Table 1.
Proteins identified by MS-analysis of anti-otoferlin immuno-affinity capture from both rat (CL-48) and mouse (CL-99) cochlea membranes
| Accession | Protein | CL-99 mouse Specificity-ratio AP-Otof_vs_IgG | Identification MS/MS matches | Abundance normalized OT | CL-48 rat Specificity-ratio AP-Otof_vs_IgG | Identification MS/MS matches | Abundance normalized FT |
|---|---|---|---|---|---|---|---|
| OTOF_RAT | Otoferlin | 5337.72 | 77 | 471850 | 337.79 | 76 | 104813 |
| AT1A1_RAT | Sodium/potassium-transporting ATPase subunit α-1 | 3122.83 | 50 | 1205148 | 30.40 | 96 | 1255648 |
| AT1A3_RAT | Sodium/potassium-transporting ATPase subunit α-3 | 1465.36 | 43 | 879001 | 1837.14 | 88 | 1033972 |
| E41L2_MOUSE | Band 4.1-like protein 2 | 2140.55 | 84 | 1095333 | 1841.11 | 24 | 60963 |
| AINX_RAT | α-Internexin | 6867.19 | 50 | 685805 | 10.79 | 14 | 35343 |
| NFM_RAT | Neurofilament medium polypeptide | 416.25 | 53 | 365494 | 55.75 | 10 | 25277 |
| ZO1_MOUSE | Tight junction protein ZO-1 | 77.16 | 54 | 316586 | 268.71 | 4 | 5551 |
| NFH_MOUSE | Neurofilament heavy polypeptide | 204.23 | 43 | 778939 | 148.01 | 14 | 33070 |
| SYVC_RAT | Valine–tRNA ligase | 2213.23 | 30 | 222839 | 564.34 | 20 | 34709 |
| DYHC1_MOUSE | Cytoplasmic dynein 1 heavy chain 1 | 720.06 | 40 | 12029 | 83.15 | 5 | 259 |
| MAP1A_RAT | Microtubule-associated protein 1A | 1175.68 | 17 | 25327 | 1009.70 | 15 | 10000 |
| AP2B1_RAT | AP-2 complex subunit β | 12.80 | 18 | 77577 | 256.35 | 5 | 8702 |
| KTN1_MOUSE | Kinectin | 166.83 | 18 | 39455 | 18.94 | 5 | 3378 |
| SYEP_MOUSE | Bifunctional glutamate/proline–tRNA ligase | 220.31 | 15 | 30906 | 182.44 | 6 | 2017 |
| AT1B1_RAT | Sodium/potassium-transporting ATPase subunit β-1 | 2655.44 | 12 | 528908 | 163.22 | 9 | 960020 |
| THOC2_MOUSE | THO complex subunit 2 | 350.05 | 19 | 32697 | 128.76 | 1 | 1228 |
| SYDC_RAT | Aspartate–tRNA ligase, cytoplasmic | 663.92 | 15 | 40889 | 226.76 | 5 | 6012 |
| AP2M1_RAT | AP-2 complex subunit μ | 34.01 | 13 | 71248 | 349.04 | 7 | 31463 |
| G3P_RAT | Glyceraldehyde-3-phosphate dehydrogenase | 138.76 | 18 | 385951 | 116.67 | 1 | 5214 |
| DHB12_RAT | Estradiol 17-β-dehydrogenase 12 | 792.80 | 13 | 226082 | 204.47 | 5 | 14065 |
| TECR_RAT | Trans-2,3-enoyl-CoA reductase | 91.09 | 9 | 340731 | 201.07 | 9 | 109375 |
| S4A11_MOUSE | Sodium bicarbonate transporter-like protein 11 | 285.68 | 7 | 22901 | 574.01 | 10 | 25618 |
| G3BP1_MOUSE | Ras GTPase-activating protein-binding protein 1 | 1936.53 | 10 | 133366 | 249.11 | 6 | 12032 |
| AT2A2_RAT | Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 | 343.57 | 5 | 8408 | 312.43 | 11 | 21373 |
| SYIC_MOUSE | Isoleucine–tRNA ligase, cytoplasmic | 897.52 | 12 | 19129 | 172.17 | 3 | 2509 |
| AP2A2_RAT | AP-2 complex subunit α-2 | 18.04 | 8 | 25002 | 52.97 | 6 | 5130 |
| VDAC2_RAT | Voltage-dependent anion-selective channel protein 2 | 1296.57 | 8 | 234270 | 463.79 | 5 | 48350 |
| RAB10_MOUSE | Ras-related protein Rab-10 OS = Mus musculus GN = Rab10 | 93.03 | 7 | 284745 | 205.67 | 6 | 56357 |
| CPT1A_RAT | Carnitine O-palmitoyltransferase 1, liver isoform | 252.10 | 6 | 18780 | 323.36 | 7 | 16289 |
| ABD12_MOUSE | Monoacylglycerol lipase ABHD12 | 39.37 | 5 | 34497 | 379.34 | 7 | 25231 |
| B3AT_RAT | Band 3 anion transport protein | 384.25 | 6 | 15168 | 66.29 | 5 | 2122 |
