Publication Information

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2195, 2203, 2351, 2383, 2402, 2427, 2439, 2462, 2498, 2531, 2546, 2557, 2569, 2594, 2629, 2634, 2643, 2658, 2666, 2778, 2785, 2843, 2852, 2976, 3003, 3053, 3147, 3196, 3249, 3328, 3423, 3476, 3504, 3511, 3539, 3665, 3672, 3682, 3694, 3698, 3720, 3772, 3779, 3791, 3805, 3808, 3824, 3854, 3857, 3865, 3879, 3894, 3910, 3959, 3968, 3984, 3990, 4009, 4021, 4034, 4041, 4055, 4068, 4081, 4101, 4134, 4144, 4154, 4165, 4172, 4181, 4184, 4198, 4223, 4258, 4277, 4282, 4292, 4301, 4309, 4314, 4404, 4427, 4486, 4515, 4544, 4603, 4662, 4675, 4695, 4761, 4816, 4879, 4919, 4985, 5004, 5021, 5052, 5064, 5069, 5079, 5097, 5102, 5126, 5176, 5242, 5250, 5256, 5291, 5335, 5371, 5411, 5466, 5516, 5545, 5585, 5618, 5627, 5684, 5698, 5728, 5783, 5808, 5835, 5850, 5854, 5857, 5863, 5869, 5878, 5891, 5897, 5915, 5924, 5980, 6001, 6013, 6060, 6078, 6083, 6100, 6114, 6154, 6166], 'endogenous': [2, 60, 76, 134, 212, 4274, 5836], 'ubiquitination': [3, 61, 77, 135, 214, 327, 358, 440, 449, 513, 640, 803, 872, 1016, 1217, 1298, 1461, 1572, 1776, 3153, 3255, 3482, 4334, 4354, 4521, 4885, 5182, 5417, 5517, 5591, 5734, 5837, 6031, 6061], 'sites': [4, 62, 78, 136, 215, 285, 514, 526, 598, 830, 1102, 1175, 1299, 1364, 1462, 1520, 3106, 3189, 3211, 4355, 5023, 5068, 5129, 5146, 5212, 5222, 5293, 5375, 5518, 5549, 5621, 5628, 5643, 5656, 5838, 5935, 6009, 6032, 6062], 'by': [5, 79, 169, 191, 216, 359, 724, 760, 1026, 1049, 1463, 1899, 2003, 2161, 2395, 2564, 2690, 2788, 2982, 3428, 3711, 3828, 3999, 4287, 4368, 4490, 4832, 5493, 5498, 5704, 5883, 5948, 6033, 6098, 6106], 'mass': [6, 80, 217, 2696, 2772, 2914, 3011, 3025, 3430, 3548, 3658, 4838, 5949], 'spectrometry': [7, 81, 218, 3431], 'has': [8, 82, 206, 769, 1007, 1287, 3945], 'dramatically': [9, 83], 'improved': [10, 41, 84, 115, 5263], 'with': [11, 85, 157, 1072, 1529, 1614, 1647, 1680, 1704, 1736, 1803, 1912, 1947, 1958, 1976, 1996, 2029, 2037, 2118, 2284, 2380, 2424, 2448, 2503, 2523, 2543, 2554, 2614, 2626, 2655, 2663, 2726, 2738, 2999, 3388, 3801, 3914, 3975, 4269, 4306, 4460, 4595, 4627, 4753, 4785, 4915, 5036, 5075, 5615, 5678, 5921, 6090, 6178], 'the': [12, 27, 86, 101, 209, 402, 421, 445, 508, 516, 519, 690, 775, 922, 993, 1010, 1068, 1073, 1076, 1087, 1267, 1303, 1357, 1437, 1492, 1497, 1503, 1511, 1822, 1937, 2024, 2201, 2204, 2243, 2253, 2301, 2307, 2352, 2372, 2452, 2759, 2771, 2815, 2833, 2868, 2876, 2886, 2900, 2948, 2967, 2988, 2992, 3000, 3019, 3034, 3075, 3084, 3103, 3175, 3186, 3207, 3220, 3224, 3313, 3389, 3421, 3448, 3521, 3613, 3617, 3630, 3652, 3657, 3663, 3670, 3673, 3683, 3696, 3706, 3718, 3760, 3768, 3780, 3792, 3795, 3806, 3822, 3855, 3895, 3908, 3950, 3957, 3966, 3976, 3982, 3988, 4018, 4031, 4099, 4132, 4141, 4152, 4170, 4192, 4212, 4221, 4252, 4280, 4290, 4456, 4471, 4484, 4676, 4842, 4920, 4986, 5084, 5124, 5233, 5238, 5254, 5277, 5467, 5504, 5514, 5682, 5696, 5784, 5812, 5822, 5833, 5851, 5855, 5892, 5905, 5909, 5922, 5995, 5999, 6017, 6058, 6076, 6122, 6140, 6150], 'commercialization': [13, 87, 149], 'anti-di-glycine': [15, 89], 'remnant': [16, 90, 160, 361, 1022, 1045, 2310], '(K-ε-GG)': [17, 91, 161, 2312], 'antibodies.': [18, 92, 6158], 'Here,': [19, 93, 3954], 'we': [20, 94, 1506, 3595, 3775, 3955, 4129, 4295, 4475, 4548, 5041, 5048, 5207, 5488, 5637, 5803, 5845], 'describe': [21, 95], 'a': [22, 64, 96, 138, 158, 732, 1105, 1361, 1522, 1539, 1886, 1985, 2053, 2067, 2122, 2162, 2217, 2235, 2285, 2295, 2512, 2693, 2705, 2713, 2775, 2782, 2789, 3058, 3199, 3215, 3356, 3543, 3724, 3863, 3943, 4014, 4178, 4227, 4420, 4673, 4835, 5025, 5045, 5076, 5120, 5131, 5152, 5248, 5295, 5806, 6111], 'number': [23, 97, 3002, 3823, 3989, 4100, 4133, 4153, 4171, 4281, 4485, 5125, 5249, 5807, 6059, 6113], 'improvements': [25, 99, 1430, 5844], 'to': [26, 45, 100, 119, 420, 432, 436, 737, 772, 996, 1083, 1096, 1435, 1653, 1877, 1943, 1966, 2049, 2146, 2172, 2178, 2251, 2292, 2675, 2704, 2735, 2749, 2791, 2874, 2882, 2987, 2997, 3007, 3015, 3030, 3041, 3073, 3081, 3198, 3355, 3529, 3537, 3679, 3723, 3783, 3794, 3904, 3928, 3932, 3980, 4029, 4059, 4065, 4187, 4210, 4219, 4250, 4352, 4365, 4462, 4482, 4493, 4554, 4652, 4669, 4852, 5008, 5136, 5304, 5485, 5503, 5520, 5811, 5830, 5881, 5888, 5931, 5998, 6117, 6136], 'K-ε-GG': [28, 102, 1101, 1519, 2226, 2258, 2282, 2560, 3094, 3117, 3210, 3366, 3426, 3540, 3610, 3666, 3688, 3721, 3773, 3825, 3905, 3992, 4036, 4061, 4136, 4199, 4224, 4284, 4303, 4405, 4487, 4560, 4670, 4707, 4714, 4811, 4846, 5010, 5022, 5055, 5067, 5128, 5211, 5243, 5292, 5620, 5642, 5655, 5813], 'enrichment': [29, 103, 2283, 3309, 3689, 3769, 3873, 4241, 4561, 4671, 4708, 5239, 5862, 5942], 'workflow,': [30, 104, 1505, 4434, 4998], 'including': [31, 105, 2803, 5253, 5848], 'optimized': [32, 106, 4330, 4399, 4546, 4845, 5002, 5257, 5929], 'antibody': [33, 38, 107, 112, 995, 1499, 1636, 2303, 2370, 2374, 2397, 2453, 2506, 3391, 3450, 3516, 3523, 3606, 3675, 3684, 3782, 3793, 3860, 3897, 3916, 3931, 4026, 4056, 4110, 4145, 4166, 4193, 4214, 4247, 4317, 4820, 5007, 5258, 5858, 6019, 6142], 'and': [34, 40, 49, 55, 108, 114, 123, 129, 330, 398, 515, 643, 686, 734, 783, 875, 918, 989, 1001, 1220, 1263, 1485, 1494, 1575, 1623, 1635, 1676, 1678, 1689, 1707, 1713, 1720, 1730, 1779, 1806, 1859, 1923, 1953, 1981, 2011, 2035, 2115, 2175, 2187, 2271, 2317, 2348, 2408, 2433, 2483, 2501, 2533, 2592, 2624, 2639, 2661, 2688, 2747, 2758, 2806, 2848, 2885, 2889, 2916, 2964, 3027, 3043, 3068, 3083, 3088, 3097, 3107, 3115, 3156, 3258, 3280, 3325, 3348, 3396, 3405, 3432, 3485, 3513, 3570, 3579, 3619, 3629, 3661, 3701, 3734, 3743, 3770, 3810, 3820, 3884, 3962, 3994, 4047, 4071, 4086, 4115, 4123, 4215, 4238, 4271, 4311, 4321, 4398, 4442, 4454, 4524, 4685, 4703, 4844, 4888, 5040, 5061, 5090, 5092, 5114, 5144, 5149, 5185, 5220, 5240, 5267, 5270, 5289, 5420, 5463, 5495, 5525, 5594, 5690, 5737, 5780, 5826, 5978, 6003, 6064, 6124, 6163], 'peptide': [35, 109, 1630, 2227, 2491, 2887, 2909, 2943, 3077, 3089, 3200, 4082, 4117, 4237, 4663, 4687, 5870, 6107], 'input': [36, 110, 1081, 1449, 1631, 1905, 3881, 3969, 4083, 4111, 4118, 4142, 4167, 4217, 4260, 4310, 4428, 6015, 6084], 'requirements,': [37, 111], 'cross-linking,': [39, 113, 2371], 'off-line': [42, 116, 2137, 4477, 5264], 'fractionation': [43, 117, 2063, 4481, 5265, 6109], 'prior': [44, 118, 1652, 3536, 4668, 5880, 6116], 'enrichment.': [46, 120, 6118], 'This': [47, 121, 1537, 3849, 4176, 4230, 4325, 5116], 'refined': [48, 122, 4397, 4843], 'practical': [50, 124, 5827], 'workflow': [51, 125, 4400, 4847], 'enables': [52, 126, 2907, 4710], 'routine': [53, 127, 1514], 'identification': [54, 128, 244, 433, 509, 557, 967, 1134, 2910, 3070, 3096, 5334], 'quantification': [56, 130, 320, 633, 768, 865, 1210, 1515, 1565, 1769, 3098, 3146, 3248, 3475, 4514, 4878, 5175, 5288, 5410, 5584, 5727], '∼20,000': [58, 132, 1517], 'distinct': [59, 133, 4035, 5054, 5066], 'in': [63, 137, 172, 194, 282, 322, 325, 521, 595, 635, 638, 727, 763, 801, 827, 867, 870, 1029, 1052, 1104, 1172, 1212, 1215, 1337, 1367, 1403, 1431, 1440, 1491, 1521, 1567, 1570, 1604, 1662, 1674, 1771, 1774, 1818, 1936, 2052, 2093, 2216, 2234, 2247, 2294, 2399, 2436, 2459, 2480, 2495, 2683, 2814, 3148, 3151, 3223, 3250, 3253, 3288, 3402, 3435, 3477, 3480, 3583, 3627, 3651, 3747, 3963, 4017, 4158, 4226, 4289, 4339, 4357, 4412, 4445, 