Table 1. Human candidate retinal proteins (FDR <1%) that were A1. documented exclusively in the control group based on zero LFQ values in the glaucoma group and therefore named “unique”; A2. significantly (p < 0.05) or distinctly (p < 0.1) decreased in the glaucoma group; B1. documented exclusively in the glaucoma group based on zero LFQ values in the control group and therefore named “unique”; B2. significantly (p < 0.05) or distinctly (p < 0.1) increased in the glaucoma group.
| Protein name | Gene name | Entry | Entry name | LCM | ||
|---|---|---|---|---|---|---|
| A1: “Unique” control retinal proteins | ||||||
| V-type proton ATPase 116 kDa subunit a isoform 1 (VPP1) | ATP6V0A1 | B7Z641 | B7Z641_HUMAN | √ | ||
| Arrestin-C (cArr) | ARR3 | P36575 | ARRC_HUMAN | |||
| Protein NipSnap homolog 3A | NIPSNAP3A | Q9UFN0 | NPS3A_HUMAN | |||
| Heterogeneous nuclear ribonucleoprotein Q (hnRPQ) | SYNCRIP | F6UXX1 | F6UXX1_HUMAN | |||
| 6-phosphofructokinase, liver type | PFKL | P17858 | K6PL_HUMAN | |||
| Elongation factor Tu, mitochondrial | TUFM | P49411 | EFTU_HUMAN | |||
| 40S ribosomal protein S19 | RPS19 | P39019 | RS19_HUMAN | √ | ||
| Peripherin-2 | PRPH2 | P23942 | PRPH2_HUMAN | |||
| Protein SET | SET | Q01105 | SET_HUMAN | |||
| Reticulocalbin-2 | RCN2 | Q14257 | RCN2_HUMAN | |||
| A2: Glaucoma decreased retinal proteins | Glaucoma/Control | p-value | ||||
| Calcium-binding mitochondrial carrier protein Aralar2 | SLC25A13 | Q9UJS0 | CMC2_HUMAN | 0,15 | 0,0060 | |
| Methyl-CpG-binding protein 2 (MeCp2) | MECP2 | P51608 | MECP2_HUMAN | 0,15 | 0,0117 | √ |
| NADH dehydrogenase [ubiquinone] 1 ß subcomplex sub. 9 (CI-B22) | NDUFB9 | Q9Y6M9 | NDUB9_HUMAN | 0,15 | 0,0157 | |
| 40S ribosomal protein S7 | RPS7 | P62081 | RS7_HUMAN | 0,17 | 0,0748 | |
| 3-hydroxyacyl-CoA dehydrogenase type-2 | HSD17B10 | Q99714 | HCD2_HUMAN | 0,18 | 0,0357 | |
| Trifunctional enzyme subunit α, mitochondrial | HADHA | P40939 | ECHA_HUMAN | 0,19 | 0,0498 | |
| Myosin-11/9 | MYH11 | P35749 | MYH11_HUMAN | 0,21 | 0,0968 | |
| 60S acidic ribosomal protein P0; P0-like | RPLP0 | P05388 | RLA0_HUMAN | 0,27 | 0,0238 | √ |
| Pyruvate dehydrogenase E1 comp. sub. ß, mitochondrial (PDHE1-B) | PDHB | P11177 | ODPB_HUMAN | 0,31 | 0,0274 | √ |
| High mobility group protein HMG-I/HMG-Y | HMGA1 | P17096 | HMGA1_HUMAN | 0,40 | 0,0239 | |
| Small nuclear ribonucleoprotein Sm D3 | SNRPD3 | P62318 | SMD3_HUMAN | 0,43 | 0,0109 | |
| (ATP-dependent) 6-phosphofructokinase, muscle type | PFKM | P08237 | PFKAM_HUMAN | 0,47 | 0,0743 | √ |
| Vesicle-fusing ATPase | NSF | P46459 | NSF_HUMAN | 0,49 | 0,0657 | √ |
| Heterogeneous nuclear ribonucleoprotein L | HNRNPL | P14866 | HNRPL_HUMAN | 0,51 | 0,0777 | |
| PC4 and SFRS1-interacting protein (DFS70) | PSIP1 | O75475 | PSIP1_HUMAN | 0,56 | 0,0271 | |
| Cytochrome c oxidase subunit 7A2, mitochondrial (COX7A2) | COX7A2 | P14406 | CX7A2_HUMAN | 0,58 | 0,0893 | |
| ADP/ATP translocase 3 (ANT3) | SLC25A6 | P12236 | ADT3_HUMAN | 0,61 | 0,0199 | √ |
| Ras-related protein Rab-11A; B | RAB11A | Q15907 | RB11B_HUMAN | 0,62 | 0,0174 | |
| Heterogeneous nuclear ribonucleoprotein U | HNRNPU | Q00839 | HNRPU_HUMAN | 0,62 | 0,0494 | |