| DHB11_RAT | Estradiol 17-β-dehydrogenase 11 | 617.70 | 7 | 63653 | 245.96 | 3 | 7379 |
| S61A1_RAT | Protein transport protein Sec61 subunit α isoform 1 | 3168.89 | 6 | 144024 | 361.26 | 4 | 23034 |
| S4A4_RAT | Electrogenic sodium bicarbonate cotransporter 1 | 281.99 | 5 | 7828 | 116.72 | 5 | 4033 |
| GTR1_RAT | Solute carrier family 2, facilitated glucose transporter member 1 | 443.08 | 5 | 56109 | 94.27 | 4 | 26919 |
| ALG2_MOUSE | α-1,3/1,6-mannosyltransferase ALG2 | 390.40 | 5 | 8839 | 28.93 | 4 | 8633 |
| NSF_MOUSE | Vesicle-fusing ATPase | 483.27 | 6 | 11228 | 99.26 | 2 | 1225 |
| VDAC3_RAT | Voltage-dependent anion-selective channel protein 3 | 1165.88 | 5 | 53167 | 519.99 | 3 | 36158 |
| SYRC_RAT | Arginine–tRNA ligase, cytoplasmic | 431.76 | 3 | 5835 | 147.08 | 5 | 1974 |
| THOC6_MOUSE | THO complex subunit 6 homolog | 1172.00 | 5 | 26504 | 68.87 | 2 | 1519 |
| TMM33_MOUSE | Transmembrane protein 33 | 263.85 | 4 | 55563 | 218.08 | 1 | 9988 |
| ZNT1_MOUSE | Zinc transporter 1 | 465.97 | 3 | 9477 | 463.94 | 2 | 9665 |
| PTSS1_RAT | Phosphatidylserine synthase 1 | 299.75 | 2 | 19963 | 374.61 | 3 | 9647 |
| SRP72_HUMAN | Signal recognition particle 72 kDa protein | 288.12 | 2 | 4206 | 362.12 | 3 | 10462 |
| NCKP1_RAT | Nck-associated protein 1 | 250.09 | 2 | 2138 | 60.87 | 1 | 526 |
| MBB1A_RAT | Myb-binding protein 1A | 175.19 | 2 | 2179 | 34.85 | 1 | 223 |
| MYP0_RAT | Myelin protein P0 | 16.21 | 43 | 37234494 | 2.61 | 68 | 10627302 |
| PLEC_RAT | Plectin | 33.62 | 102 | 51673 | 0.02 | 2 | 1297 |
| TBB5_MOUSE | Tubulin β-5 chain | 229.06 | 78 | 2449670 | 2.44 | 18 | 133357 |
| CN37_RAT | 2′,3′-cyclic-nucleotide 3′-phosphodiesterase | 23.19 | 37 | 1789388 | 3.25 | 37 | 423459 |
| NFL_RAT | Neurofilament light polypeptide | 617.59 | 44 | 1387637 | 3.47 | 21 | 90778 |
| MBP_RAT | Myelin basic protein | 16.88 | 43 | 10126599 | 2.94 | 9 | 326297 |
| HSP7C_RAT | Heat shock cognate 71 kDa protein | 90.86 | 36 | 489906 | 7.47 | 8 | 29964 |
| COCH_MOUSE | Cochlin | 40.67 | 24 | 241722 | 1.24 | 13 | 57796 |
| CKAP4_MOUSE | Cytoskeleton-associated protein 4 | 28.46 | 24 | 206725 | 2.56 | 5 | 12684 |
| MYO6_MOUSE | Unconventional myosin-VI | 13.15 | 25 | 84374 | 0.11 | 2 | 2127 |
| MYPR_MOUSE | Myelin proteolipid protein | 14.54 | 12 | 1413421 | 2.98 | 11 | 251283 |
| HHATL_MOUSE | Protein-cysteine N-palmitoyltransferase HHAT-like protein | 2549.21 | 11 | 207284 | 4.96 | 12 | 90049 |
| S12A2_MOUSE | Solute carrier family 12 member 2 | 454.19 | 13 | 33522 | 2.75 | 5 | 2656 |
| MYO1C_RAT | Unconventional myosin-Ic | 398.84 | 6 | 3033 | 0.29 | 2 | 2183 |
| S27A1_RAT | Long-chain fatty acid transport protein 1 | 0.00 | 5 | 8032 | 223.58 | 2 | 2935 |
| EAA1_RAT | Excitatory amino acid transporter 1 | 0.00 | 2 | 208 | 4.91 | 3 | 13989 |
| UIF_RAT | UAP56-interacting factor | 0.00 | 2 | 1783 | 97.93 | 1 | 3176 |
Columns (left to right): database entry, protein name, purification specificity by the respective protein ratio (rPV, see Materials and Methods), identification by the number of database-matched MS/MS spectra and estimated molecular abundance based on the abundancenorm score (calculated as the sum of PVs divided by the number of MS-accessible amino acids of the respective protein; Müller et al., 2010). Proteins with specificity ratios >10 (bold) were displayed in Fig. 1C.