Publication Information

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[8, 252, 520, 555, 582, 649, 768, 771, 1082, 1096, 1263, 1276, 1421, 2949, 3547, 3561, 3957, 4007], 'tags': [9, 253, 556, 610, 656, 691, 807], '(TMTs)': [10, 254, 557], 'is': [11, 255, 745, 1106, 1638], 'increasingly': [12, 256], 'being': [13, 257], 'applied': [14, 258, 1320], 'large-scale': [16, 260], 'proteomic': [17, 261, 1628], 'studies.': [18, 262], 'Experiments': [19, 263], 'focusing': [20, 264], 'on': [21, 235, 265, 479, 819, 1515, 1545, 1607, 1739, 2202, 2929, 2983, 2990, 3574, 3587, 3616, 3634, 3649, 3736, 4204, 4282, 4349], 'proteoform': [22, 266, 811, 847, 1353], 'analysis': [23, 203, 267, 447, 590, 960, 986, 1824, 1898, 2683, 3384, 4366], 'in': [24, 32, 176, 197, 268, 276, 420, 441, 502, 522, 618, 643, 671, 704, 720, 726, 738, 795, 1119, 1198, 1394, 1495, 1524, 1584, 1640, 1643, 1667, 1696, 1711, 1762, 1793, 1954, 1991, 2167, 2171, 2281, 2415, 2434, 2476, 2497, 2507, 2575, 2611, 2713, 2744, 2812, 2910, 2955, 3032, 3034, 3040, 3099, 3115, 3128, 3134, 3424, 3803, 4042, 4149, 4169, 4173, 4253, 4357], 'drug': [25, 269], 'time': [26, 270, 3170, 3475], 'course': [27, 271], 'or': [28, 31, 272, 275, 1691, 1704, 1726, 1789, 2178, 2239, 2260, 2292, 2319, 2353, 2409, 2485, 2545, 2581, 2933, 2945, 3080, 3117, 3164, 3175, 3212, 3609, 3626, 3652, 4355, 4421, 4436], 'perturbation': [29, 273], 'studies': [30, 49, 274, 293], 'large': [33, 277], 'patient': [34, 278], 'cohorts': [35, 279, 989], 'greatly': [36, 280, 729], 'benefit': [37, 281], 'from': [38, 113, 138, 282, 357, 382, 527, 665, 688, 717, 1500, 1937, 2494, 2598, 3021, 3089, 3109, 3122, 3418, 4336, 4414], 'the': [39, 61, 71, 92, 191, 211, 216, 222, 283, 305, 315, 336, 435, 455, 460, 466, 503, 530, 622, 625, 644, 648, 651, 655, 672, 689, 694, 705, 710, 721, 731, 752, 781, 844, 979, 985, 1107, 1121, 1128, 1350, 1425, 1516, 1525, 1530, 1539, 1546, 1556, 1562, 1595, 1601, 1608, 1611, 1620, 1623, 1635, 1644, 1668, 1684, 1734, 1745, 1764, 1810, 1813, 1917, 1930, 2231, 2236, 2282, 2443, 2453, 2508, 2528, 2702, 2723, 2761, 2863, 2978, 2984, 3141, 3218, 3228, 3265, 3270, 3523, 3566, 3579, 3683, 3758, 3940, 3954, 3983, 4037, 4177, 4184, 4190, 4264, 4337, 4358, 4406, 4419, 4462, 4491], 'reproducible': [40, 284], 'quantification': [41, 285, 586, 714, 736, 743, 821, 1102, 3491], 'of': [42, 53, 55, 57, 74, 94, 101, 110, 116, 127, 159, 179, 190, 204, 224, 286, 297, 299, 301, 318, 338, 345, 354, 360, 371, 403, 423, 434, 448, 468, 493, 505, 547, 560, 591, 607, 654, 661, 681, 697, 715, 733, 751, 784, 799, 822, 846, 870, 889, 961, 981, 987, 990, 1101, 1110, 1123, 1154, 1191, 1229, 1330, 1352, 1389, 1427, 1520, 1532, 1538, 1541, 1564, 1581, 1600, 1610, 1622, 1634, 1652, 1660, 1736, 1747, 1786, 1812, 1899, 1939, 2142, 2230, 2383, 2488, 2535, 2543, 2548, 2572, 2601, 2684, 2716, 2730, 2737, 2769, 2852, 2974, 3013, 3078, 3152, 3162, 3172, 3188, 3205, 3210, 3238, 3243, 3256, 3282, 3287, 3303, 3385, 3430, 3452, 3466, 3471, 3670, 3713, 3752, 3801, 3838, 3852, 3855, 3858, 3866, 3884, 3902, 3915, 3929, 4032, 4048, 4164, 4166, 4176, 4201, 4241, 4250, 4367, 4398, 4408, 4444, 4465, 4490], 'single': [43, 287, 823, 3810], 'peptides': [44, 58, 111, 288, 302, 355, 548, 716, 824, 1585, 1935, 2431, 2596, 2710, 2825, 2923, 2964, 2987, 3410, 4313, 4333, 4391], 'across': [45, 289, 825, 1432, 4454], 'samples.': [46, 290], 'However,': [47, 291, 1513], 'such': [48, 59, 292, 303, 552, 1321], 'often': [50, 294], 'require': [51, 295], 'hundreds': [54, 298], 'micrograms': [56, 300], 'that': [60, 90, 304, 334, 817, 1577, 3793, 4277, 4301, 4314, 4341], 'cost': [62, 73, 306, 317, 1109], 'reagents': [65, 309, 551, 786, 2490, 2734], 'represents': [66, 310], 'a': [67, 82, 99, 198, 311, 