Table 4.
iTRAQ identification of proteins with >20% decreased expression and peptide count >1 in regenerating sciatic nerve from ApoE4 mice compared with ApoE3 mice
| Protein name | Accession number | Protein MW | Protein PI | Peptide count | Total ion score, CI percentage | Best ion score | Average ratio (E4/E3) | Standard deviation (E4/E3) |
|---|---|---|---|---|---|---|---|---|
| Myosin, light polypeptide 3, isoform CRA_a | 148677054 | 27359.4 | 5.0 | 5 | 100.00 | 54.09 | 0.38 | 1.11 |
| Troponin T | 2340048 | 34082.0 | 9.4 | 4 | 100.00 | 78.26 | 0.39 | 0.50 |
| Myozenin 1 | 10946924 | 34319.7 | 8.6 | 3 | 100.00 | 58.73 | 0.41 | 0.23 |
| Myosin-binding protein C | 81910387 | 143381.3 | 6.0 | 10 | 100.00 | 100.37 | 0.41 | 0.71 |
| Myosin light chain, phosphorylatable, fast skeletal muscle | 7949078 | 21485.1 | 4.8 | 11 | 100.00 | 99.81 | 0.42 | 0.94 |
| Myomesin 2 | 170763465 | 179757.5 | 5.6 | 11 | 100.00 | 72.44 | 0.42 | 0.63 |
| Calsequestrin 1 | 127798794 | 49034.3 | 3.9 | 3 | 100.00 | 83.23 | 0.43 | 0.28 |
| Troponin C | 6678371 | 19609.3 | 4.1 | 4 | 100.00 | 106.88 | 0.43 | 0.27 |
| Fast skeletal myosin alkali light chain 1 isoform 1f | 29789016 | 23699.5 | 5.0 | 14 | 100.00 | 97.84 | 0.43 | 0.82 |
| Troponin I, skeletal, fast 2 | 123242973 | 25972.9 | 9.1 | 3 | 100.00 | 65.23 | 0.46 | 0.60 |
| LIM domain binding 3 isoform f | 84872217 | 33857.8 | 9.2 | 2 | 100.00 | 93.78 | 0.47 | 0.55 |
| Muscle creatine kinase | 6671762 | 48101.2 | 6.6 | 14 | 100.00 | 101.99 | 0.47 | 0.56 |
| Myomesin 1 isoform 2 | 145279198 | 194032.5 | 6.0 | 7 | 100.00 | 81.84 | 0.48 | 0.54 |
| Actinin alpha 3 | 7304855 | 110400.7 | 5.3 | 34 | 100.00 | 112.37 | 0.49 | 0.69 |
| Nebulin | 123857937 | 157734.8 | 8.8 | 2 | 100.00 | 45.87 | 0.51 | 0.63 |
| Titin | 123232572 | 3312853.3 | 6.2 | 2 | 100.00 | 37.84 | 0.53 | 0.25 |
| Igh protein | 62028521 | 56919.8 | 7.5 | 3 | 100.00 | 71.06 | 0.54 | 0.34 |
| Alpha cardiac myosin heavy chain | 191618 | 253883.5 | 5.6 | 18 | 100.00 | 91.72 | 0.55 | 0.25 |
| Myh7 protein | 187956918 | 252607.1 | 5.6 | 20 | 100.00 | 91.72 | 0.56 | 0.26 |
| Myosin, heavy polypeptide 4, skeletal muscle | 67189167 | 254149.5 | 5.6 | 86 | 100.00 | 127.38 | 0.56 | 0.38 |
| LIM domain binding 3 isoform b | 84872213 | 76092.4 | 8.3 | 3 | 100.00 | 70.38 | 0.56 | 0.10 |
| Calcium/calmodulin-dependent protein kinase II alpha isoform 1 | 6753250 | 24580.7 | 6.5 | 1 | 99.85 | 50.17 | 0.56 | 0.02 |
| Myosin, heavy polypeptide 8, skeletal muscle, perinatal | 71143152 | 253848.8 | 5.7 | 46 | 100.00 | 106.43 | 0.56 | 0.41 |
| Myosin heavy chain IIa | 205830428 | 254268.0 | 5.6 | 58 | 100.00 | 123.29 | 0.56 | 0.38 |
| Myosin, heavy polypeptide 8, skeletal muscle, perinatal | 187956525 | 253835.8 | 5.7 | 47 | 100.00 | 106.43 | 0.57 | 0.40 |