| Histone H1.0 | H1F0 | P07305 | H10_HUMAN | 0,67 | 0,0729 | |
| Putative elongation factor 1-α-2;1; like 3 | EEF1A1P5 | Q5VTE0 | EF1A3_HUMAN | 0,69 | 0,0148 | √ |
| Guanine nucleotide-binding protein G(i) subunit α-2 | GNAI2 | P04899 | GNAI2_HUMAN | 0,69 | 0,0930 | √ |
| B1: “Unique” glaucoma retinal proteins | ||||||
| Protein name | Gene name | Entry | Entry name | LCM | ||
| Glutathione synthetase | GSS | P48637 | GSHB_HUMAN | |||
| Septin-8 | SEPT8 | Q92599 | SEPT8_HUMAN | |||
| Opticin | OPTC | Q9UBM4 | OPT_HUMAN | |||
| Calcium-binding mitochondrial carrier protein Aralar1 | SLC25A12 | O75746 | CMC1_HUMAN | √ | ||
| Serpin B6 | SERPINB6 | P35237 | SPB6_HUMAN | |||
| Neuroplastin | NPTN | Q9Y639 | NPTN_HUMAN | |||
| Carbonyl reductase [NADPH] 1 | CBR1 | P16152 | CBR1_HUMAN | |||
| 4-trimethylaminobutyraldehyde dehydrogenase | ALDH9A1 | B4DXY7 | B4DXY7_HUMAN | |||
| ß-crystallin A3;isoform A1/Σ4/Σ7/Σ8 | CRYBA1 | P05813 | CRBA1_HUMAN | |||
| Ig γ-2 chain C region | IGHG2 | P01859 | IGHG2_HUMAN | |||
| ß-crystallin B1 | CRYBB1 | P53674 | CRBB1_HUMAN | |||
| Phakinin | BFSP2 | Q13515 | BFSP2_HUMAN | |||
| α-1-antitrypsin;Short peptide from AAT | SERPINA1 | P01009 | A1AT_HUMAN | |||
| Sideroflexin-1 | SFXN1 | Q9H9B4 | SFXN1_HUMAN | √ | ||
| X-ray repair cross-complementing protein 5 | XRCC5 | P13010 | XRCC5_HUMAN | |||
| N(G), N(G)-dimethylarginine dimethylaminohydrolase 1 | DDAH1 | B4DGT0 | B4DGT0_HUMAN | |||
| Hippocalcin-like protein 1 | HPCAL1 | P37235 | HPCL1_HUMAN | |||
| Thy-1 membrane glycoprotein | THY1 | J3QRJ3 | J3QRJ3_HUMAN | |||
| V-type proton ATPase subunit G 1/G2 | ATP6V1G1 | O75348 | VATG1_HUMAN | |||
| Cytosolic non-specific dipeptidase | CNDP2 | Q96KP4 | CNDP2_HUMAN | |||
| B2: Glaucoma increased retinal proteins | Glaucoma/Control | p-value | ||||
| Retinal dehydrogenase 1 (RALDH 1) | ALDH1A1 | P00352 | AL1A1_HUMAN | 11,73 | 0,0080 | |
| High mobility group protein B1; Putative B1-like 1 | HMGB1 | Q5T7C4 | Q5T7C4_HUMAN | 7,39 | 0,0745 | |
| Vesicle-associated membrane protein-associated protein B/C | VAPB | O95292 | VAPB_HUMAN | 6,51 | 0,0023 | √ |
| Annexin A2; Putative A2-like | ANXA2 | P07355; | ANXA2_HUMAN | 4,81 | 0,0962 | |
| Reticulon-3 | RTN3 | O95197-3 | RTN3_HUMAN | 3,69 | 0,0922 | √ |
| Glutathione S-transferase Mu 3 (hGSTM3-3) | GSTM3 | P21266 | GSTM3_HUMAN | 3,61 | 0,0529 | |
| Dihydropteridine reductase | QDPR | P09417 | DHPR_HUMAN | 2,37 | 0,0950 | |
| Retinol-binding protein 3 (IRBP) | RBP3 | P10745 | RET3_HUMAN | 2,12 | 0,0427 | |
| α-crystallin B chain (HspB5) | CRYAB | P02511 | CRYAB_HUMAN | 1,66 | 0,0599 | √ |
| Endoplasmin | HSP90B1 | P14625 | ENPL_HUMAN | 1,58 | 0,0575 | √ |
| Serotransferrin | TF | P02787 | ENPL_HUMAN | 1,46 | 0,0872 | √ |
| Rab GDP dissociation inhibitor α | GDI1 | P31150 | ENPL_HUMAN | 1,40 | 0,0541 | |
In case of multiple isoforms, only the first gene, entry accession and entry name are given. In case of candidate recovery in the porcine retinal GCL using LCM, candidates are highlighted by check mark in the LCM column. ANT3, MECP2 and DFS70 presence was supported by MS detection of diagnostic m/z peaks in human LCM preparation (illustrated in Fig. 10, not highlighted in the table).