4516, 4519, 4855, 4880, 4883, 5018, 5044, 5081, 5107, 5123, 5151, 5177, 5180, 5215, 5225, 5237, 5372, 5412, 5415, 5546, 5586, 5589, 5649, 5662, 5729, 5732, 5821, 6057, 6066, 6093, 6127, 6134, 6149], 'single': [65, 139, 1106, 1369, 1523, 4015, 5026, 5046, 5132, 5153, 5296, 6067], 'SILAC': [66, 140, 1524, 1535, 1656, 1695, 1725, 1894, 1907, 2535, 4422, 5027, 5037, 5133], 'experiment': [67, 141, 1108, 1527, 4160, 4423], 'using': [68, 142, 1444, 1885, 1926, 1984, 2066, 2242, 2578, 2598, 2692, 2781, 2838, 2899, 3214, 3312, 3332, 3370, 3454, 3555, 3677, 3876, 4424, 4813, 4834, 4848, 5927, 6016, 6139], 'moderate': [69, 143, 1445, 5913], 'amounts': [70, 144, 1446, 3510, 4164, 4447, 5914, 6012], 'protein': [72, 146, 213, 326, 639, 787, 871, 1019, 1216, 1448, 1533, 1571, 1775, 1890, 1904, 2918, 3045, 3152, 3254, 3481, 3530, 3798, 3880, 3970, 4043, 4188, 4216, 4259, 4429, 4450, 4520, 4884, 5181, 5416, 5590, 5733, 5933, 6014, 6085], 'input.': [73, 147], 'The': [148, 2139, 2275, 2751, 2796, 2809, 2857, 3009, 3061, 3926, 4415, 4802, 4996, 5842, 5940], 'antibodies': [151, 499], 'that': [152, 797, 1291, 1424, 1700, 3353, 3393, 3508, 3524, 3597, 3615, 3763, 3788, 3891, 4004, 4072, 4131, 4162, 4206, 4264, 4328, 4341, 4349, 4362, 4646, 4709, 5043, 5209, 5490, 5639, 5668, 5675, 5873, 5908, 6054, 6121], 'recognize': [153], 'lysine': [154, 357, 473, 3202], 'residues': [155], 'modified': [156], 'di-glycine': [159, 1021, 1044, 4472], '1The': [162, 184], 'abbreviations': [163, 185], 'used': [164, 186, 2199, 3861, 4476], 'are:K-ε-GGdi-glycine': [165, 187], 'remnantSILACstable': [166, 188], 'isotope': [167, 189, 722, 758, 1024, 1047, 2890], 'labeling': [168, 190, 723, 759, 1025, 1048, 1696], 'amino': [170, 192, 725, 761, 1027, 1050, 3086], 'acids': [171, 193, 726, 762, 1028, 1051], 'cell': [173, 195, 728, 764, 1030, 1053, 1809, 1812, 1823, 5650], 'cultureDMPdimethyl': [174, 196], 'pimelimidatebasic': [175, 197], 'RPbasic': [176, 198], 'pH': [177, 199, 1035, 1058, 1833, 1951, 2107, 2158, 2388, 2431, 2470, 3453, 3816], 'reversed': [178, 200, 1036, 1059], 'phaseHCDhigh': [179, 201], 'energy': [180, 202, 1039, 1062, 2871], 'collision-induced': [181, 203, 1040, 1063], 'dissociationFAformic': [182, 204], 'acid.': [183, 205, 1043, 1066], 'significantly': [207, 3900, 4107, 4139, 5640, 5680], 'transformed': [208], 'detection': [210, 1292, 3422, 3664, 3771, 4197, 5020, 5241, 5290], '(1Emanuele': [219, 532, 942, 1109, 5309], 'M.J.': [220, 392, 533, 680, 912, 943, 1110, 1257, 2342, 5310, 5457, 5774], 'Elia': [221, 534, 944, 1111, 5311], 'A.E.': [222, 535, 945, 1112, 5312], 'Xu': [223, 536, 946, 1113, 5313], 'Q.': [224, 537, 947, 1114, 5314], 'Thoma': [225, 538, 948, 1115, 5315], 'C.R.': [226, 539, 949, 1116, 5316], 'Izhar': [227, 540, 950, 1117, 5317], 'L.': [228, 541, 951, 1118, 5318], 'Leng': [229, 542, 952, 1119, 5319], 'Y.': [230, 543, 953, 1120, 1455, 2586, 3566, 3730, 4565, 4571, 4577, 4618, 4723, 4729, 4735, 4776, 5320, 5967, 6025], 'Guo': [231, 379, 544, 667, 899, 954, 1121, 1244, 2329, 5321, 5444, 5761], 'A.': [232, 380, 384, 545, 668, 672, 718, 900, 904, 955, 1122, 1245, 1249, 2330, 2334, 2934, 5322, 5445, 5449, 5762, 5766], 'Chen': [233, 546, 956, 1123, 5323], 'Y.N.': [234, 547, 957, 1124, 5324], 'Rush': [235, 389, 548, 677, 909, 958, 1125, 1254, 2339, 5325, 5454, 5771], 'J.': [236, 272, 382, 390, 549, 585, 670, 678, 817, 902, 910, 959, 1126, 1162, 1247, 1255, 1457, 2332, 2340, 2582, 2903, 2930, 3564, 3728, 4949, 5326, 5362, 5447, 5455, 5536, 5764, 5772, 5937, 6027], 'Hsu': [237, 550, 960, 1127, 5327], 'P.W.': [238, 551, 961, 1128, 5328], 'Yen': [239, 552, 962, 1129, 5329], 'H.C.': [240, 553, 963, 1130, 5330], 'Elledge': [241, 554, 964, 1131, 5331], 'S.J.': [242, 555, 965, 1132, 4937, 5332], 'Global': [243, 354, 556, 966, 1133, 5333], 'modular': [246, 559, 969, 1136, 5336], 'Cullin-RING': [247, 560, 970, 1003, 1014, 1137, 4377, 5337], 'ligase': [248, 561, 971, 1004, 1015, 1138, 5338], 'substrates.Cell.': [249, 562, 972, 1139, 5339], '2011;': [250, 292, 406, 563, 605, 694, 837, 926, 973, 1140, 1182, 1271, 2356, 2953, 4607, 4765, 4970, 5340, 5382, 5471, 5556, 5788], '147:': [251, 564, 974, 1141, 5341], '459-474Abstract': [252, 565, 975, 1142, 5342], 'Full': [253, 255, 294, 296, 338, 340, 409, 411, 484, 486, 566, 568, 607, 609, 651, 653, 697, 699, 745, 747, 839, 841, 883, 885, 929, 931, 976, 978, 1143, 1145, 1184, 1186, 1228, 1230, 1274, 1276, 1345, 1347, 1411, 1413, 1472, 1474, 1583, 1585, 1787, 1789, 2359, 2361, 3164, 3166, 3266, 3268, 3493, 3495, 4386, 4388, 4532, 4534, 4896, 4898, 4973, 4975, 5193, 5195, 5343, 5345, 5384, 5386, 5428, 5430, 5474, 5476, 5558, 5560, 5602, 5604, 5745, 5747, 5791, 5793, 6042, 6044], 'Text': [254, 256, 295, 297, 339, 341, 410, 412, 485, 487, 567, 569, 608, 610, 652, 654, 698, 700, 746, 748, 840, 842, 884, 886, 930, 932, 977, 979, 1144, 1146, 1185, 1187, 1229, 1231, 1275, 1277, 1346, 1348, 1412, 1414, 1473, 1475, 1584, 1586, 1788, 1790, 2360, 2362, 3165, 3167, 3267, 3269, 3494, 3496, 4387, 4389, 4533, 4535, 4897, 4899, 4974, 4976, 5194, 5196, 5344, 5346, 5385, 5387, 5429, 5431, 5475, 5477, 5559, 5561, 5603, 5605, 5746, 5748, 5792, 5794, 6043, 6045], 'PDF': [257, 298, 342, 413, 488, 570, 611, 655, 701, 749, 843, 887, 933, 980, 1147, 1188, 1232, 1278, 1349, 1415, 1476, 1587, 1791, 2363, 3168, 3270, 3497, 4390, 4536, 4900, 4977, 5197, 5347, 5388, 5432, 5478, 5562, 5606, 5749, 5795, 6046], 'PubMed': [258, 299, 343, 368, 414, 489, 571, 612, 656, 702, 750, 844, 888, 934, 981, 1148, 1189, 1233, 1279, 1350, 1416, 1477, 1588, 1792, 2364, 2604, 2924, 2956, 3169, 3271, 3299, 3340, 3498, 3589, 3753, 4391, 4537, 4610, 4639, 4768, 4797, 4901, 4978, 5198, 5348, 5389, 5433, 5479, 5563, 5607, 5750, 5796, 5955, 5989, 6047], 'Scopus': [259, 344, 369, 415, 490, 572, 657, 703, 751, 889, 935, 982, 1149, 1234, 1280, 1351, 1417, 1478, 1589, 1793, 2365, 2605, 2925, 2957, 3170, 3272, 3300, 3341, 3499, 3590, 3754, 4392, 4538, 4611, 4640, 4769, 4798, 4902, 4979, 5199, 5349, 5434, 5480, 5608, 5751, 5797, 5956, 5990, 6048], '(318)': [260, 573, 983, 1150, 5350], 'Google': [261, 300, 346, 371, 417, 492, 574, 613, 659, 705, 753, 845, 891, 937, 984, 1151, 1190, 1236, 1282, 1353, 1419, 1480, 1591, 1795, 2367, 2607, 2927, 2959, 3172, 3274, 3302, 3343, 3501, 3592, 3756, 4394, 4540, 4613, 4642, 4771, 4800, 4904, 4981, 5201, 5351, 5390, 5436, 5482, 5564, 5610, 5753, 5799, 5958, 5992, 6050], 'Scholar,': [262, 301, 347, 372, 575, 614, 660, 706, 846, 892, 1152, 1191, 1237, 2928, 3275, 4614, 4772, 5352, 5391, 5437, 5565, 5754, 5959], '2Wagner': [263, 576, 1153, 5353], 'S.A.': [264, 317, 577, 630, 809, 862, 1154, 1207, 1311, 1377, 1562, 1766, 3143, 3245, 3472, 4511, 4875, 5172, 5354, 5407, 5528, 5581, 5724], 'Beli': [265, 578, 810, 1155, 1312, 1378, 5355, 5529], 'P.': [266, 309, 579, 622, 811, 854, 1156, 1199, 1313, 1379, 1554, 1758, 3135, 3237, 3464, 4503, 4867, 5164, 5356, 5399, 5530, 5573, 5716], 'Weinert': [267, 580, 812, 1157, 1314, 1380, 5357, 5531], 'B.T.': [268, 581, 813, 1158, 1315, 1381, 3321, 5358, 5532], 'Nielsen': [269, 467, 582, 814, 1159, 1322, 1388, 5359, 5533], 'M.L.': [270, 468, 583, 815, 1160, 1323, 1389, 5360, 5534], 'Cox': [271, 584, 816, 1161, 5361, 5535], 'Mann': [273, 586, 719, 818, 1163, 2583, 2904, 2939, 3567, 3731, 5363, 5537], 'M.': [274, 587, 720, 819, 1164, 2584, 2905, 2940, 3568, 3732, 4927, 5364, 5538], 'Choudhary': [275, 588, 820, 