| Alpha-tropomyosin | 157787199 | 38470.8 | 4.7 | 14 | 100.00 | 105.62 | 0.58 | 0.35 |
| Myosin, heavy polypeptide 1, skeletal muscle, adult | 82524274 | 254200.7 | 5.6 | 71 | 100.00 | 127.38 | 0.58 | 0.38 |
| Ig H-C allotype gamma2b | 223428 | 40724.8 | 7.2 | 2 | 100.00 | 90.21 | 0.59 | 0.26 |
| Sarcalumenin, isoform CRA_a | 148664814 | 59761.7 | 6.2 | 4 | 100.00 | 60.15 | 0.60 | 0.36 |
| mCG18455 | 148678485 | 256334.6 | 5.5 | 22 | 100.00 | 84.80 | 0.60 | 0.39 |
| Tropomyosin 1, alpha, isoform CRA_b | 148694194 | 37823.3 | 4.7 | 12 | 100.00 | 105.62 | 0.60 | 0.39 |
| Predicted: similar to tropomyosin 2 (beta) isoform 2 isoform 15 | 73971296 | 38348.4 | 4.6 | 17 | 100.00 | 86.54 | 0.61 | 0.30 |
| Adenylate kinase 1 | 10946936 | 26311.9 | 5.7 | 5 | 100.00 | 77.64 | 0.63 | 0.25 |
| Tropomyosin 1, alpha isoform i | 78000203 | 32304.2 | 4.7 | 11 | 100.00 | 105.62 | 0.63 | 0.44 |
| Muscle glycogen phosphorylase | 6755256 | 104509.5 | 6.7 | 18 | 100.00 | 93.56 | 0.63 | 0.32 |
| Myoglobin | 21359820 | 20131.1 | 7.1 | 10 | 100.00 | 143.49 | 0.64 | 0.43 |
| RIKEN cDNA 8030451F13, isoform CRA_c | 148689541 | 142202.0 | 5.7 | 4 | 100.00 | 52.26 | 0.64 | 0.50 |
| Enolase 3, beta muscle, isoform CRA_a | 148680653 | 54402.9 | 6.8 | 15 | 100.00 | 112.63 | 0.64 | 0.60 |
| Actin, alpha 1, skeletal muscle | 4501881 | 45181.8 | 5.2 | 12 | 100.00 | 91.76 | 0.65 | 0.46 |
| mCG2006, isoform CRA_a | 148680420 | 187536.8 | 6.3 | 2 | 100.00 | 60.73 | 0.65 | 0.06 |
| Actinin alpha 2 | 58476244 | 111806.5 | 5.3 | 20 | 100.00 | 112.37 | 0.65 | 0.39 |
| ATPase, Ca++ transporting, ubiquitous isoform a | 254039658 | 116671.4 | 5.5 | 2 | 100.00 | 48.16 | 0.66 | 0.09 |
| Alpha actin 1 proprotein | 4885049 | 45033.8 | 5.2 | 12 | 100.00 | 91.76 | 0.66 | 0.45 |
| Alpha 2 actin | 4501883 | 45185.8 | 5.2 | 12 | 100.00 | 91.76 | 0.66 | 0.48 |
| Methylthioadenosine phosphorylase, isoform CRA_b | 148699009 | 36228.5 | 6.5 | 2 | 100.00 | 43.65 | 0.67 | 0.19 |
| Actinin alpha 2 | 157951643 | 112009.7 | 5.3 | 23 | 100.00 | 112.37 | 0.67 | 0.34 |
| Myosin | 1945080 | 253502.8 | 5.4 | 17 | 100.00 | 83.10 | 0.67 | 0.39 |
| Heat shock protein, alpha-crystallin-related, B6 | 59958370 | 18132.5 | 5.6 | 3 | 100.00 | 54.71 | 0.67 | 0.17 |
| Sarcomeric mitochondrial creatine kinase precursor | 38259206 | 51557.9 | 8.6 | 2 | 100.00 | 46.62 | 0.69 | 0.37 |
| Adenylosuccinate synthase like 1 | 6671519 | 54920.1 | 8.6 | 2 | 100.00 | 81.76 | 0.69 | 0.07 |
| Growth factor receptor bound protein 2 | 6680083 | 27765.1 | 5.7 | 2 | 100.00 | 45.66 | 0.69 | 0.41 |
| ATPase, Ca++ transporting, cardiac muscle, fast twitch 1 | 148685412 | 116243.4 | 5.3 | 12 | 100.00 | 114.25 | 0.70 | 0.14 |
| PDZ and LIM domain protein 3 | 7948997 | 36807.6 | 8.1 | 3 | 100.00 | 68.49 | 0.70 | 0.13 |