326, 343, 442, 491, 659, 796, 871, 1328, 1570, 1649, 1774, 1821, 1958, 2339, 2356, 2486, 2540, 2834, 2940, 2971, 2991, 3010, 3017, 3049, 3075, 3085, 3105, 3118, 3150, 3208, 3236, 3241, 3254, 3301, 3406, 3427, 3434, 3469, 3631, 3638, 3646, 3665, 3737, 3743, 3787, 3809, 4021, 4198, 4426, 4430, 4438], 'major': [68, 312], 'contribution': [69, 313], 'to': [70, 140, 153, 314, 384, 397, 498, 529, 562, 614, 658, 693, 748, 1326, 1529, 1553, 1626, 1678, 1720, 1732, 1743, 1751, 1770, 1817, 1929, 2206, 2218, 2224, 2307, 2388, 2391, 2460, 2539, 2579, 2939, 2961, 3023, 3054, 3091, 3111, 3124, 3190, 3197, 3289, 3405, 3420, 3478, 3599, 3688, 3698, 3705, 3731, 3873, 3890, 3919, 3945, 3962, 3965, 3971, 3987, 3989, 3992, 3996, 4011, 4211, 4226, 4247, 4263, 4344, 4418], 'overall': [72, 316, 1547], 'an': [75, 319, 2930, 2958, 3155, 3201, 3278, 3402, 3414, 3448, 3462, 4172], 'experiment.': [76, 320, 741], 'Here,': [77, 321], 'we': [78, 220, 322, 464, 1559], 'describe': [79, 323], 'and': [80, 84, 103, 108, 118, 130, 133, 145, 156, 164, 182, 185, 201, 232, 324, 328, 347, 352, 362, 374, 377, 389, 400, 408, 426, 429, 445, 476, 507, 635, 668, 700, 712, 770, 867, 877, 958, 977, 1057, 1113, 1202, 1226, 1231, 1244, 1302, 1318, 1497, 1518, 1568, 1572, 1618, 1629, 1648, 1658, 1663, 1688, 1694, 1723, 1730, 1742, 1896, 1926, 1942, 1950, 1962, 1971, 1977, 1986, 1993, 2003, 2010, 2013, 2161, 2182, 2195, 2343, 2349, 2369, 2395, 2425, 2437, 2468, 2482, 2503, 2511, 2524, 2527, 2554, 2562, 2587, 2603, 2681, 2722, 2757, 2760, 2786, 2819, 2862, 2917, 3016, 3072, 3083, 3136, 3167, 3207, 3382, 3468, 3484, 3490, 3603, 3618, 3655, 3668, 3672, 3701, 3717, 3724, 3760, 3767, 3783, 3806, 3825, 3831, 3840, 3864, 3870, 3877, 3881, 3887, 3905, 3924, 3927, 3969, 3975, 3999, 4005, 4034, 4220, 4228, 4231, 4266, 4287, 4379, 4382, 4400, 4474, 4483], 'evaluate': [81, 325, 1809], 'robust': [83, 327, 820, 1571], 'cost-effective': [85, 329], 'protocol': [86, 193, 330, 437, 1576, 1602, 1625, 1749, 1816, 1919], 'TMT': [88, 144, 155, 217, 332, 388, 399, 461, 740, 785, 872, 982, 1124, 1306, 1574, 1590, 1686, 1718, 1765, 1924, 2704, 2733, 2742, 3485, 3882, 3925, 3974, 4281, 4306, 4319, 4348, 4409, 4427, 4457, 4468], 'reduces': [91, 335, 730], 'quantity': [93, 337, 1689, 1766], 'required': [95, 339], 'reagent': [97, 341, 1125, 1591, 2484], 'by': [98, 215, 342, 459, 595, 964, 1103, 1127, 1594, 1902, 1983, 2139, 2210, 2235, 2333, 2354, 2381, 2427, 2470, 2533, 2589, 2687, 2728, 2788, 2821, 2919, 3388, 3862, 3922, 4189, 4461, 4480], 'factor': [100, 344], 'eight': [102, 346, 1587], 'achieves': [104, 348, 1578], 'complete': [105, 349, 1579], 'labeling.': [106, 350], 'Under-': [107, 351], 'overlabeling': [109, 353, 3623, 3883, 3926, 4359], 'derived': [112, 356, 1936, 2597], 'complex': [114, 358, 592, 1155], 'digests': [115, 359, 620, 1157, 1938, 2600], 'tissues': [117, 361, 963, 1901, 2686, 3387], 'cell': [119, 363, 1193], 'lines': [120, 364], 'were': [121, 151, 365, 395, 1681, 1709, 1780, 1791, 1802, 1952, 1981, 1989, 2019, 2165, 2200, 2247, 2305, 2379, 2420, 2432, 2474, 2567, 2607, 2711, 2749, 2780, 2794, 2826, 2847, 2855, 2866, 2897, 2927, 2988, 3132, 3147, 3193, 3222, 3233, 3248, 3275, 3295, 3311, 3411, 3442, 3456, 3492, 3563, 3597, 3719, 3729, 3755, 3816, 3893, 3907, 3931, 4009, 4050, 4224, 4237, 4269, 4278, 4295, 4307, 4321, 4325, 4334, 4342, 4361, 4374, 4392, 4403, 4448, 4459, 4477], 'systematically': [122, 366, 1560], 'evaluated': [123, 367, 1561], 'using': [124, 368, 549, 1274, 1586, 1683, 1916, 1921, 1964, 2249, 2284, 2312, 2362, 2397, 2442, 2766, 2796, 2833, 2875, 2883, 2899, 3154, 3200, 3217, 3240, 3253, 3277, 3300, 3401, 3433, 3447, 3461, 3494, 3746, 3776, 4024, 4183, 4405], 'peptide': [125, 146, 157, 242, 369, 390, 401, 486, 