1165, 1328, 1394, 5365, 5539], 'C.': [276, 589, 821, 1166, 1317, 1321, 1327, 1329, 1383, 1387, 1393, 1395, 5366, 5540], 'A': [277, 590, 822, 1167, 2100, 2120, 2128, 2192, 2754, 2942, 2974, 3531, 3799, 3838, 4189, 5367, 5541], 'proteome-wide,': [278, 591, 823, 1168, 5368, 5542], 'quantitative': [279, 399, 592, 687, 824, 919, 1169, 1264, 1441, 2349, 5369, 5464, 5543, 5781], 'survey': [280, 593, 825, 1170, 5370, 5544], 'vivo': [283, 323, 596, 636, 828, 868, 1173, 1213, 1568, 1772, 3149, 3251, 3478, 4517, 4881, 5178, 5373, 5413, 5547, 5587, 5730], 'ubiquitylation': [284, 474, 597, 829, 1174, 1334, 1400, 5374, 5548], 'reveals': [286, 475, 599, 831, 1176, 5376, 5550], 'widespread': [287, 600, 832, 1177, 5377, 5551], 'regulatory': [288, 601, 833, 1178, 5378, 5552], 'roles.Mol.': [289, 602, 834, 1179, 5379, 5553], 'Cell.': [290, 333, 405, 480, 603, 646, 693, 740, 835, 878, 925, 1180, 1223, 1270, 1340, 1406, 1467, 1578, 1782, 2355, 3159, 3261, 3488, 4381, 4527, 4891, 5188, 5380, 5423, 5470, 5554, 5597, 5740, 5787, 6037], 'Proteomics.': [291, 334, 481, 604, 647, 741, 836, 879, 1181, 1224, 1341, 1407, 1468, 1579, 1783, 3160, 3262, 3489, 4382, 4528, 4635, 4793, 4892, 5189, 5381, 5424, 5555, 5598, 5741, 6038], '10M111.013284Abstract': [293, 606, 838, 1183, 5383, 5557], '3Udeshi': [302, 615, 847, 1192, 5392, 5566], 'N.D.': [303, 616, 848, 1193, 1548, 1752, 3129, 3231, 3458, 4497, 4861, 5158, 5393, 5567, 5710], 'Mani': [304, 617, 849, 1194, 1549, 1753, 3130, 3232, 3459, 4498, 4862, 5159, 5394, 5568, 5711], 'D.R.': [305, 618, 850, 1195, 1550, 1754, 3131, 3233, 3460, 4499, 4863, 5160, 5395, 5569, 5712], 'Eisenhaure': [306, 619, 851, 1196, 1551, 1755, 3132, 3234, 3461, 4500, 4864, 5161, 5396, 5570, 5713], 'T.': [307, 620, 852, 1197, 1552, 1756, 3133, 3235, 3462, 4501, 4573, 4575, 4583, 4731, 4733, 4741, 4865, 5162, 5397, 5571, 5714], 'Mertins': [308, 621, 853, 1198, 1553, 1757, 3134, 3236, 3463, 4502, 4866, 5163, 5398, 5572, 5715], 'Jaffe': [310, 623, 855, 1200, 1555, 1759, 3136, 3238, 3465, 4504, 4868, 5165, 5400, 5574, 5717], 'J.D.': [311, 624, 856, 1201, 1556, 1760, 3137, 3239, 3466, 4505, 4869, 5166, 5401, 5575, 5718], 'Clauser': [312, 625, 857, 1202, 1557, 1761, 3138, 3240, 3467, 4506, 4870, 5167, 5402, 5576, 5719], 'K.R.': [313, 626, 858, 1203, 1558, 1762, 3139, 3241, 3468, 4507, 4871, 5168, 5403, 5577, 5720], 'Hacohen': [314, 627, 859, 1204, 1559, 1763, 3140, 3242, 3469, 4508, 4872, 5169, 5404, 5578, 5721], 'N.': [315, 466, 628, 860, 1205, 1560, 1764, 2932, 3141, 3243, 3470, 4509, 4873, 5170, 5405, 5579, 5722], 'Carr': [316, 629, 861, 1206, 1561, 1765, 3142, 3244, 3471, 4510, 4874, 5171, 5406, 5580, 5723], 'Methods': [318, 631, 863, 1208, 1563, 1767, 3144, 3246, 3473, 4512, 4876, 5173, 5408, 5582, 5725], 'for': [319, 632, 767, 864, 1209, 1428, 1510, 1564, 1644, 1733, 1768, 1808, 1872, 1917, 1930, 2136, 2200, 2257, 2281, 2413, 2443, 2487, 2508, 2534, 2588, 2596, 2862, 3018, 3023, 3033, 3065, 3145, 3247, 3284, 3365, 3375, 3474, 3546, 3574, 3686, 3738, 3949, 4013, 4234, 4401, 4419, 4513, 4559, 4600, 4630, 4706, 4713, 4758, 4788, 4810, 4877, 4912, 4966, 5083, 5130, 5174, 5287, 5409, 5583, 5726, 5832, 5860, 5894, 5904, 5944, 5975, 5982, 6096, 6152, 6170], 'changes': [324, 637, 800, 869, 1214, 1569, 1773, 3150, 3252, 3479, 4518, 4882, 5179, 5414, 5502, 5588, 5731], 'following': [328, 641, 873, 1218, 1573, 1777, 2787, 3154, 3256, 3483, 4522, 4886, 5183, 5418, 5592, 5631, 5735], 'proteasome': [329, 642, 781, 874, 1219, 1574, 1778, 3155, 3257, 3484, 3977, 4293, 4346, 4370, 4523, 4887, 4987, 5184, 5419, 5491, 5593, 5676, 5736], 'deubiquitinase': [331, 644, 876, 1221, 1576, 1780, 3157, 3259, 3486, 4525, 4889, 4922, 5186, 5421, 5496, 5595, 5702, 5738], 'inhibition.Mol.': [332, 645, 877, 1222, 1577, 1781, 3158, 3260, 3487, 4526, 4890, 5187, 5422, 5596, 5739], '2012;': [335, 648, 880, 1225, 1342, 1408, 1469, 1580, 1784, 3161, 3263, 3490, 4383, 4529, 4636, 4794, 4893, 5190, 5425, 5599, 5742, 6039], '11:': [336, 649, 881, 1226, 1343, 1409, 1470, 1581, 1785, 3162, 3264, 3491, 4384, 4530, 4608, 4766, 4894, 5191, 5426, 5600, 5743, 6040], '148-159Abstract': [337, 650, 882, 1227, 1582, 1786, 3163, 3265, 3492, 4531, 4895, 5192, 5427, 5601, 5744], '(123)': [345, 658, 890, 1235, 1590, 1794, 3171, 3273, 3500, 4539, 4903, 5200, 5435, 5609, 5752, 5991], '4Xu': [348], 'G.': [349, 5963], 'Paige': [350], 'J.S.': [351], 'Jaffrey': [352], 'S.R.': [353], 'analysis': [355, 471, 517, 1304, 1370, 3327, 5814, 5834, 5882, 5947], 'ubiquitin': [360, 505, 778, 1433, 2309, 5505, 6008], 'immunoaffinity': [362, 1465, 6035], 'profiling.Nat.': [363], 'Biotechnol.': [364, 2920], '2010;': [365, 482], '28:': [366], '868-873Crossref': [367], '(395)': [370], '5Kim': [373, 661, 893, 1238, 5438, 5755], 'W.': [374, 662, 894, 1239, 2324, 3319, 5439, 5756], 'Bennett': [375, 663, 895, 1240, 2325, 5440, 5757], 'E.J.': [376, 664, 896, 1241, 2326, 5441, 5758], 'Huttlin': [377, 665, 897, 1242, 2327, 5442, 5759], 'E.L.': [378, 666, 898, 1243, 2328, 5443, 5760], 'Li': [381, 669, 901, 1246, 2331, 5446, 5763], 'Possemato': [383, 671, 903, 1248, 2333, 5448, 5765], 'Sowa': [385, 673, 905, 1250, 2335, 5450, 5767], 'M.E.': [386, 674, 906, 1251, 2336, 4579, 4737, 5451, 5768], 'Rad': [387, 675, 907, 1252, 2337, 5452, 5769], 'R.': [388, 676, 908, 1253, 2338, 4941, 4943, 5453, 5770], 'Comb': [391, 679, 911, 1256, 2341, 5456, 5773], 'Harper': [393, 681, 913, 1258, 2343, 5458, 5775], 'J.W.': [394, 460, 682, 914, 1259, 2344, 4373, 5459, 5776], 'Gygi': [395, 683, 915, 1260, 2345, 5460, 5777, 5938], 'S.P.': [396, 684, 916, 1261, 2346, 5461, 5778, 5939], 'Systematic': [397, 685, 917, 1262, 2347, 3324, 5462, 5779], 'assessment': [400, 688, 920, 1265, 2350, 5465, 5782], 'ubiquitin-modified': [403, 691, 923, 1268, 2353, 5468, 5785], 'proteome.Mol.': [404, 692, 924, 1269, 2354, 5469, 5786], '44:': [407, 695, 927, 1272, 2357, 5472, 5789], '325-340Abstract': [408, 696, 928, 1273, 2358, 5473, 5790], '(1183)': [416, 704, 936, 1281, 2366, 5481, 5798], 'Scholar).': [418, 493, 754, 938, 1283, 1354, 1420, 1481, 1592, 1796, 2368, 2608, 3173, 3303, 3344, 3502, 3593, 3757, 3848, 4395, 4541, 4643, 4801, 4905, 5202, 5483, 5611, 5800, 6051], 'Prior': [419], 'development': [422, 4965], 'these': [424, 525, 3505, 3985], 'highly': [425, 4701, 5928, 6147], 'specific': [426, 5843], 'reagents,': [427, 5636], 'proteomics': [428, 990, 2597, 4962], 'experiments': [429, 1443, 4096, 6068, 6138], 'were': [430, 1602, 1642, 1660, 1702, 1731, 1800, 1814, 1866, 1883, 1910, 1940, 1974, 1994, 2047, 2214, 2232, 2273, 2279, 2290, 2376, 2419, 2455, 2493, 2521, 2550, 2562, 2576, 2647, 2673, 2681, 2710, 2768, 2893, 2897, 3047, 3092, 3100, 3119, 3204, 3212, 3399, 3406, 3552, 4910, 4991, 5072, 5147, 5622, 5629, 5644, 5657], 'limited': [431, 444, 5303, 6133], 'up': [435, 3678, 4064], 'only': [437, 1360, 3637, 4005, 4077, 4116, 5142, 6137], 'several': [438], 'hundred': [439], 'sites,': [441], 'which': [442, 1006, 3715, 4195, 4680, 4999, 5070], 'severely': [443], 'scope': [446], 'global': [448, 1432, 4333, 5945], 'studies': [450, 496], '(6Danielsen': [451], 'J.M.': [452], 'Sylvestersen': [453], 'K.B.': [454], 'Bekker-Jensen': [455], 'S.': [456], 'Szklarczyk': [457], 'D.': [458, 1451, 3835, 4581, 4739, 6021], 'Poulsen': [459], 'Horn': [461], 'H.': [462, 716], 'Jensen': [463], 'L.J.': [464], 'Mailand': [465], 'Mass': [469], 'spectrometric': [470, 3549], 'promiscuity': [476], 'at': [477, 1816, 1868, 1875, 1920, 1933, 1956, 1963, 2121, 2410, 2446, 2485, 2515, 2774, 3383, 3451, 5216, 5512, 5694], 'site': [478, 1335, 1401, 3069, 3095, 3179], 'level.Mol.': [479], '10M110.003590Abstract': [483], '(248)': [491], 'Recent': [494], 'proteomic': [495, 1442, 1504, 4632, 4790], 'employing': [497], 'anti-K-ε-GG': [498, 994, 1077, 1498, 2302, 2373, 2505, 3390, 3449, 3522, 3674, 3781, 3859, 3896, 3952, 3960, 4819, 6018, 6141], 'have': [500, 986, 1093, 1507, 3766, 3929, 4342, 4549, 5804, 5819, 5846, 5902], 'enhanced': [501], 'our': [502, 1543, 3409, 4093, 4246, 4545, 4653, 4856, 5137, 5669], 'understanding': [503], 'biology': [506], 'through': [507, 5247], 'thousands': [511, 1363], 'change': [520, 4108], 'relative': [522, 4492, 5135, 5519], 'abundance': [523], 'after': [527, 2825, 3644, 3920], 'chemical': [528, 3777, 3789, 3892, 4961], 'or': [529, 794, 1716, 1746, 2528, 3869, 4024, 4990, 6105], 'biological': [530, 3306, 4849, 5034, 5205], 'perturbation': [531], '7Ong': [707], 'S.