Table 1. Comparison of AMPA-R and KA-R interactomes by Mass Spectrometry.
Known primary interactors (left) as well as candidate interactors (right) are listed by common name and IPI number. The spectrum count (spec), peptide count (pep) and % coverage (%AA) identified by LC-MS/MS as well as the normalized (norm) abundance of the protein relative to the IPed target protein are listed for proteins in both the GluA2 (A2) and GluK2 (K2) preparations. The current annotated rat protein database does not provide complete representation of the proteins in the rat genome. Thus, to identify Shisa-6, 9, and Neto-1 (shown in italics) we searched against a concatenated database consisting of the humanmouse-rat protein databases. References of known and candidate interactors are provided in the supplementary material.
known primary interactors | |||||
---|---|---|---|---|---|
IPI | GluA2 spec,pep (%AA) |
GluA2 norm |
GluK2 spec,pep (%AA) |
GluK2 norm |
Common Name |
IPI00780113.1 | 2526, 193 (71.3)• | 1.0000 | 17, 11 (17.2)• | 0.0215 | GluA2 |
IPI00324555.2 | 876, 129 (60.4)• | 0.3468 | 6, 3 (5.1) | 0.0076 | GluA1 |
IPI00231095.1 | 873, 121 (56.5)• | 0.3456 | 6, 4 (4.8) | 0.0076 | GluA3 |
IPI00195445.1 | 585, 91 (48.7)• | 0.2316 | 3, 2 (2.4) | 0.0038 | GluA4 |
IPI00207460.1 | 212, 26 (34.0)• | 0.0839 | 0, 0 (0.0) | 0.0000 | TARP gamma-3 |
IPI00201313.4 | 193, 28 (39.6)• | 0.0764 | 0, 0 (0.0) | 0.0000 | TARP gamma-2 |
IPI00207426.1 | 162, 28 (36.8)• | 0.0641 | 5, 2 (8.3) | 0.0063 | TARP gamma-8 |
IPI00207431.1 | 78, 13 (32.4)• | 0.0309 | 0, 0 (0.0) | 0.0000 | TARP gamma-4 |
IPI00214444.1 | 11, 4 (23.30• | 0.0044 | 0, 0 (0.0) | 0.0000 | TARP gamma-7 |
IPI00207430.1 | 3, 2 (6.9) | 0.0012 | 0, 0 (0.0) | 0.0000 | TARP gamma-5 |
IPI00366152.2 | 18, 6 (13.1)• | 0.0071 | 0, 0 (0.0) | 0.0000 | CNIH-2 |
IPI00358957.3 | 11, 4 (9.0) | 0.0044 | 0, 0 (0.0) | 0.0000 | CNIH-3 |
IPI00956073.1 | 147, 13 (26.2) | 0.0582 | 0, 0 (0.0) | 0.0000 | Shisa-9/CKAMP-44 |
IPI00566635.2 | 255, 61 (65.1)• | 0.1010 | 28, 10 (16.0)• | 0.0354 | PSD-95 |
IPI00777470.1 | 80, 31 (40.7)• | 0.0317 | 208, 62 (62.7)• | 0.2633 | SAP-97 |
IPI00650099.1 | 53, 21 (27.9)• | 0.0210 | 140, 48 (42.4)• | 0.1772 | PSD-93 |