619, 663, 676, 735, 1090, 1156, 1161, 1616, 1675, 1724, 1753, 1776, 2438, 2454, 3179, 3291, 3483, 3488, 3518, 3619, 3738, 3822, 3833, 3867, 4205, 4243, 4275, 4292], 'quantities': [126, 370, 1517, 1676, 1729], 'between': [128, 372, 1603], '12.5': [129, 373], '800': [131, 375, 1679, 1692], 'μg': [132, 376, 2462, 2709, 2732, 4255], 'TMT-to-peptide': [134, 168, 378, 412, 1543], 'ratios': [135, 169, 379, 413, 1544, 4413], '(wt/wt)': [136, 174, 380, 418], 'ranging': [137, 381], '8:1': [139, 383], '1:2': [141, 385], 'at': [142, 160, 386, 404, 2212, 2221, 2253, 2264, 2278, 2338, 2346, 2359, 2422, 2465, 2521, 2559, 2584, 2754, 2783, 2816, 2914, 3074, 3149, 3195, 3235, 3250, 3297, 3426, 3444, 3458, 3714, 4316, 4350, 4387], 'different': [143, 241, 387, 485, 682, 690, 695, 1615, 1717, 2979, 3799], 'concentrations.': [147, 391], 'When': [148, 392], 'reaction': [149, 226, 393, 470, 623, 1566, 2530, 2725, 2763], 'volumes': [150, 394, 2502], 'reduced': [152, 396, 1131, 2248], 'maintain': [154, 398], 'concentrations': [158, 402, 1519, 1659, 1731, 2504], 'least': [161, 405, 3715, 4317, 4351, 4388], '10': [162, 406, 1433, 2217, 2250, 2293, 3191, 3244, 4467], 'mm': [163, 407, 2173, 2180, 2184, 2251, 2262, 2286, 2294, 2314, 2321, 2478, 2718, 2739], '2': [165, 409, 2309, 2367, 3479], 'g/l,': [166, 410], 'respectively,': [167, 411, 1997, 3880], 'as': [170, 172, 414, 416, 553, 1700, 1714, 1783, 1804, 1827, 2021, 2609, 3224, 3264, 3313, 3437, 3613, 3630, 3645, 3664, 3676, 3682, 3817, 3844, 3895, 3909, 3939, 4297, 4309, 4327, 4363], 'low': [171, 415], '1:1': [173, 417], 'resulted': [175, 419], 'efficiencies': [178, 422], '>': [180, 424], '99%': [181, 425], 'excellent': [183, 427], 'intra-': [184, 428, 866], 'interlaboratory': [186, 430, 868, 1757], 'reproducibility.': [187, 431], 'The': [188, 432, 864, 1632, 2513, 3043, 3259, 3542, 3813, 4239], 'utility': [189, 433, 1811], 'optimized': [192, 436, 1323, 1612, 1748, 1814, 1918, 2703], 'was': [194, 438, 1130, 1767, 1825, 2233, 2276, 2331, 2440, 2456, 2492, 2516, 2531, 2726, 2764, 2881, 2965, 3046, 3262, 3476, 3611, 3628, 3662, 3680, 3696, 3842, 3917, 3937, 3960, 3985, 4045, 4181, 4209, 4245], 'further': [195, 439, 636, 2867, 4478], 'demonstrated': [196, 440, 883], 'deep-scale': [199, 443, 875, 956, 1822, 1894, 2679, 3308, 3380], 'proteome': [200, 444, 790, 876, 957, 1189, 1230, 1499, 1895, 1976, 2680, 2860, 3381, 3569, 3582, 3952, 4180], 'phosphoproteome': [202, 446, 878, 959, 1234, 1897, 1979, 2682, 3383, 3899, 3981], 'patient-derived': [205, 449, 885, 1088], 'xenograft': [206, 450, 886, 1089], 'tumor': [207, 451, 962, 1900, 2685, 3386], 'tissue': [208, 452, 2164], 'benchmarked': [209, 453], 'against': [210, 454, 1773, 3565, 3757], 'procedure': [213, 457], 'recommended': [214, 458, 1126, 1593], 'vendor.': [218, 462, 1596], 'Finally,': [219, 463], 'discuss': [221, 465], 'impact': [223, 467, 1563, 1735], 'parameters': [227, 471, 1567, 1738, 1750, 2976], 'N-hydroxysuccinimide': [229, 473, 1087], 'ester-based': [230, 474, 627], 'chemistry': [231, 475], 'provide': [233, 477, 1605], 'guidance': [234, 478, 1606], 'adopting': [236, 480], 'efficient': [237, 481, 1227, 1268, 1573], 'protocols': [239, 483, 1118], 'quantities.': [243, 487, 1754], 'In': [488, 779, 1555, 1670, 2981], 'bottom-up': [489], 'proteomics,': [490], 'variety': [492, 1329], 'strategies': [494], 'can': [495, 611], 'be': [496, 612, 4345], 'followed': [497, 2209, 3861, 3921], 'determine': [499], 'quantitative': [500, 1184, 1271, 4452], 'differences': [501], 'abundance': [504, 1426], 'proteins': [506, 1431, 4031, 4236, 4384, 4399], 'posttranslational': [508, 814], 'modifications': [509, 815, 3790, 3802], '(PTMs)': [510], '(1Bantscheff': [511], 'M.': [512, 836, 927, 1023, 1039, 1342, 1373, 