-E.': [708], 'Blagoev': [709], 'B.': [710, 4957], 'Kratchmarova': [711], 'I.': [712], 'Kristensen': [713], 'D.B.': [714], 'Steen': [715], 'Pandey': [717], 'Stable': [721], 'culture,': [729], 'SILAC,': [730, 6104], 'as': [731, 790, 1356, 1500, 1502, 2320, 3049, 3057, 3125, 3227, 4140, 4466, 4468, 4672, 5865, 5867], 'simple': [733], 'accurate': [735], 'approach': [736, 5943], 'expression': [738, 3287], 'proteomics.Mol.': [739], '2002;': [742], '1:': [743], '376-386Abstract': [744], '(4577)': [752], 'Use': [755], 'stable': [757, 1023, 1046], 'culture': [765, 1031, 1054], '(SILAC)': [766], 'enabled': [770], 'researchers': [771], 'better': [773], 'understand': [774], 'extent': [776], 'regulation': [779], 'upon': [780, 805, 3814], 'inhibition': [782, 5492, 5497, 5677, 5703], 'precisely': [784], 'identify': [785, 997], 'those': [786, 4361, 4853], 'classes,': [788], 'such': [789, 1699, 3942], 'newly': [791], 'synthesized': [792], 'proteins': [793, 3395, 4457, 5647, 5660], 'chromatin-related': [795], 'proteins,': [796], 'see': [798], 'overt': [799], 'their': [802], 'levels': [804, 4276, 5515, 5683, 5697], 'drug': [806], 'treatment': [807, 4348, 5614], '(2Wagner': [808, 5527], 'Emanuel': [939], 'et': [940], 'al.': [941], 'Scholar)': [985, 2960], 'combined': [987, 4444, 6089], 'genetic': [988], 'assays': [991, 4335], 'implementing': [992], 'hundreds': [998], 'known': [1000], 'putative': [1002], 'substrates,': [1005], 'clearly': [1008], 'demonstrated': [1009], 'extensive': [1011], 'role': [1012], 'on': [1017, 2082, 2511, 2702, 2832, 3122, 3373, 3408, 3656, 3767, 3987, 4449, 5646, 5659, 5919], 'cellular': [1018, 4275, 4408, 5613, 5840], 'regulation.': [1020, 5664], 'dimethyl': [1032, 1055, 1748, 2405], 'pimelimidate': [1033, 1056, 2406], 'basic': [1034, 1057, 2061, 2097, 2130, 2211, 2229, 2538, 4551, 4647, 4697, 4804, 5014, 5058], 'phase': [1037, 1060], 'high': [1038, 1061, 2618, 2908, 4179], 'dissociation': [1041, 1064], 'formic': [1042, 1065, 1977], 'Despite': [1067], 'successes': [1069], 'recently': [1070, 1289], 'achieved': [1071, 4076, 5246], 'use': [1074, 1495, 5255, 5868, 6077, 6099], 'antibody,': [1078, 2532, 3695, 3961, 5262, 5852], 'increased': [1079, 4147], 'sample': [1080, 1375, 1896, 2090, 2208, 2804, 3581, 3745, 4683, 5134, 5298, 5879, 6094], '(up': [1082], '∼35': [1084], 'mg)': [1085], 'and/or': [1086, 4191], 'completion': [1088], 'numerous': [1090], 'experimental': [1091], 'replicates': [1092, 5035, 5228], 'been': [1094, 1288, 3947, 4267], 'necessary': [1095], 'achieve': [1097, 4030], 'large': [1098, 3329, 3509], 'numbers': [1099], '(>5,000)': [1103], 'SILAC-based': [1107, 3176], 'For': [1284, 1626, 1655, 1692, 2225, 2369, 2517, 2677, 2990, 3110, 3174], 'example,': [1285], 'it': [1286, 4207], 'shown': [1290, 4411, 5106], 'more': [1294, 5510, 5692, 6079], 'than': [1295, 3624, 3713, 5701, 6080], '20,000': [1296, 1869], 'unique': [1297], 'is': [1300, 1422, 1426, 3525, 3851, 3874, 3937, 4011, 4027, 4057, 4112, 4119, 4208, 4231, 4350, 4410, 4417, 4650, 4665, 5245, 5302, 5509, 5691, 5918], 'possible': [1301], 'from': [1302, 1667, 2168, 2306, 3102, 3185, 3206, 3219, 3447, 3520, 3608, 3972, 4038, 4063, 4092, 4255, 4262, 4407, 5012, 5024, 5294, 5839, 5912, 6010], 'five': [1306], 'different': [1307], 'murine': [1308, 1338, 1404], 'tissues': [1309], '(8Wagner': [1310, 1376], 'Schölz': [1316, 1382], 'Kelstrup': [1318, 1384], 'C.D.': [1319, 1385], 'Young': [1320, 1386], 'Olsen': [1324, 1390, 2937], 'J.V.': [1325, 1391, 2938], 'Brakebusch': [1326, 1392], 'Proteomic': [1330, 1396], 'analyses': [1331, 1397], 'reveal': [1332, 1398], 'divergent': [1333, 1399], 'patterns': [1336, 1402], 'tissues.Mol.': [1339, 1405], '1578-1585Abstract': [1344, 1410], '(225)': [1352, 1418], 'However,': [1355], 'authors': [1358], 'indicate,': [1359], 'few': [1362], 'are': [1365, 3381, 3444, 3518, 3622, 3917, 4075, 4437, 4458, 4807, 5105, 5213, 5223, 6069], 'detected': [1366, 4135, 4489, 5148, 6063], 'any': [1368], 'an': [1372, 1964, 2083, 2143, 2727, 2839, 2849, 3361, 4299, 5001, 5050, 5062], 'individual': [1373], 'tissue': [1374], 'It': [1421], 'recognized': [1423], 'there': [1425], 'need': [1427, 3927], 'further': [1429, 4244, 6055, 6091], 'technology': [1434, 5893], 'increase': [1436, 2145, 3850, 4483, 5122], 'depth-of-coverage': [1438, 4253, 4712, 5910], 'attainable': [1439], '(9Bustos': [1450, 6020], 'Bakalarski': [1452, 6022], 'C.E.': [1453, 6023], 'Yang': [1454, 4566, 4724, 6024], 'Peng': [1456, 6026], 'Kirkpatrick': [1458, 6028], 'D.S.': [1459, 6029], 'Characterizing': [1460, 6030], 'peptide-based': [1464, 6034], 'enrichment.Mol.': [1466, 6036], '1529-1540Abstract': [1471, 6041], '(47)': [1479, 6049], 'Through': [1482], 'systematic': [1483], 'study': [1484, 3944, 3981, 4002, 4249], 'optimization': [1486, 5853, 5979, 6153], 'key': [1488], 'pre-analytical': [1489], 'variables': [1490], 'preparation': [1493, 1666], 'well': [1501, 3939, 4467, 5866], 'now': [1508], 'achieved,': [1509], 'first': [1512, 2254, 3020, 5906], 'time,': [1513, 5907], 'nonredundant': [1518, 4704], 'triple': [1525], 'encoded': [1526], 'starting': [1528, 3858, 4069, 4305, 5300, 5916], '5': [1530, 1738, 1742, 1901, 1913, 1997, 2004, 2079, 2103, 2154, 2853, 4425, 4917, 4983, 5305, 6081], 'mg': [1531, 1902, 3878, 4040, 4067, 4080, 4257, 4308, 4426, 5306, 6082], 'per': [1534, 1906, 4430, 4821, 5057, 5307, 6086], 'channel.': [1536], 'represents': [1538, 5118], '10-fold': [1540, 5121], 'improvement': [1541, 5235], 'over': [1542, 3414, 3862], 'previously': [1544, 2322, 3127, 3229, 4654, 4857, 5138, 5284], 'published': [1545, 4655, 4858, 5139], 'method': [1546, 2133, 4659, 5828], '(3Udeshi': [1547, 1751, 3128, 3230, 3457, 4496, 4860, 5157, 5709], 'To': [1593, 3758], 'generate': [1594, 2252, 4463, 4555], 'titration': [1595, 1627, 2518, 3111, 4095, 4248], 'curve': [1596, 3112], 'data,': [1597], 'Jurkat': [1598, 1640, 1658, 4908], 'E6-1': [1599], 'cells': [1600, 1641, 1659, 1701, 1726, 1799, 1865, 3973, 4263, 4436, 4909], '(ATCC)': [1601], 'grown': [1603, 1703], 'Roswell': [1605], 'Park': [1606], 'Memorial': [1607], 'Institute': [1608], '(RPMI)': [1609], '1640': [1610], 'media': [1611, 1664], '(Invitrogen)': [1612], 'supplemented': [1613, 1679], '10%': [1615, 1681], 'dialyzed': [1616, 1682], 'fetal': [1617, 1683], 'bovine': [1618, 1684], 'serum': [1619, 1685], '(Sigma-Aldrich),': [1620, 