IPI00568474.1 | 28, 14 (19.6)• | 0.0111 | 27, 11 (10.0) | 0.0342 | SAP-102 |
IPI00208830.1 | 2,.2 (3.0) | 0.0008 | 0, 0 (0.0) | 0.0000 | Grip1 |
IPI00409970.1 | 0, 0 (0.0) | 0.0000 | 2, 2 (6.3) | 0.0025 | Grip2 |
IPI00204506.1 | 5, 5 (6.7)• | 0.0020 | 42, 20 (22.8)• | 0.0532 | protein4.1 |
IPI00210635.2 | 16, 13 (19.5)• | 0.0063 | 32, 20 (36.0)• | 0.0405 | NSF |
IPI00471901.3 | 11, 6 (8.4)• | 0.0044 | 10, 6 (10.2)• | 0.0127 | AP-2 alpha2 |
IPI00389753 1 | 6, 6 (9.3)• | 0.0024 | 10, 6 (7.6) | 0.0127 | AP-2 beta |
IPI00203346.4 | 5, 4 (6.3)• | 0 0020 | 8, 6 (10.1)• | 0.0101 | AP-2 alpha1 |
IPI00196530.1 | 4, 3 (5.7) | 0.0016 | 5, 4 (11.5)• | 0.0063 | AP-2 mu |
IPI00198371.1 | 2, 2 (14.1) | 0.0008 | 4, 3 (24.6) | 0.0051 | AP-2 sigma |
IPI00324708.1 | 0, 0 (0.0) | 0.0000 | 790, 88 (47.8)• | 1.0000 | GluK2 |
IPI00207006.1 | 0, 0 (0.0) | 0.0000 | 190, 52 (48.0)• | 0.2405 | GluK5 |
IPI00231400.2 | 0, 0 (0.0) | 0.0000 | 187, 36 (29.1)• | 0.2367 | GluK1 |
IPI00231277.4 | 2, 2 (2.2)• | 0.0006 | 686, 77 (45.4)• | 0.8684 | GluK3 |
IPI00326553.1 | 0, 0 (0.0) | 0.0000 | 105, 32 (34 5)• | 0.1329 | GluK4 |
IPI00359373.3 | 0, 0 (0.0) | 0.0000 | 125, 37 (59.7)• | 0.1582 | Neto-2 |
IPI00367046.2 | 0, 0 (0.0) | 0.0000 | 37, 14 (38.3) | 0 0468 | Neto-1 |
IPI00370061.1 | 0, 0 (0.0) | 0.0000 | 19, 14 (22.8)• | 0.0241 | Kelch |
candidate interactors | |||||
---|---|---|---|---|---|
IPI | GluA2 spec,pep (%AA) |
GluA2 norm |
GluK2 spec,pep (%AA) |
GluK2 norm |
Common Name |
IPI00763858.2 | 0, 0 (0.0) | 0.0000 | 9, 5 (13.3) • | 0.0114 | MAGUK p55 |
IPI00365736.3 | 14, 11 (12.0)• | 0.0055 | 5, 5 (6.1) | 0.0063 | Liprin alpha 3 |
IPI00392157.3 | 0, 0 (0.0) | 0.0000 | 14, 13 (13.9)• | 0.0177 | Liprin alpha 4 |
IPI00388795.3 | 11, 8 (12.6) | 0.0044 | 94, 32 (36.6) | 0.1190 | CASK |
IPI00214300.1 | 0, 0 (0.0) | 0.0000 | 37, 12 (42.6) | 0.0342 | Lin 7 |
IPI00367477.1 | 56, 21 (29.8)• | 0.0222 | 0, 0 (0.0) | 0.0000 | NGL-3 (LRRC 4b) |
IPI00207958.1 | 11, 7 (11.4)• | 0.0044 | 0, 0 (0.0) | 0.0000 | NGL-l (LRRC 4c) |
IPI00360822.3 | 4, 3 (5.1) | 0.0018 | 0, 0 (0.0) | 0.0000 | LRRTM3 |
IPI00454354.1 | 3, 3 (4.3) | 0.0012 | 8, 6 (5.3)• | 0.0101 | LRRC 7 |
IPI00206020.1 | 3, 3 (19.2) | 0.0012 | 5, 3 (11.1) | 0.0063 | LRRC 59 |