1379, 1446, 1466, 1468, 1865, 2055, 2102, 2650, 3351, 3515, 4070, 4124], 'Lemeer': [513], 'S.': [514, 572, 1137, 1139, 1377, 1381, 1429, 2025, 2039, 2120, 3537, 4056, 4060, 4100], 'Savitski': [515], 'M.M.': [516], 'Kuster': [517, 837, 1217, 1343, 1382], 'B.': [518, 838, 1212, 1218, 1344, 1375, 1383, 4094], 'Quantitative': [519, 1420], 'spectrometry': [521, 772, 1083], 'proteomics:': [523], 'Critical': [524], 'review': [525], 'update': [526], '2007': [528], 'present.Anal.': [531], 'Bioanalytical': [532], 'Chem.': [533, 597], '2012;': [534], '404:': [535], '939-965Crossref': [536], 'PubMed': [537, 601, 859, 972, 1075, 1174, 1285, 1313, 1365, 1403, 1440, 1508, 1910, 2154, 2695, 3396, 3531, 3555, 4157], 'Scopus': [538, 602, 860, 973, 1076, 1175, 1286, 1314, 1366, 1404, 1441, 1509, 1911, 2155, 2696, 3397, 3532, 3556, 4158], '(581)': [539], 'Google': [540, 604, 862, 975, 1078, 1177, 1288, 1316, 1368, 1406, 1443, 1511, 1913, 2157, 2698, 3399, 3534, 3558, 4160], 'Scholar).': [541, 605, 863, 1079, 1512, 2158, 3559, 4161], 'Among': [542], 'those,': [543], 'isobaric': [550, 652, 806, 1104], 'enables': [558, 709, 787], 'multiplexing': [559, 782, 1423], 'up': [561, 3189, 3288, 3687, 3944, 3970, 3995], '11': [563, 609, 1698], 'samples': [564, 632, 670, 794, 1708, 2793], '(2Thompson': [565], 'A.': [566, 1009, 1035, 1180, 2035, 2083, 2124, 3509, 4106, 4114], 'Schäfer': [567], 'J.': [568, 574, 828, 1027, 1029, 1031, 1196, 1214, 1254, 1334, 1415, 2029, 2041, 2061, 2089, 3505, 3541, 4072, 4082, 4090], 'Kuhn': [569, 1144], 'K.': [570, 897, 1001, 1021, 1145, 1835, 2116, 2620, 3321, 4108], 'Kienle': [571], 'Schwarz': [573], 'Schmidt': [575], 'G.': [576, 1133], 'Neumann': [577], 'T.': [578, 949, 995, 1887, 2057, 2075, 2100, 2672, 3373, 3539], 'Hamon': [579], 'C.': [580, 830, 1336, 2043, 2049, 2067, 2073, 2077, 2079, 2085, 2098, 2128, 4078, 4132], 'Tandem': [581, 3560], 'tags:': [583], 'A': [584, 1300, 3517], 'novel': [585], 'strategy': [587, 1269, 1304, 3792], 'comparative': [589], 'protein': [593, 1297, 3674, 3748, 3849, 4026, 4039, 4170, 4420], 'mixtures': [594], 'MS/MS.Anal.': [596], '2003;': [598], '75:': [599], '1895-1904Crossref': [600], '(1709)': [603], 'Each': [606], 'these': [608, 803, 1737], 'used': [613, 758, 3720, 4246], 'label': [615, 3633], 'primary': [616, 1582, 3635, 4202], 'amines': [617, 1583, 3636, 4203], 'via': [621, 2828, 3181], 'with': [624, 1158, 1999, 2569, 2891, 3001, 3048, 3064, 3227, 3269, 3498, 3592, 3686, 3772, 3798, 3943, 4014, 4213, 4280, 4347, 4386], 'NHS': [626], 'reactive': [628], 'group.': [629], 'Subsequently,': [630, 2791, 2895], 'all': [631, 666, 718, 3658, 3819, 4258, 4283, 4415, 4445, 4466], 'are': [633, 686, 1665, 2505], 'pooled': [634, 2848, 2868], 'processed': [637, 2608], 'together,': [638], 'thus': [639], 'reducing': [640, 1542], 'technical': [641], 'variation': [642], 'experimental': [645, 1636], 'workflow.': [646], 'Inside': [647], 'spectrometer,': [650], 'nature': [653], 'leads': [657], 'summation': [660], 'each': [662, 739, 3804, 4471], 'signal': [664], 'labeled': [667, 1682, 1710, 1953, 4324, 4346], 'combined': [669], 'MS1': [673, 3145, 3231, 3273, 3440], 'spectrum.': [674], 'Following': [675], 'fragmentation,': [677], 'sample-specific': [678], 'reporter': [679, 706, 3639, 4371, 4410], 'ions': [680], 'mass-to-charge': [683], '(m/z)': [684], 'values': [685, 737], 'generated': [687, 2020], 'owing': [692], 'combinations': [696], 'heavy': [698], 'carbon': [699, 1434], 'nitrogen': [701], 'isotopes': [702], 'present': [703, 1557], 'ions.': [707, 2894], 'This': [708], 'differentiation': [711], 'relative': [713], 'conditions': [719, 826, 1654, 1699], 'same': [722, 1685], 'MS2': [723, 3186, 3285, 3454, 3641], 'scan.': [724], 'Multiplexing': [725], 