1686, 1844], 'penicillin,': [1621, 1687], 'streptomycin,': [1622, 1688], 'glutamine': [1624, 1690], '(Invitrogen).': [1625, 1691], 'data': [1628, 2896, 3380, 5671], 'where': [1629, 5141, 5299], 'was': [1632, 1638, 1697, 1897, 2021, 2064, 2091, 2134, 2198, 2304, 2318, 2393, 2541, 2612, 2755, 2762, 2800, 2812, 2865, 2872, 2880, 2984, 2995, 3013, 3028, 3055, 3071, 3079, 3182, 3310, 3997, 4146, 4829], 'held': [1633], 'constant': [1634, 4114], 'amount': [1637, 3697, 3856, 3958, 3967, 4143, 5003, 5856], 'varied,': [1639], 'treated': [1643, 1732, 3974, 4268, 4911], '4': [1645, 1734, 4913, 5524], 'h': [1646, 1735, 2445, 2510, 4914], '2': [1648, 1841, 1944, 2444, 3349, 4320], 'μm': [1649, 1739, 1743, 1857, 2717, 2722, 2742, 4918, 4984], 'MG-132': [1650, 3979, 4270, 5494, 5508, 5679], '(Calbiochem)': [1651], 'harvest.': [1654], 'experiments,': [1657, 2519, 2536, 3113, 3178, 3965], 'cultured': [1661], 'RPMI': [1663], '(custom': [1665], 'Caisson': [1668], 'Laboratories,': [1669], 'North': [1670], 'Logan,': [1671], 'UT)': [1672], 'deficient': [1673], 'l-arginine': [1675, 1705, 1710, 1717], 'l-lysine': [1677, 1708, 1721], 'each': [1693, 2537, 2826, 3687, 4159, 4827], 'experiment,': [1694], 'completed': [1698, 2065, 2394, 3311, 3875, 4338, 5031], '(Arg-0)': [1706], '(Lys-0),': [1709], '[13C6]HCl': [1711], '(Arg-6)': [1712], 'l-lysine-4,4,5,5-d4': [1714], '(Lys-4),': [1715], '[13C6,15N4]HCl': [1718], '(Arg-10)': [1719], '[13C6,15N2]HCl': [1722], '(Lys-8)': [1723], '(Sigma-Aldrich).': [1724], 'underwent': [1727], '∼6': [1728], 'doublings': [1729], 'either': [1737, 2524, 4022, 4916], 'MG132': [1740], '(Calbiochem),': [1741], 'PR-619': [1744, 5499, 5521, 5632, 5705], '(LifeSensors),': [1745], '0.5%': [1747], 'sulfoxide': [1749], '(DMSO)': [1750], 'Following': [1797, 1863, 1971, 4452, 5612], 'treatment,': [1798], 'washed': [1801, 2028, 2377, 2421, 2456, 2551, 2652], 'twice': [1802], '1×': [1804], 'PBS': [1805], 'pelleted': [1807], 'lysis.': [1810], 'SILAC-labeled': [1811, 4435, 4907, 5297], 'pellets': [1813], 'lysed': [1815, 4438], '4°C': [1817, 1876, 2447, 2486], 'denaturing': [1819, 4440], 'conditions.': [1820], 'Specifically,': [1821, 2250, 4906], 'lysis': [1824], 'buffer': [1825, 2465, 2500, 3635], 'contained': [1826], '8': [1827], 'm': [1828, 1945], 'urea,': [1829], '50': [1830, 1856, 1948, 2476, 2567, 2664], 'mm': [1831, 1836, 1839, 1852, 1861, 1914, 1928, 1949, 2104, 2155, 2385, 2404, 2429, 2441, 2468, 2473, 2477], 'Tris-HCl,': [1832, 1950], '7.5,': [1834, 1952], '150': [1835], 'NaCl,': [1837], '1': [1838, 1851, 1860, 2381, 2400, 2425, 2437, 2509, 3347, 3877, 4039, 4256, 4307], 'EDTA,': [1840], 'μg/ml': [1842, 1846], 'aprotinin': [1843], '10': [1845, 1927, 2472, 4066, 4079], 'leupeptin': [1847], '(Roche': [1848], 'Applied': [1849], 'Science),': [1850], 'phenylmethylsulfonyl': [1853], 'fluoride': [1854], '(PMSF),': [1855], 'PR-619,': [1858], 'chloroacetamide.': [1862], 'lysis,': [1864], 'centrifuged': [1867], '×': [1870, 2074, 2720, 2845, 2854], 'g': [1871], '15': [1873, 2030], 'min': [1874, 1919, 1932, 2415], 'remove': [1878, 3605], 'insoluble': [1879], 'material.': [1880], 'Protein': [1881], 'concentrations': [1882], 'estimated': [1884], 'bicinchoninic': [1887], 'acid': [1888, 1978, 2018, 3087], '(BCA)': [1889], 'assay': [1891, 4016], '(Pierce).': [1892], 'Each': [1893, 2089, 2609], 'triple-encoded': [1895, 4421, 5028], 'prepared': [1898], 'combining': [1900], 'state.': [1908], 'Proteins': [1909], 'reduced': [1911], 'dithiothreitol': [1915], '(DTT)': [1916], '45': [1918], 'room': [1921, 1934, 2411], 'temperature': [1922, 1935, 2412], 'subsequently': [1924, 1982, 2434], 'carbamidomethylated': [1925], 'iodoacetamide': [1929], '30': [1931, 2414], 'dark.': [1938], 'Lysates': [1939], 'then': [1941, 2420, 4443], 'diluted': [1942], 'urea': [1946], 'digested': [1954, 4042, 4459], 'overnight': [1955, 2051], '25°C': [1957], 'sequencing': [1959], 'grade': [1960], 'trypsin': [1961, 2998, 4461], '(Promega)': [1962], 'enzyme': [1965, 2993], 'substrate': [1967, 4379], 'ratio': [1968], '1:50.': [1970], 'digestion,': [1972], 'samples': [1973, 2046, 3404, 3551, 3611, 3654, 4495, 4705, 4850, 5899], 'acidified': [1975], '(FA)': [1979], '(Sigma-Aldrich)': [1980], 'desalted': [1983, 2577, 3554], '500-mg': [1986], 'tC18': [1987], 'Sep-Pak': [1988], 'SPE': [1989], 'cartridge': [1990], '(Waters).': [1991], 'C18': [1992, 2026, 2579, 2616, 3412, 3599, 3632, 3708, 3725], 'cartridges': [1993], 'conditioned': [1995, 2025, 2625, 2650], 'ml': [1998, 2005, 2014, 2031, 2039, 2095, 2382, 2401, 2426, 2438, 2461, 2497, 2556], '100%': [2000, 2630], 'MeCN,': [2001, 2008, 2042, 2102, 2153, 2631, 2636, 2668, 2685, 2764], 'followed': [2002, 2160], '50%': [2007, 2041, 2635, 2667, 3638], '0.1%': [2009, 2016, 2033, 2043, 2637, 2644, 2659, 2669, 2756, 2765], 'FA,': [2010, 2638, 2660, 2757], 'finally': [2012], '20': [2013, 2403, 2883, 3016, 3625], 'trifluoroacetic': [2017, 2571], '(TFA).': [2019, 2573], 'Sample': [2020], 'loaded': [2022, 2648], 'onto': [2023, 2649, 2712, 3542], 'cartridge,': [2027], 'TFA,': [2034], 'eluted': [2036, 2563, 2662, 2769, 3446], '6': [2038, 3031], 'FA.': [2044, 2645, 2670, 2766], 'Desalted': [2045], 'dried': [2048, 2291, 2674], 'completeness': [2050, 2293], 'Savant': [2054], 'SC210A': [2055], 'SpeedVac': [2056, 2296], 'concentrator': [2057], '(Thermo': [2058, 2698], 'Scientific).': [2059], 'Off-line': [2060], 'RP': [2062, 2098, 2131, 2212, 2230, 2539, 4552, 4648, 4698, 4805, 5015, 5059], 'custom-manufactured': [2068], 'Zorbax': [2069], '300': [2070, 2077], 'Extend-C18': [2071], 'column': [2072, 2611, 2715, 2807, 3413, 3545], '(9.4': [2073], '250': [2075, 2529, 3680, 3870], 'mm,': [2076], 'Å,': [2078], 'μm,': [2080], 'Agilent)': [2081], 'Agilent': [2084], '1100': [2085], 'series': [2086], 'HPLC': [2087, 2113, 2752], 'system.': [2088], 'resuspended': [2092, 2479, 2494, 2682], '1.8': [2094], 'solvent': [2099, 2119, 2148, 2170, 2753, 2760], '(2%': [2101], 'ammonium': [2105, 2156], 'formate,': [2106, 2157], '10),': [2108], 'separated': [2109], 'equally': [2110], 'into': [2111, 2238, 2770, 2947, 6110], 'two': [2112, 2422, 2615, 2653, 5217], 'vials': [2114], 'injected': [2116, 2711, 3655], 'successively': [2117], 'flow': [2123, 2193, 2776], 'rate': [2124, 2194, 2777, 3064], '3': [2126, 2196, 2844, 3296], 'ml/min.': [2127], '64-min': [2129], 'LC': [2132, 2205, 5271], 'utilized': [2135, 2861], 'fractionation.': [2138], 'gradient': [2140, 2165, 2784], 'consisted': [2141], 'initial': [2144, 4094], '8%': [2147, 2169], 'B': [2149, 2171, 2174, 2180, 2184, 2189, 2761, 2793], '(1.1%': [2150], 'B/min)': [2151, 2167], '(90%': [2152], '10)': [2159], '38-min': [2163], 'linear': [2164, 2783], '(0.5%': [2166, 2185], '27%': [2173], 'successive': [2176], 'ramps': [2177], '31%': [2179], '(1%': [2181], 'B/min),': [2182, 2186], '39%': [2183], '60%': [2188, 2792], '(3%': [2190], 'B/min).': [2191, 2795], 'ml/min': [2197], 'entirety': [2202], 'separation.': [2206], 'Upon': [2207], 'injection,': [2209], '80': [2210], 'fractions': [2213, 2231, 2241, 2261, 2278, 2492, 4558, 4664, 4699, 4719, 4806, 5086, 6115], 'collected': [2215], '96-well': [2218], 'polypropylene': [2219], 'round': [2220], 'bottom': [2221], 'plate': [2222], '(GE': [2223], 'Healthcare).': [2224], 'analysis,': [2228, 3550], 'pooled': [2233, 2255], 'noncontiguous': [2236], 'manner': [2237], 'eight': [2239, 4556, 4718, 4803, 