IPI00372074.1 | 2, 2 (4.0) | 0.0008 | 0, 0 (0.0) | 0.0000 | LRRC 8 |
IPI00359172.2 | 0, 0 (0.0) | 0.0000 | 3, 2 (5.9) | 0.0038 | LRRC 47 |
IPI00367715.3 | 2, 2 (3.9) | 0.0008 | 0, 0 (0.0) | 0.0000 | FLRT-2 |
IPI00829463.1 | 10, 8 (7.8)• | 0.0040 | 10, 7 (6.5)• | 0.0127 | Nrxn-1 |
IPI00195792.3 | 10, 7 (6 8)• | 0.0004 | 6, 6 (7.8)• | 0.0076 | Nrxn-2 |
IPI00829491.1 | 5, 4 (6.1) | 0.0020 | 4, 2 (2.7)• | 0.0051 | Nrxn-3 |
IPI00325649.1 | 3, 2 (4.9) | 0.0012 | 0, 0 (0.0) | 0.0000 | Nlgn-2 |
IPI00325804 1 | 0, 0 (0 0) | 0.0000 | 5, 2 (3.3)• | 0.0063 | Nlgn-3 |
IPI00764645.1 | 30, 15 (23.2)• | 0.0119 | 0, 0 (0.0) | 0.0000 | EphB2 |
IPI00189428.1 | 4, 3 (5.5) | 0.0016 | 0, 0 (0.0) | 0.0000 | EphB1 |
IPI00569433.1 | 3, 3 (6.7)• | 0.0012 | 0, 0 (0.0) | 0.0000 | EphA4 |
IPI00230960.1 | 2, 2 (4.8)• | 0.0008 | 0, 0 (0.0) | 0.0000 | EphA5 |
IPI00365395.2 | 2, 2 (13.4) | 0 0008 | 0, 0 (0.0) | 0.0000 | EphrinB2 |
IPI00411236.1 | 10, 7 (8.1)• | 0.0040 | 13, 8 (9.3)• | 0.0165 | Latrophillin 1 |
IPI00561212.4 | 9, 8 (9.2)• | 0.0036 | 0, 0 (0.0) | 0.0000 | Latrophillin 3 |
IPI00568123.2 | 4, 3 (4.3) | 0.0016 | 0, 0 (0.0) | 0.0000 | Latrophillin 2 |
IPI00568245.2 | 0, 0 (0.0) | 0.0000 | 480, 136• | 0.6076 | myosin 18 |
IPI00193933.3 | 3, 3 (6.0) | 0.0012 | 0, 0 (0.0) | 0.0000 | DHHC5 |
IPI00357941.4 | 7, 7 (5.8) | 0.0028 | 0, 0 (0.0) | 0.0000 | RTPT delta |
IPI00231945.4 | 3, 2 (3.3) | 0.0012 | 0, 0 (0.0) | 0.0000 | RTPT |
IPI00565098.2 | 30, 13 (25.8)• | 0 0119 | 0, 0 (0.0) | 0.0000 | GSG1L |
IPI00939232.1 | 2, 2 (5.1) | 0.0006 | 0, 0 (0.0) | 0.0000 | Shisa-6 |
IPI00214724.3 | 4,20 (12.1)• | 0.0016 | 0, 0 (0.0) | 0.0000 | PPRT 1 |
IPI00366048.3 | 38, 10 (38.1) | 0.0150 | 0, 0 (0.0) | 0.0000 | PPRT 2 |
IPI00207495.3 | 0, 0 (0.0) | 0.0000 | 32, 13 (24.5)• | 0.0405 | pentraxin-2 (Narp) |
IPI00192125.1 | 0, 0 (0 0) | 0.0000 | 58, 19 (29.9)• | 0.0734 | pentraxin-1 |
IPI00212317.1 | 0, 0 (0.0) | 0.0000 | 69, 16 (36.6)• | 0.0873 | pentraxin receptor |
IPI00206558.4 | 19, 9 (15.1)• | 0.0075 | 0, 0 (0.0) | 0.0000 | Olfm-1 |
IPI00337161.1 | 5, 3 (8.7) | 0.0020 | 0, 0 (0.0) | 0.0000 | Olfm-3 |
Black dots represent proteins which were also found in a smaller scale duplication experiment.