| mCG147612, isoform CRA_b | 148686595 | 58853.2 | 5.8 | 4 | 100.00 | 49.09 | 0.70 | 0.24 |
| h1-calponin alpha | 1069994 | 36759.9 | 8.8 | 4 | 100.00 | 68.12 | 0.72 | 0.23 |
| Myosin, light polypeptide kinase | 55930915 | 237267.2 | 6.0 | 2 | 100.00 | 46.40 | 0.72 | 0.24 |
| Parvalbumin | 31980767 | 14372.8 | 5.0 | 5 | 100.00 | 88.79 | 0.72 | 0.41 |
| UDP-glucose ceramide glucosyltransferase-like 1 | 45946485 | 190971.6 | 5.4 | 2 | 100.00 | 43.57 | 0.72 | 0.02 |
| Predicted: similar to tropomyosin 3 isoform 1 | 149751320 | 32645.1 | 4.8 | 10 | 100.00 | 80.10 | 0.74 | 0.37 |
| Carboxylesterase | 192854 | 65222.7 | 5.0 | 8 | 100.00 | 84.01 | 0.74 | 0.09 |
| Phosphoglycerate mutase 2 | 9256624 | 31972.9 | 8.7 | 8 | 100.00 | 89.17 | 0.74 | 0.54 |
| Skeletal muscle LIM protein | 2880031 | 38678.1 | 8.8 | 2 | 100.00 | 78.07 | 0.75 | 0.23 |
| RIKEN cDNA 1810020D17, isoform CRA_c | 148684357 | 17880.5 | 7.8 | 2 | 100.00 | 44.25 | 0.75 | 0.09 |
| Aldolase A, fructose-bisphosphate | 42490830 | 43401.8 | 8.5 | 11 | 100.00 | 91.23 | 0.75 | 0.17 |
| Albumin precursor | 163310765 | 77836.5 | 5.8 | 36 | 100.00 | 121.79 | 0.77 | 0.26 |
| SH3P9 | 1438563 | 53597.8 | 5.1 | 4 | 100.00 | 62.83 | 0.77 | 0.12 |
| Creatine kinase, mitochondrial 1, ubiquitous, isoform CRA_c | 148696104 | 50564.3 | 8.5 | 2 | 100.00 | 59.05 | 0.77 | 0.04 |
| Milk fat globule-EGF factor 8 protein isoform 2 | 113865977 | 50796.5 | 6.7 | 5 | 100.00 | 83.22 | 0.77 | 0.20 |
| ATPase, Ca++ transporting, slow twitch 2 isoform a | 158635979 | 124907.5 | 5.2 | 5 | 100.00 | 68.51 | 0.78 | 0.32 |
| Proteasome alpha 6 subunit | 6755198 | 30608.7 | 6.3 | 2 | 100.00 | 75.58 | 0.78 | 0.18 |
| Liver glycogen phosphorylase | 18875342 | 107417.7 | 6.6 | 5 | 100.00 | 58.28 | 0.78 | 0.28 |
| Solute carrier family 4 (anion exchanger), member 1 | 6755560 | 108215.2 | 5.4 | 2 | 100.00 | 50.97 | 0.78 | 0.06 |
| Coagulation factor II | 123227411 | 76215.8 | 6.0 | 4 | 100.00 | 61.55 | 0.79 | 0.08 |
| TRIO and F-actin binding protein isoform 3 | 88501749 | 234306.2 | 8.4 | 2 | 100.00 | 36.79 | 0.79 | 0.04 |
| Ig gamma-3 chain C region | 121044 | 47963.7 | 6.7 | 3 | 100.00 | 46.58 | 0.79 | 0.01 |
| Filamin, alpha | 125347376 | 305825.3 | 5.7 | 29 | 100.00 | 89.05 | 0.79 | 0.20 |
| Glyceraldehyde-3-phosphate-dehydrogenase isoform 1 | 149272161 | 40122.8 | 7.1 | 3 | 100.00 | 86.97 | 0.79 | 0.05 |
| Phosphoglucomutase 2 | 55824767 | 66748.2 | 6.0 | 10 | 100.00 | 75.31 | 0.80 | 0.23 |
| C-1-tetrahydrofolate synthase, cytoplasmic | 34921990 | 110015.8 | 6.9 | 2 | 100.00 | 40.34 | 0.80 | 0.31 |
| Alpha actinin 1a | 82659196 | 111086.8 | 5.3 | 32 | 100.00 | 112.37 | 0.80 | 0.33 |
| Acyl-CoA thioesterase 2 | 39992610 | 52675.7 | 7.2 | 2 | 100.00 | 53.32 | 0.80 | 0.22 |