglobin subunit beta [5]	Yes	16	9	3.31E-08	VNVDEVGGEALGR
A0N071	Hemoglobin subunit delta [5]	Yes	16	4	7.12E-06	VLGAFSDGLAHLDNLK
P02790	Hemopexin	Yes	52	14	2.24E-08	GECQAEGVLFFQGDR
P04196	Histidine-rich glycoprotein	Yes	60	3	2.98E-06	DSPVLIDFFEDTER
Q0VAC5	HP protein	NF	38	7	1.10E-06	TEGDGVYTLNNEK
P10745	Interphotoreceptor retinoid-binding protein	NF	135	11	2.03E-07	TAVDLESLASQLTADLQEVSGDHR
Q2XP30	Mutant beta-globin	NF	2	2	4.24E-05	VHLTPEEK
Q9UBM4	Opticin	NF	37	2	1.51E-07	EGDSFEVLPLR
P36955	Pigment epithelium-derived factor	Yes	46	12	0.00E+00	DTDTGALLFIGK
P05155	Plasma protease C1 inhibitor	Yes	55	4	2.98E-06	LEDMEQALSPSVFK
Q9P173	PRO2275	NF	13	5	3.20E-10	VFSNGADLSGVTEEAPLK
P41222	Prostaglandin-H2 D-isomerase	Yes	21	10	0.00E+00	EAQVSVQPNFQQDK
P02787	Serotransferrin [1]	Yes	77	50	2.57E-11	FDEFFSEGCAPGSK
P02766	Transthyretin [1,15,16]	Yes	16	12	2.24E-08	KAADDTWEPFASGK
P68871	Unnamed protein product	NF	16	8	3.31E-08	VNVDEVGGEALGR
P02774	Vitamin D-binding protein [1,16]	Yes	53	7	3.22E-08	VPTADLEDVLPLAEDITNILSK

NF, not found in current list of identified plasma proteins from Anderson et al. [21]. Proteins identified by previous AH proteome analyses (Stastna et al. [1], Rohde et al. [5], Funding et al. [15], and Duan et al. [16]) are marked at the end of the protein name by the appropriate reference.