5013, 5085], 'total': [2240, 2797, 4557, 5082], 'pooling': [2244, 2287, 4694], 'scheme': [2245], 'diagramed': [2246], 'Fig.': [2248, 3924, 4319, 4413, 5109, 5111, 5707], '2.': [2249, 3008, 4414], 'fraction': [2256, 2540, 4597, 4628, 4755, 4786, 4822, 4828, 5060], 'enrichment,': [2259, 2590, 3441, 4826], 'original': [2260], '1,': [2262], '9,': [2263], '17,': [2264], '25,': [2265], '33,': [2266], '41,': [2267], '49,': [2268], '57,': [2269], '65,': [2270], '73': [2272], 'combined.': [2274], 'remaining': [2276], 'seven': [2277], 'created': [2280], 'similar': [2286], 'strategy.': [2288], 'Fractions': [2289], 'concentrator.': [2297], 'In': [2298, 3668, 4432, 5801], 'this': [2299, 3692, 4433, 6128], 'study,': [2300], 'obtained': [2305, 3101, 3183, 5926], 'PTMScan®': [2308], 'motif': [2311], 'kit': [2313], '(Cell': [2314], 'Signaling': [2315, 6168], 'Technology)': [2316], 'produced': [2319], 'described': [2321, 3126, 3228, 4854, 5805, 5829, 6126], '(5Kim': [2323], 'beads': [2375, 2398, 2454, 2507, 2549, 2743, 3532, 3800, 4190], 'three': [2378, 2457, 5032, 5204, 5227], 'times': [2379, 2423, 2458, 2553, 2654], '100': [2384, 2627, 2632, 2641, 2656], 'sodium': [2386, 2474], 'borate,': [2387], '9.0.': [2389], 'After': [2390, 2450, 3440, 4825], 'washing,': [2391], 'cross-linking': [2392, 3778, 3790, 3893, 3922, 5849], 'resuspending': [2396], '(DMP)': [2407], 'incubated': [2409, 2435, 2502, 2522, 2542], 'while': [2416], 'rotating.': [2417], 'Beads': [2418], '200': [2428, 2440, 2779], 'ethanolamine,': [2430], '8.0,': [2432], 'ethanolamine': [2442], 'rotation.': [2449], 'blocking,': [2451], '1.5': [2460, 2496, 2555], 'ice-cold': [2463, 2558], 'immunoprecipitation': [2464], '(IAP)': [2466], '(50': [2467], 'MOPS,': [2469], '7.2,': [2471], 'phosphate,': [2475], 'NaCl),': [2478], 'IAP': [2481, 2499], 'buffer,': [2482], 'stored': [2484], 'future': [2488, 5889, 6151], 'use.': [2489], 'Dried': [2490], 'cross-linked': [2504, 4023, 4316, 4818, 5006, 5261], 'rotating': [2513], 'unit': [2514], '4°C.': [2516], 'peptides': [2520, 2561, 2595, 2672, 2680, 3118, 3398, 3427, 3443, 3541, 3722, 3826, 3906, 3911, 3993, 3996, 4037, 4062, 4104, 4137, 4156, 4186, 4200, 4225, 4285, 4304, 4406, 4465, 4469, 4488, 4715, 4812, 5011, 5056, 5104, 5244], '31,': [2525, 3866], '62,': [2526, 3867], '125,': [2527, 3868], 'μg': [2530, 2545, 3681, 3871, 4007, 4054, 4313, 4815], '31': [2544, 4053, 4149, 4312, 4814], 'antibody.': [2547, 3953], 'Antibody': [2548], 'four': [2552], 'PBS.': [2559], 'adding': [2565], '2×': [2566, 2640], 'μl': [2568, 2628, 2633, 2642, 2657, 2665], '0.15%': [2570, 3455], 'acetic': [2572], 'Peptide': [2574], 'supernatants': [2575], 'StageTips': [2580], '(10Rappsilber': [2581], 'Ishihama': [2585, 3565, 3729], 'Protocol': [2587], 'micro-purification,': [2589], 'pre-fractionation,': [2591], 'storage': [2593], 'StageTips.Nat.': [2599], 'Protoc.': [2600, 3336, 5951], '2007;': [2601], '2:': [2602], '1896-1906Crossref': [2603], '(2590)': [2606], 'StageTip': [2610, 3600, 3633, 3645, 3709, 3726], 'packed': [2613, 2734], 'EmporeTM': [2617], 'performance': [2619], 'extraction': [2620, 3572, 3736], 'disks': [2621], '(3': [2622], 'm)': [2623], 'Peptides': [2646, 2767], 'StageTips,': [2651], 'Eluted': [2671], 'completeness.': [2676], 'MS': [2678, 2895, 5269], 'analyses,': [2679], '3%': [2684], '1%': [2686], 'FA': [2687], 'analyzed': [2689, 2898, 4831], 'nanoflow-UPLC-HCD-MS/MS': [2691], 'Q': [2694, 2810, 4836], 'Exactive': [2695, 2811, 4837], 'spectrometer': [2697, 2773, 3659], 'Fisher': [2699], 'Scientific)': [2700], 'coupled': [2701], 'line': [2703], 'Proxeon': [2706], 'Easy-nLC': [2707], '1000.': [2708], 'Samples': [2709], 'microcapillary': [2714, 3411, 3544], '(360': [2716], 'outer': [2718], 'diameter': [2719], '75': [2721], 'inner': [2723], 'diameter)': [2724], 'equipped': [2725], 'integrated': [2728, 2946], 'electrospray': [2729, 3429], 'emitter': [2730], 'tip': [2731], '(10': [2732], 'μm),': [2733], '24': [2736], 'cm': [2737], 'ReproSil-Pur': [2739], 'C18-AQ': [2740], '1.9': [2741], '(Dr.': [2744], 'Maisch': [2745], 'GmbH)': [2746], 'heated': [2748], '50°C.': [2750], '90%': [2763], 'nl/min': [2780], '0.3%B/min,': [2786], 'ramp': [2790], '(10%': [2794], 'run': [2798], 'time': [2799, 2860, 2879], '∼150': [2801], 'min,': [2802], 'loading': [2805], 'conditioning.': [2808], 'operated': [2813], 'data-dependent': [2816], 'mode': [2817], 'acquiring': [2818], 'HCD': [2819, 5099], 'MS/MS': [2820, 2863, 3363, 5100], 'scans': [2821, 2864], '(R': [2822, 2829], '=': [2823, 2830], '17,500)': [2824], 'MS1': [2827, 2840], 'scan': [2828], '70,000)': [2831], '12': [2834], 'most': [2835, 5823], 'abundant': [2836, 3418, 3425, 3647], 'ions': [2837, 2847], 'ion': [2841, 2859], 'target': [2842, 2851, 3935], '106': [2846], 'MS2': [2850], '104': [2855], 'ions.': [2856], 'maximum': [2858, 3001, 4032], '120': [2866], 'ms;': [2867], 'HCD-normalized': [2869], 'collision': [2870], 'set': [2873, 2881, 2996, 3006, 3014, 3029, 3072, 3080], '25;': [2875], 'dynamic': [2877], 'exclusion': [2878, 2891], 's,': [2884], 'match': [2888], 'functions': [2892, 3091, 4359], 'enabled.': [2894, 3093], 'MaxQuant': [2901, 2906, 2949, 2983, 3104, 3187], '(11Cox': [2902], 'rates,': [2911], 'individualized': [2912], 'p.p.b.-range': [2913], 'accuracies,': [2915], 'proteome-wide': [2917], 'quantification.Nat.': [2919], '2008;': [2921, 5952], '26:': [2922], '1367-1372Crossref': [2923], '(9223)': [2926], '12Cox': [2929], 'Neuhauser': [2931], 'Michalski': [2933], 'Scheltema': [2935], 'R.A.': [2936, 3323], 'Andromeda:': [2941], 'search': [2944, 3021], 'engine': [2945], 'environment.J.': [2950], 'Proteome': [2951], 'Res.': [2952], '10:': [2954], '1794-1805Crossref': [2955], '(3474)': [2958], 'software': [2961], 'version': [2962], '1.3.0.5': [2963], 'searched': [2965, 3048, 3056], 'against': [2966], 'human': [2968, 4604, 4762], 'Uniprot': [2969], 'database': [2970], 'containing': [2971, 4470], '81,470': [2972], 'entries.': [2973], 'list': [2975], '248': [2977], 'common': [2978], 'laboratory': [2979], 'contaminants': [2980, 3419, 3607, 3765], 'provided': [2981, 4012], 'also': [2985, 3889, 3918, 5666, 6145], 'added': [2986], 'database.': [2989], 'searching,': [2991], 'specificity': [2994], 'missed': [3004], 'cleavages': [3005], 'precursor': [3010], 'tolerance': [3012], 'ppm': [3017, 3032], '(used': [3022], 'nonlinear': [3024], 're-calibration)': [3026], 'main': [3035], 'search.': [3036], 'Oxidized': [3037], 'methionines,': [3038], 'Gly-Gly': [3039, 3105, 3188], 'addition': [3040], 'lysines,': [3042], 'N-terminal': [3044], 'acetylation': [3046], 'variable': [3050], 'modifications.': [3051], 'Carbamidomethylation': [3052], 'cysteines': [3054], 'fixed': [3059], 'modification.': [3060], 'false': [3062], 'discovery': [3063], 'peptide,': [3066], 'protein,': [3067], '1%;': [3074], 'minimum': [3076], 'length': [3078], '6,': [3082], 'filter-labeled': [3085], 'requantification': [3090], 'information': [3099, 3124, 3181], 'evidence': [3108], 'tables.': [3109], 'identified': [3114, 3827, 3913, 3919, 3991, 3998, 4102, 4157, 4173, 4283, 4298], 'nondistinct': [3116], 'grouped': [3120], 'based': [3121, 4448], 'localization': [3123, 5077], 'benchmarking': [3177], 'level': [3180, 3693, 6007, 6108], 'directly': [3184, 4808], 'table.': [3190], 'Sites': [3191], 'confidently': [3192, 5073], 'localized': [3193, 5074], '(localization': [3194], 