'this': [727], 'manner': [728], 'number': [732], 'missing': [734], 'Further,': [742], 'reproducibility': [744, 869], 'less': [746, 1589, 1923], 'sensitive': [747], 'performance': [749, 1549, 1741], 'variations': [750], 'liquid': [753, 965, 1080, 1903, 2688, 3389], 'chromatography': [754, 1081, 2832], '(LC)': [755], '1The': [756], 'abbreviations': [757], 'are:LCliquid': [759], 'chromatographyMSmass': [760], 'spectrometryNCEnormalized': [761], 'collision': [762, 1085], 'energyNHSN-hydroxysuccinimidePDXpatient-derived': [763], 'xenograftPSMpeptide': [764], 'spectrum': [765, 1091, 3739], 'matchRPreversed': [766], 'phaseTMTtandem': [767], 'tags.': [769, 1097], '(MS)': [773], 'systems': [774], 'than': [775, 1592], 'label-free': [777], 'measurements.': [778], 'addition,': [780], 'capability': [783], 'achieving': [788], 'deep': [789], 'coverage': [791], 'multiple': [793], 'reasonable': [797], 'amount': [798, 1122, 1777, 2959], 'measurement': [800], 'time.': [801], 'Together': [802], 'advantages': [804], 'render': [805], 'attractive': [808], 'MS-based': [810], 'studies,': [812], 'including': [813, 1655], 'analyses': [816, 879, 1059, 2926, 3310], 'depend': [818], '(3Zecha': [827, 1333], 'Meng': [829, 1335], 'Zolg': [831, 1215, 1337], 'D.P.': [832, 1216, 1338], 'Samaras': [833, 1339], 'P.': [834, 893, 909, 1013, 1033, 1135, 1241, 1340, 1831, 1847, 2616, 2632, 3317, 3333, 4058, 4086, 4092], 'Wilhelm': [835, 1341, 1372], 'Peptide': [839, 1345, 2565, 2778], 'level': [840, 1346, 3741], 'turnover': [841, 1347], 'measurements': [842, 1348, 3216], 'enable': [843, 1349], 'study': [845, 1351], 'dynamics.Mol.': [848, 1354], 'Cell': [849, 1355], 'Proteomics.': [850, 1356, 1436], '2018;': [851, 969, 1067, 1282, 1310, 1357, 1907, 2692, 3393], '17:': [852, 1283, 1311, 1358], '974Abstract': [853, 1359], 'Full': [854, 856, 1070, 1072, 1360, 1362, 2149, 2151], 'Text': [855, 857, 1071, 1073, 1361, 1363, 2150, 2152], 'PDF': [858, 1074, 1364, 2153], '(66)': [861, 1367], 'high': [865, 1108, 1965, 2829], 'workflow': [873, 953, 1891, 2450, 2676, 3377], 'has': [880, 1550], 'recently': [881], 'been': [882, 1551], '(PDX)': [887], 'models': [888, 1948, 2018], 'breast': [890, 1945, 2015, 4150], 'cancer': [891, 1396, 1946, 2016, 4151], '(4Mertins': [892, 1830, 2615, 3316], 'Tang': [894, 1024, 1832, 2617, 3318], 'L.C.': [895, 1025, 1833, 2618, 3319], 'Krug': [896, 1000, 1834, 2619, 3320], 'Clark': [898, 1836, 2621, 3322], 'D.J.': [899, 1837, 2622, 3323], 'Gritsenko': [900, 1838, 2623, 3324], 'M.A.': [901, 911, 1019, 1417, 1839, 1849, 2624, 2634, 3325, 3335, 4084, 4118], 'Chen': [902, 1840, 2625, 3326, 4136], 'L.': [903, 1237, 1462, 1841, 2045, 2071, 2110, 2626, 3327, 4076, 4143], 'Clauser': [904, 1020, 1842, 2627, 3328, 4067], 'K.R.': [905, 1843, 2628, 3329, 4068], 'Clauss': [906, 1844, 2629, 3330], 'T.R.': [907, 1845, 2630, 3331], 'Shah': [908, 1846, 2631, 3332], 'Gillette': [910, 1018, 1848, 2633, 3334, 4117], 'Petyuk': [912, 1850, 2635, 3336], 'V.A.': [913, 1851, 2636, 3337], 'Thomas': [914, 1852, 2637, 3338], 'S.N.': [915, 1853, 2638, 3339], 'Mani': [916, 936, 1014, 1854, 1874, 2639, 2659, 3340, 3360, 4065], 'D.R.': [917, 1015, 1855, 2640, 3341, 4066], 'Mundt': [918, 996, 1856, 2641, 3342], 'F.': [919, 997, 1857, 2642, 3343], 'Moore': [920, 1858, 2643, 3344], 'R.J.': [921, 1859, 2644, 3345], 'Hu': [922, 1860, 2645, 3346], 'Y.': [923, 1454, 1464, 1472, 1861, 2063, 2096, 2646, 3347], 'Zhao': [924, 1862, 2647, 3348], 'R.': [925, 1480, 1863, 2031, 2065, 2104, 2106, 2108, 2112, 2648, 3349, 4135], 'Schnaubelt': [926, 1864, 2649, 3350], 'Keshishian': [928, 1866, 2651, 3352], 'H.': [929, 947, 1017, 1371, 1867, 1885, 2652, 2670, 3353, 3371, 4126], 'Monroe': [930, 1868, 2653, 3354], 'M.E.': [931, 1869, 2654, 