Table 2. Identification by mass spectrometry of proteins differentially expressed in the retina of parkinsonian monkeys.
| Spot no. | Protein | Accession no. a | pI exp. / pI theor. b | Mr exp. / Mr theor. b | Analysis methodb | MALDI-TOFc Score / Sequence coverage / Number of peptides | LC-MS/MSd Score / Sequence coverage / Number of peptides |
|---|---|---|---|---|---|---|---|
| 1 | α-Enolase | P06733 (S, Hs), NP_001419 (N, Hs) | 4.75/6.99 | 48.2/47.1 | LC-MS/MS, MALDI-TOF | 133/53/16 | 244.30/39/12 |
| 2 | ATP synthase, subunit β | P06576 (S, Hs) | 4.75/5.00 | 52.4/51.8 | LC-MS/MS | 378.20/52/21 | |
| 3 | S-Arrestin | P10523 (S, Hs) | 6.25/6.14 | 51.5/45.1 | LC-MS/MS | 67.24/10/5 | |
| 5 | β-Crystallin B2 | XP_001098886 (N, Mm) | 6.14/6.54 | 27.7/23.2 | MALDI-TOF | 261/60/15 | |
| 7 | Heat shock 70 kDa protein 8 (HSC70) | P11142 (N, Hs) | 5.08/5.37 | 75.0/70.8 | LC-MS/MS | 65.84/8/4 | |
| 12 | Stathmin | P16949 (N, Hs) | 5.53/5.77 | 16.5/17.2 | LC-MS/MS | 31.58/15/2 | |
| 13 | NG,NG-Dimethylarginine dimethylaminohydrolase 1 (DDAH1) | O94760 (S, Hs) | 4.93/5.53 | 15.2/30.1 | LC-MS/MS | 152.41/34/8 | |
| 18 | DDAH1 | O94760 (S, Hs), NP_036269 (N, Hs) | 5.32/5.53 | 36.9/30.1 | LC-MS/MS, MALDI-TOF | 171/63/16 | 218.67/58/13 |
| 20 | γ-Enolase | P09104 (S, Hs) | 5.44/4.91 | 32.2/47.1 | LC-MS/MS | 23.87/6e / 2e | |
| 21 | Glucose-regulated 78 kDa protein (GRP78) | P11021 (S, Hs) | 4.67/5.01 | 82.1/72.3 | LC-MS/MS | 68.31/9/4 | |
| 31 | Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) | P04406 (S, Hs) | 5.49/8.58 | 37.4/35.6 | LC-MS/MS | 53.30/10/3 | |
| 33 | Inorganic pyrophosphatase (PPA1) | Q4R543 (S, Mf), XP_001164495 (N, Pt) | 5.33/5.54 | 34.1/32.6 | LC-MS/MS, MALDI-TOF | 231/65/18 | 135.79/35/8 |
| 34 | Calbindin | P05937 (S, Hs) | 4.16/4.70 | 25.6/29.9 | LC-MS/MS | 17.43/8e/ 2e | |
| 37 | Nucleoside diphosphate kinase B (NDPK B) | P22392 (S, Hs) | 5.30/8.52 | 16.8/17.3 | LC-MS/MS | 44.49/25/3 | |
| 42 | Cytochrome c oxidase (COX), subunit 5A | Q53CF8 (S, Mm) | 4.69/5.01 | 13.1/12.5 | LC-MS/MS | 36.40/16/2 | |
| 91 | γ-Synuclein | Q2PFW6 (S, Mf) | 4.50/4.98 | 15.4/13.3 | LC-MS/MS | 96.86/49/6 | |
| 115 | S-Arrestin | P10523 (S, Hs) | 6.06/6.14 | 50.6/45.1 | LC-MS/MS | 177.66/27/10 | |
| 237 | γ-Enolase | P09104 (S, Hs), AAV67362 (N, Mf) | 4.54/4.91 | 48.5/47.1 | LC-MS/MS, MALDI-TOF | 294/73/21 | 204.93/44/13 |
For each spot the protein identified is indicated together with its accession number in the interrogated polypeptide database (N, NCBInr; S, Swiss-Prot) and the corresponding primate species (Hs, human; Mf, long-tailed macaque; Mm, rhesus macaque; Pt, chimpanzee).
The isoelectric point (pI) and relative molecular mass (Mr) are also given, both experimental and theoretical, together with the MS method(s) used for its identification.
The MOWSE score is indicated together with the fraction (%) of protein sequence covered by the identified peptides and the number of these represented in the mass fingerprint.
The corresponding score is indicated together with the fraction (%) of sequence and the number of peptides identified.
Peptides identified by de novo sequencing using the Sherenga algorithm.