'probability': [3195, 5078], '≥0.75)': [3197], 'C-terminal': [3201], 'residue': [3203], 'removed': [3205], 'dataset.': [3208], 'Regulated': [3209], 'determined': [3213], 'moderated': [3216], 'T-statistic': [3217], 'calculated': [3218], 'limma': [3221], 'package': [3222], 'R': [3225], 'environment': [3226], '13Smyth': [3276], 'G.K.': [3277], 'Linear': [3278], 'models': [3279], 'empirical': [3281], 'bayes': [3282], 'methods': [3283, 5872, 5930], 'assessing': [3285], 'differential': [3286], 'microarray': [3289], 'experiments.Stat.': [3290], 'Appl.': [3291], 'Genet.': [3292], 'Mol.': [3293], 'Biol.': [3294, 4969], '2004;': [3295], '(Article': [3297], '3)Crossref': [3298], '(9178)': [3301], 'Gene': [3304], 'ontology': [3305], 'process': [3307, 4416], 'term': [3308], 'DAVID': [3314, 3333], 'bioinformatics': [3315, 3334], 'resource': [3316], '(14Huang': [3317], 'da': [3318], 'Sherman': [3320], 'Lempicki': [3322], 'integrative': [3326], 'gene': [3330], 'lists': [3331], 'resources.Nat.': [3335], '2009;': [3337, 5986], '4:': [3338], '44-57Crossref': [3339], '(25496)': [3342], 'Supplemental': [3345], 'Tables': [3346], 'contain': [3350], 'embedded': [3351], 'hyperlinks': [3352], 'link': [3354], 'Spectrum': [3357], 'Mill': [3358], 'viewer': [3359], 'showing': [3360], 'annotated': [3362, 5098], 'spectrum': [3364], 'peptides.': [3367, 3667, 4175], 'We': [3368, 3786, 3888, 4243, 4644, 4840, 5030, 5665, 5901, 6052, 6119, 6159], 'recommend': [3369], 'Internet': [3371], 'Explorer': [3372], 'Windows': [3374], 'best': [3376], 'results.': [3377], 'All': [3378], 'raw': [3379], 'available': [3382], 'ftp://ftp.broadinstitute.org/distribution/proteomics/public_datasets/.': [3384], 'Our': [3385, 4001, 4203, 4396], 'previous': [3386, 5486, 5673], 'work': [3387, 4859, 5140, 6129], 'indicated': [3392], 'contaminant': [3394], 'nontryptic': [3397], 'frequently': [3400], 'present': [3401], 'K-ε-GG-enriched': [3403], 'retained': [3407], 'on-line': [3410, 3547], 'multiple': [3415, 4596, 4754], 'runs.': [3416], 'These': [3417], 'compromised': [3420], 'lower': [3424], 'often': [3433], 'resulted': [3434, 5017, 5820], 'poor': [3436], 'chromatographic': [3437], 'peak': [3438], 'shapes.': [3439], 'K-ε-GG-modified': [3442, 5103], 'typically': [3445, 3553], 'low': [3452, 3815, 6006], 'TFA': [3456], 'Analysis': [3503], 'eluates': [3506], 'indicates': [3507, 4177, 4327], 'light': [3512, 3618, 3702, 3811], 'heavy': [3514, 3620, 3700, 3809], 'chain': [3515, 3703, 3812], 'subunits': [3517], 'released': [3519, 3699], 'supplied': [3526, 3797], 'noncovalently': [3527], 'bound': [3528], '(Fig.': [3533, 3640, 3818, 3830, 3882, 4045, 4084, 4097, 4121, 4201, 4562, 4720, 4823, 4994, 5087, 5155, 5229], '1a).': [3534, 3641], 'Furthermore,': [3535], 'injection': [3538], 'C18-based': [3556], 'STop': [3557], 'And': [3558], 'Go': [3559], 'Extraction': [3560], 'Tips': [3561], '(StageTips)': [3562], '(15Rappsilber': [3563, 3727], 'Stop': [3569, 3733], 'go': [3571, 3735], 'tips': [3573, 3737], 'matrix-assisted': [3575, 3739], 'laser': [3576, 3740], 'desorption/ionization,': [3577, 3741], 'nanoelectrospray,': [3578, 3742], 'LC/MS': [3580, 3744], 'pretreatment': [3582, 3746], 'proteomics.Anal.': [3584, 3748], 'Chem.': [3585, 3749, 5985], '2003;': [3586, 3750], '75:': [3587, 3751], '663-670Crossref': [3588, 3752], '(1804)': [3591, 3755], 'Surprisingly,': [3594], 'find': [3596, 3787, 4645, 5208], 'conventional': [3598, 3707], 'desalting': [3601, 4661, 5877], 'does': [3602, 3898, 4105], 'not': [3603, 3899, 3946, 4106, 4266, 4343, 4666, 5875, 6131], 'effectively': [3604], 'enriched': [3609, 4809, 5645, 5658], 'despite': [3612], 'fact': [3614], 'both': [3616, 5635], 'chains': [3621, 5700], 'greater': [3623, 3712], 'kDa': [3626], 'size,': [3628], 'final': [3631, 3653], 'elution': [3634, 3817], 'contains': [3636], 'acetonitrile': [3639], 'Therefore,': [3642], 'even': [3643, 6005], 'desalting,': [3646], 'non-K-ε-GG': [3648, 3995, 4103, 4155, 4174, 4185, 4464], 'species': [3649], 'remain': [3650], '(MS)': [3660], 'hamper': [3662], 'addition,': [3669], 'manufacturer': [3671], 'suggests': [3676], 'reagent': [3685], 'experiment.': [3690, 4229], 'With': [3691, 5634], 'fragments': [3704, 3813], 'surpasses': [3705], 'capacity': [3710], '10×,': [3714], 'likely': [3716, 4232, 6074], 'compromises': [3717], 'binding': [3719, 3903, 4183], 'diminish': [3759], 'deleterious': [3761], 'effects': [3762], 'antibody-derived': [3764], 'peptides,': [3774], 'evaluated': [3776], 'solid': [3784], 'support.': [3785], 'commercially': [3796], 'DMP': [3802, 3921, 4817], 'prevents': [3803], 'release': [3804], 'majority': [3807, 3909], '1b)': [3819], 'increases': [3821, 4169, 5681, 6056], '∼25%': [3829], '1c)': [3831], '(16Harlow': [3832], 'E.': [3833, 4945], 'Lane': [3834], 'Using': [3836], 'Antibodies:': [3837], 'Laboratory': [3839, 3844], 'Manual.': [3840], 'Cold': [3841], 'Spring': [3842], 'Harbor': [3843], 'Press,': [3845], '1999:': [3846], '321-325Google': [3847], 'largely': [3852], 'independent': [3853], 'range': [3864], 'when': [3872, 4109], '1c': [3883, 4046], 'supplemental': [3885, 4048, 4087, 4124, 4322, 5093, 5108], 'Table': [3886, 4049, 4088, 4125, 4323, 5094, 5274], '1).': [3887, 3925, 4050, 4089, 4126, 4324], 'show': [3890, 4205, 5489], 'alter': [3901], 'its': [3902], 'because': [3907, 4660], '(62%)': [3912], 'noncross-linked': [3915, 4025], '(supplemental': [3923, 4318, 5273, 5522, 5706], 'sufficient': [3930, 4058], 'capture': [3933], 'all': [3934, 4717, 5226, 5283, 5686, 5885], 'antigen': [3936], 'generally': [3938], 'understood,': [3940], 'but': [3941, 5507, 6071, 6143], 'reported': [3948, 5279, 5285], 'commercial': [3951, 4019], 'titrated': [3956], 'parallel': [3964, 5895], 'derived': [3971, 4261], 'inhibitor': [3978, 4347, 4923, 4964, 4988], 'interplay': [3983], 'factors': [3986], 'LC-MS/MS.': [4000], 'revealed': [4003, 4161], '∼31': [4006], '(1/8': [4008], 'what': [4010], 'product)': [4020], 'needed': [4028, 5859], 'yield': [4033, 4222], 'lysate': [4044], 'Remarkably,': [4051], 'just': [4052], 'enrich': [4060, 5009], 'material': [4070, 5301, 5917], 'saturating': [4073], 'conditions': [4074, 4441, 5272], 'above': [4078], '1d': [4085, 4122], 'As': [4090, 4542], 'expected': [4091], '1c),': [4098], 'kept': [4113], 'varied': [4120], 'Quite': [4127], 'unexpectedly,': [4128], 'found': [4130, 5042, 5638], 'decreased': [4138, 4286], 'beyond': [4148], 'μg.': [4150], 'Tracking': [4151], 'increasing': [4163, 5513, 5695], 'steadily': [4168], 'degree': [4180, 5923], 'nonspecific': [4182], 'itself,': [4194], 'impedes': [4196], '1c).': [4202], 'results': [4204, 5278], 'imperative': [4209], 'determine': [4211], 'optimal': [4213], 'combination': [4218], 'maximize': [4220], 'given': [4228], 'true': [4233], 'other': [4235, 6155], 'antibody-based': [4236], 'post-translational': [4239, 6156], 'modification': [4240], 'protocols.': [4242], 'extended': [4245], 'compare': [4251], 'obtainable': [4254, 5911], 'had': [4265, 4273], 'therefore': [4272], 'ubiquitination.': [4278], 'Although': [4279], '∼40%': [4288], 'absence': [4291], 'inhibitor,': [4294], 'still': [4296], 'successfully': [4297], 'average': [4300, 5051, 5063], '5,030': [4302], 'chemically': [4315, 5005, 5260], 'result': [4326, 4674, 5117], 'under': [4329, 4439, 4690], 'technical': [4331, 5251], 'conditions,': [4332], 'can': [4336], 'be': [4337, 6132, 6146], 'systems': [4340], 'undergone': [4344], 'prolonged': [4345], 'important': [4351], 'differentiate': [4353], 'involved': [4356, 5648, 5661], 'physiological': [4358], 'versus': [4360, 6102], 'occur': [4363], 'due': [4364], 'stress': [4366], 'induced': [4367], 'inhibiting': [4369], 'function': [4371], '(17Harper': [4372], 'Tan': [4374], 'M.