3355], 'Zhang': [932, 946, 1016, 1870, 1884, 2088, 2655, 2669, 3356, 3370], 'Z.': [933, 1871, 2656, 3357, 4096], 'Udeshi': [934, 1872, 2657, 3358], 'N.D.': [935, 1873, 2658, 3359], 'D.': [937, 1011, 1143, 1875, 2027, 2051, 2093, 2660, 3361, 4120], 'Davies': [938, 1876, 2086, 2661, 3362, 4127], 'S.R.': [939, 1877, 2087, 2662, 3363, 4128], 'Townsend': [940, 1878, 2663, 3364, 4134], 'R.R.': [941, 1879, 2664, 3365], 'Chan': [942, 1880, 2665, 3366], 'D.W.': [943, 1881, 2666, 3367], 'Smith': [944, 1882, 2667, 3368], 'R.D.': [945, 1883, 2668, 3369], 'Liu': [948, 1886, 2032, 2038, 2671, 3372], 'Carr': [950, 1046, 1888, 2673, 3374, 4138], 'S.A.': [951, 1047, 1889, 2674, 3375, 4139], 'Reproducible': [952, 1890, 2675, 3376], 'multiplexed': [955, 1165, 1893, 2678, 3379], 'chromatography–mass': [966, 1904, 2689, 3390], 'spectrometry.Nat.': [967, 1905, 2690, 3391], 'Protoc.': [968, 1906, 2691, 3392, 3551], '13:': [970, 1908, 2693, 3394], '1632-1661Crossref': [971, 1909, 2694, 3395], '(198)': [974, 1912, 2697, 3398], 'Scholar),': [976], 'motivates': [978], 'use': [980], 'larger': [988], 'patients': [991], '(5Archer': [992], 'T.C.': [993], 'Ehrenberger': [994], 'Gold': [998], 'M.P.': [999, 1478], 'Mah': [1002], 'C.K.': [1003], 'Mahoney': [1004], 'E.L.': [1005], 'Daniel': [1006], 'C.J.': [1007], 'LeNail': [1008], 'Ramamoorthy': [1010], 'Mertins': [1012, 2612, 4057], 'Noble': [1022], 'Pierre-François': [1026], 'Silterra': [1028], 'Jensen': [1030], 'Tamayo': [1032], 'Korshunov': [1034], 'Pfister': [1036], 'S.M.': [1037, 4074], 'Kool': [1038], 'Northcott': [1040], 'P.A.': [1041, 1476], 'Sears': [1042], 'R.C.': [1043], 'Lipton': [1044], 'J.O.': [1045], 'Mesirov': [1048], 'J.P.': [1049], 'Pomeroy': [1050], 'S.L.': [1051, 1486], 'Fraenkel': [1052], 'E.': [1053, 1291, 1460, 4102], 'Proteomics,': [1054], 'post-translational': [1055], 'modifications,': [1056, 3912], 'integrative': [1058], 'reveal': [1060], 'molecular': [1061, 1387], 'heterogeneity': [1062], 'within': [1063, 1957, 3637], 'medulloblastoma': [1064], 'subgroups.Cancer': [1065], 'Cell.': [1066], '34:': [1068], '396-410.e398Abstract': [1069], '(90)': [1077], 'normalized': [1084, 4479], 'energy': [1086, 3183], 'match': [1092, 3740], 'reversed': [1093, 3747, 4025], 'phase': [1094], 'One': [1098], 'substantial': [1099], 'shortcoming': [1100], 'reagents.': [1111], 'We': [1112, 1597], 'others': [1114], 'have': [1115], 'previously': [1116, 1828, 2022, 4051], 'reported': [1117, 1552], 'which': [1120, 1763, 1787, 2853, 4049], 'vendor': [1129], '(6Böhm': [1132], 'Prefot': [1134], 'Jung': [1136], 'Selzer': [1138], 'Mitra': [1140], 'V.': [1141], 'Britton': [1142], 'Pike': [1146], 'I.': [1147], 'Thompson': [1148], 'A.H.': [1149], 'Low-pH': [1150], 'solid-phase': [1151, 2400, 2799], 'amino': [1152, 4251], 'TMTs': [1159], 'improves': [1160], 'identification': [1162, 3489], 'rates': [1163], 'global': [1166], 'phosphopeptide': [1167, 1972, 2873], 'analysis.J.': [1168], 'Proteome': [1169, 1280, 1308, 1398, 3526], 'Res.': [1170, 1281, 1309, 1399, 3527], '2015;': [1171], '14:': [1172], '2500-2510Crossref': [1173], '(24)': [1176], 'Scholar,': [1178, 1210, 1252, 1289, 1369, 1407, 1444, 3535], '7Edwards': [1179], 'Haas': [1181], 'W.': [1182, 2033, 2114], 'Multiplexed': [1183], 'proteomics': [1185], 'high-throughput': [1187], 'comprehensive': [1188], 'comparisons': [1190], 'human': [1192, 1501, 3567, 3759, 3766, 4033, 4178, 4381], 'lines.in:': [1194], 'Reinders': [1195], 'Proteomics': [1197], 'Systems': [1199], 'Biology:': [1200], 'Methods': [1201, 1243], 'Protocols.': [1203, 1245], 'Springer': [1204, 1246], 'New': [1205, 1207, 1247, 1249, 3059], 'York,': [1206, 1248], 'York2016:': [1208], '1-13Google': [1209], '8Ruprecht': [1211], 'Zecha': [1213], 'High': [1219], 'pH': [1220, 1966, 2175, 2186, 2316, 2323, 2552, 2830], 'reversed-phase': [1221], 'micro-columns': [1222], 'simple,': [1224], 'sensitive,': [1225], 'fractionation': [1228], '(TMT': [1232], 'labeled)': [1233], 'digests.in:': [1235], 'Comai': [1236], 'Katz': [1238], 'J.E.': [1239, 4088], 'Mallick': [1240], 'Proteomics:': [1242], 'York2017:': [1250], '83-98Google': [1251], '9Navarrete-Perea': [1253], 'Yu': [1255], 'Q.': [1256], 'Gygi': [1257, 1292, 1416, 1418, 1483], 'S.P.': [1258, 1293, 1419, 1484], 'Paulo': [1259, 1294], 'J.A.': [1260, 1295, 1409], 'Streamlined': [1261], 'tag': [1264], '(SL-TMT)': [1265], 'protocol:': [1266], 'An': [1267, 4488], '(phospho)proteome': [1272, 1823, 2594, 3309], 'profiling': [1273, 1385], 'tag-synchronous': [1277], 'precursor': [1278, 3956, 4431], 'selection-MS3.J.': [1279], '2226-2236Crossref': [1284], '(133)': [1287], '10Stepanova': [1290], 'Filter-based': [1296], 'digestion': [1298, 2358], '(FPD):': [1299], 'detergent-free': [1301], 'scaffold-based': [1303], 'workflows.J.': [1307], '1227-1234Crossref': [1312], '(13)': [1315, 1405], 'Scholar)': [1317, 1914, 2699, 3400], 'successfully': [1319], 'economically': [1322], 'workflows': [1325], 'address': [1327], 'biological': [1331], 'questions': [1332], '11Koch': [1370], 'Ruprecht': [1374], 'Beck': [1376], 'Frejno': [1378], 'Klaeger': [1380], 'Phosphoproteome': [1384], 'reveals': [1386, 4146], 'mechanisms': [1388], 'growth-factor-mediated': [1390], 'kinase': [1391], 'inhibitor': [1392, 2194, 2197], 'resistance': [1393], 'EGFR-overexpressing': [1395], 'cells.J.': [1397], '2016;': [1400, 1437, 3552], '15:': [1401], '4490-4504Crossref': [1402], '12Paulo': [1408], "O'Connell": [1410], 'J.D.': [1411], 'Everley': [1412], 'R.A.': [1413, 3511], "O'Brien": [1414], 'spectrometry-based': [1422, 3548], 'compares': [1424], '5000': [1428], 'cerevisiae': [1430], 'sources.J.': [1435], '148:': [1438], '85-93Crossref': [1439], '(102)': [1442], '13Mirzaei': [1445], 'Gupta': [1447, 1487], 'V.B.': [1448], 'Chick': [1449], 'J.M.': [1450, 4116], 'Greco': [1451], 'T.M.': [1452], 'Wu': [1453], 'Chitranshi': [1455], 'N.': [1456, 1470, 3507], 'Wall': [1457], 'R.V.': [1458], 'Hone': [1459], 'Deng': [1461], 'Dheer': [1463], 'Abbasi': [1465], 'Rezaeian': [1467], 'Braidy': [1469], 'You': [1471], 'Salekdeh': [1473], 'G.H.': [1474], 'Haynes': [1475], 'Molloy': [1477], 'Martins': [1479], 'Cristea': [1481], 'I.M.': [1482], 'Graham': [1485], 'V.K.': [1488], 'Age-related': [1489], 'neurodegenerative': [1490], 'disease': [1491], 'associated': [1492], 'pathways': [1493], 'identified': [1494, 4343, 4385], 'retinal': [1496], 'vitreous': [1498], 'glaucoma': [1502], 'eyes.Scientific': [1503], 'Reports.': [1504], '2017;': [1505, 4154], '7:': [1506], '12685Crossref': [1507], '(75)': [1510], 'details': [1514, 4047], 'reactants': [1521], 'vary': [1522], 'widely': [1523], 'published': [1526], 'literature': [1527], 'and,': [1528, 3643], 'best': [1531], 'our': [1533], 'knowledge,': [1534], 'no': [1535, 4214], 'systematic': [1536], 'evaluation': [1537], 'influence': [1540], 'date.': [1554], 'study,': [1558], 'established': [1569], 'times': [1588], 'demonstrate': [1598], 'transferability': [1599], 'laboratories,': [1604], 'adoption': [1609], 'approach': [1613, 3745, 4023], 'quantities,': [1617, 1656], 'show': [1619], 'applicability': [1621], 'improved': [1624], 'in-depth': [1627, 2593], 'phosphoproteomic': [1630], 'analyses.': [1631, 4339], 'rationale': [1633], 'design': [1637], 'described': [1639, 1829, 2023, 2610, 3225, 3314, 3438, 4052], 'more': [1641], 'detail': [1642], 'respective': [1645], 'results': [1646, 2509], 'sections,': [1647], 'detailed': [1650, 2972], 'overview': [1651, 2973], 'volumes,': [1657], 'reactants,': [1661], 