-K.': [4375], 'Proteomics-based': [4376], 'E3': [4378], 'identification.Mol.': [4380], '1541-1550Abstract': [4385], '(56)': [4393], 'deep': [4402], 'coverage': [4403, 5925], 'lysates': [4409], 'illustrated': [4418], 'label/condition.': [4431], 'equal': [4446], 'content.': [4451], 'reduction': [4453], 'alkylation,': [4455], 'remnant.': [4473], 'Previously,': [4474], 'strong': [4478, 4656], 'cation': [4479, 4657], 'exchange': [4480, 4658], '3–4-fold': [4491], 'nonfractionated': [4494], 'part': [4543], 'protocol,': [4547], 'implemented': [4550], 'chromatography': [4553, 4594, 4626, 4649, 4752, 4784], '2)': [4563], '(18Wang': [4564, 4722], 'F.': [4567, 4616, 4725, 4774], 'Gritsenko': [4568, 4726], 'M.A.': [4569, 4727], 'Wang': [4570, 4728], 'Clauss': [4572, 4730], 'Liu': [4574, 4732], 'Shen': [4576, 4617, 4734, 4775], 'Monroe': [4578, 4736], 'Lopez-Ferrer': [4580, 4738], 'Reno': [4582, 4740], 'Moore': [4584, 4742], 'R.J.': [4585, 4743], 'Klemke': [4586, 4744], 'R.L.': [4587, 4745], 'Camp': [4588, 4619, 4746, 4777], '2nd,': [4589, 4620, 4747, 4778], 'D.G.': [4590, 4621, 4748, 4779], 'Smith': [4591, 4622, 4749, 4780], 'R.D.': [4592, 4623, 4750, 4781], 'Reversed-phase': [4593, 4751], 'concatenation': [4598, 4629, 4756, 4787], 'strategy': [4599, 4757], 'proteome': [4601, 4759], 'profiling': [4602, 4760], 'MCF10A': [4605, 4763], 'cells.Proteomics.': [4606, 4764], '2019-2026Crossref': [4609, 4767], '(403)': [4612, 4770], '19Yang': [4615, 4773], 'High-pH': [4624, 4782], 'reversed-phase': [4625, 4783], '2D': [4631, 4789], 'analysis.Expert': [4633, 4791], 'Rev.': [4634, 4792], '9:': [4637, 4795], '129-134Crossref': [4638, 4796], '(203)': [4641, 4799], 'superior': [4651], 'required': [4667], 'volatile': [4677], 'buffers': [4678], 'used,': [4679], 'greatly': [4681], 'simplifies': [4682], 'handling': [4684], 'improves': [4686], 'recovery': [4688], '(see': [4689], '"Experimental': [4691], 'Procedures").': [4692], 'Additionally,': [4693], 'nonadjacent': [4696], 'generates': [4700], 'uniform': [4702], 'consistent': [4711], 'across': [4716], '3b)': [4721], '2).': [4824, 5095], 'individually': [4830], 'UPLC-HCD-MS/MS': [4833], 'spectrometer.': [4839], 'benchmarked': [4841], 'identical': [4851], 'reversible': [4921], '2,6-diaminopyradine-3,5-bis(thiocynate)': [4924], '(PR-619)': [4925], '(20Altun': [4926], 'Kramer': [4928], 'H.B.': [4929], 'Willems': [4930], 'L.I.': [4931], 'McDermott': [4932], 'J.L.': [4933, 4953], 'Leach': [4934], 'C.A.': [4935], 'Goldenberg': [4936], 'Kumar': [4938], 'K.G.': [4939], 'Konietzny': [4940], 'Fischer': [4942], 'Kogan': [4944], 'Mackeen': [4946], 'M.M.': [4947], 'McGouran': [4948], 'Khoronenkova': [4950], 'S.V.': [4951], 'Parsons': [4952], 'Dianov': [4954], 'G.L.': [4955], 'Nicholson': [4956], 'Kessler': [4958], 'B.M.': [4959], 'Activity-based': [4960], 'accelerates': [4963], 'deubiquitylating': [4967], 'enzymes.Chem.': [4968], '18:': [4971], '1401-1412Abstract': [4972], '(279)': [4980], 'Scholar),': [4982, 5993], 'MG-132,': [4989, 5616], 'left': [4992], 'untreated': [4993], '3a).': [4995], 'new': [4997], 'employs': [5000], 'fractions,': [5016], 'unparalleled': [5019], 'sample.': [5029], 'full': [5033], 'label': [5038, 6087], 'switching,': [5039], 'replicate': [5047, 5154], 'quantify': [5049], '3,143': [5053], '20,004': [5065], '18,133': [5071], '>0.75': [5080], '3,': [5088, 5112], 'b': [5089, 5113], 'c,': [5091], 'Examples': [5096], 'spectra': [5101], '3A,': [5110], 'c.': [5115], 'nearly': [5119, 5685], 'quantified': [5127, 5150, 5214, 5224, 5619, 6065], '2,931': [5143], '1,716': [5145], '3c)': [5156], 'Across': [5203], 'replicates,': [5206, 5219], '14,181': [5210], 'least': [5218], '8,269': [5221], '3d).': [5230], 'Taken': [5231], 'together,': [5232, 5818], 'marked': [5234], 'made': [5236], 'enhancements,': [5252], 'input,': [5259], 'methods,': [5266], 'advanced': [5268], '3).': [5275], 'Notably,': [5276], 'here': [5280], 'far': [5281], 'surpass': [5282], 'yields': [5286], 'channel': [5308], 'Similar': [5484], 'findings,': [5487], 'cause': [5500], 'significant': [5501], 'landscape,': [5506], 'effective': [5511, 5693], 'Figs.': [5523], '5)': [5526], '∼60%': [5617], 'reproducibly': [5623], 'regulated,': [5624], 'whereas': [5625, 5653], '∼10%': [5626], 'regulated': [5630], 'treatment.': [5633], 'up-regulated': [5641], 'cycle': [5651], 'progression,': [5652], 'down-regulated': [5654], 'translational': [5663], 'noted': [5667], 'current': [5670], 'corroborate': [5672], 'findings': [5674], 'polyubiquitin': [5687, 5699], 'linkage': [5688], 'types': [5689], '6)': [5708], 'summary,': [5802], 'critical': [5809], 'enhancements': [5810], 'pipeline': [5815], 'that,': [5816], 'taken': [5817], 'robust,': [5824], 'sensitive,': [5825], 'date': [5831], 'lysates.': [5841], 'introduced,': [5847], 'efficient': [5861], 'K-ε-GG-peptides,': [5864], 'separation': [5871], 'do': [5874], 'require': [5876, 6075], 'LC-MS/MS,': [5884], 'lend': [5886], 'themselves': [5887], 'automation': [5890], 'processing': [5896], 'many': [5898], 'simultaneously.': [5900], 'shown,': [5903], 'par': [5920], 'detect': [5932], 'phosphorylation': [5934, 5946], '(21Villén': [5936], 'SCX/IMAC': [5941], 'spectrometry.Nat.': [5950], '3:': [5953], '1630-1638Crossref': [5954], '(500)': [5957], '22Ficarro': [5960], 'S.B.': [5961], 'Adelmant': [5962], 'Tomar': [5964], 'M.N.': [5965], 'Zhang': [5966], 'Cheng': [5968], 'V.J.': [5969], 'Marto': [5970], 'J.A.': [5971], 'Magnetic': [5972], 'bead': [5973], 'processor': [5974], 'rapid': [5976], 'evaluation': [5977], 'parameters': [5981], 'phosphopeptide': [5983], 'enrichment.Anal.': [5984], '81:': [5987], '4566-4575Crossref': [5988], 'moving': [5994], 'field': [5996], 'closer': [5997], 'goal': [6000], 'detecting': [6002], 'quantifying': [6004], 'limiting': [6011], 'note': [6053], 'possible,': [6070], 'they': [6072], 'will': [6073, 6130, 6144], 'state': [6088], 'decreases': [6092], 'complexity,': [6095], 'example': [6097], 'two-state': [6101], 'three-state': [6103], 'larger': [6112], 'anticipate': [6120], 'techniques': [6123], 'refinements': [6125], 'usefulness': [6135], 'valuable': [6148], 'modification-specific': [6157], 'thank': [6160], 'Jeffrey': [6161], 'Silva': [6162], 'Charles': [6164], 'Nogawe': [6165], 'Cell': [6167], 'Technology': [6169], 'helpful': [6171], 'discussions.': [6172], 'Download': [6173], '.zip': [6174], '(99.11': [6175], 'MB)': [6176], 'Help': [6177], 'zip': [6179], 'files': [6180]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2118453371', 'counts_by_year': [{'year': 2024, 'cited_by_count': 10}, {'year': 2023, 'cited_by_count': 21}, {'year': 2022, 'cited_by_count': 38}, {'year': 2021, 'cited_by_count': 38}, {'year': 2020, 'cited_by_count': 31}, {'year': 2019, 'cited_by_count': 27}, {'year': 2018, 'cited_by_count': 32}, {'year': 2017, 'cited_by_count': 25}, {'year': 2016, 'cited_by_count': 20}, {'year': 2015, 'cited_by_count': 20}, {'year': 2014, 'cited_by_count': 20}, {'year': 2013, 'cited_by_count': 11}], 'updated_date': '2024-12-08T21:18:22.275820', 'created_date': '2016-06-24'}