'buffers,': [1662], 'solvents': [1664], 'listed': [1666], 'supplement.': [1669, 2512], 'three': [1671, 1712, 1790, 1794, 3997], 'independent': [1672, 1795], 'experiments,': [1673, 1761, 2452, 3487, 4456], 'increasing': [1674], '(12.5': [1677, 2459], 'μg)': [1680, 1693, 1722, 1728, 1772], 'concentration': [1687, 2229, 2439, 2542], '(100': [1690, 1778], 'including,': [1695], 'total,': [1697], 'technical,': [1701], 'intralaboratory': [1702], 'duplicates': [1703], 'triplicates.': [1705], 'Moreover,': [1706], '17': [1707], 'experiments': [1713, 1798], 'singlicates,': [1715], 'applying': [1716, 3009, 3084], '(40': [1719, 1725], '400': [1721, 1771, 2525, 2563, 4227], '200': [1727, 2461, 3081, 3431], 'explore': [1733], 'examine': [1744], 'adaptability': [1746], 'lower': [1752], 'To': [1755, 1808, 4028, 4196, 4450], 'assess': [1756], 'robustness,': [1758], 'four': [1759, 3795, 3814, 3946], 'titrated': [1768], '(50': [1769], 'constant': [1775], 'μg),': [1779], 'carried': [1781], 'out': [1782], 'seven': [1784], 'replicates': [1785, 1956], 'two': [1788, 3689, 3976, 4000, 4389], 'performed': [1792, 1826, 2277, 2332, 2882, 3223, 3493, 4182], 'laboratories.': [1796], 'All': [1797], 'method': [1800], 'optimization': [1801, 2451], 'analyzed': [1803, 2928], 'single-shot': [1805], 'LC-MS/MS': [1806, 2975], 'runs.': [1807], 'highly': [1818], 'fractionated': [1819, 1963, 2827, 3753, 4368], 'samples,': [1820], 'but': [1915, 2700, 4320], '(i.e.': [1920, 4289], '8x': [1922], 'reagent)': [1925], 'comparing': [1927], 'it': [1928], 'original': [1931], 'protocol.': [1933, 2706], 'Briefly,': [1934, 2707, 3409, 3786], 'basal': [1940, 2012, 2604], '(B)': [1941], 'luminal': [1943, 2014, 2602], '(L)': [1944], 'PDX': [1947, 2017, 2160, 2190, 2273, 2302, 2328, 2376, 2605, 4369], '(WHIM2': [1949], 'WHIM16)': [1951], 'five': [1955], 'TMT10-plex': [1959, 2489, 4455], 'experiment': [1960, 3642], '(B-l-B-B-l-B-l-l-B-L)': [1961], 'RP': [1967, 2399, 2798, 2831], 'chromatography.': [1968, 2879], 'After': [1969, 2953, 3178], 'pooling': [1970], 'enrichment,': [1973], '24': [1974, 2850], 'whole': [1975, 2859], '12': [1978, 2870], 'fractions': [1980, 2851, 2871], 'measured': [1982, 3312], 'LC-MS/MS.': [1984], 'HeLa': [1985], 'Jurkat': [1987], 'cells': [1988], 'cultured': [1990], 'DMEM': [1992], 'RPMI': [1994], '1640': [1995], 'medium,': [1996], 'supplemented': [1998, 3591], '10%': [2000, 2573, 2576], 'FBS': [2001], '(GibcoTM),': [2002], '1%': [2004, 3732], 'antibiotic,': [2005], 'antimycotic': [2006], 'solution': [2007, 2455], '(Sigma).': [2008], 'WHIM2': [2009], 'WHIM16': [2011], '(14Li': [2024], 'Shen': [2026], 'Shao': [2028], 'Crowder': [2030], 'Prat': [2034], 'He': [2036], 'X.': [2037, 4104, 4137], 'Hoog': [2040, 4089], 'Lu': [2042], 'Ding': [2044, 4142], 'Griffith': [2046], 'O.L.': [2047], 'Miller': [2048], 'Larson': [2050], 'Fulton': [2052], 'R.S.': [2053], 'Harrison': [2054], 'Mooney': [2056], 'McMichael': [2058], 'J.F.': [2059, 2069], 'Luo': [2060], 'Tao': [2062], 'Goncalves': [2064], 'Schlosberg': [2066], 'Hiken': [2068], 'Saied': [2070], 'Sanchez': [2072], 'Giuntoli': [2074], 'Bumb': [2076], 'Cooper': [2078], 'Kitchens': [2080], 'R.T.': [2081], 'Lin': [2082], 'Phommaly': [2084], 'Kavuri': [2090, 4073], 'M.S.': [2091], 'McEachern': [2092], 'Dong': [2094], 'Yi': [2095], 'Ma': [2097, 4131], 'Pluard': [2099], 'Naughton': [2101], 'Bose': [2103], 'Suresh': [2105], 'McDowell': [2107], 'Michel': [2109], 'Aft': [2111], 'Gillanders': [2113], 'DeSchryver': [2115], 'Wilson': [2117], 'R.K.': [2118], 'Wang': [2119, 4103], 'Mills': [2121], 'G.B.': [2122], 'Gonzalez-Angulo': [2123], 'Edwards': [2125], 'J.R.': [2126], 'Maher': [2127], 'Perou': [2129, 4129], 'C.M.': [2130, 4130], 'Mardis': [2131], 'E.R.': [2132], 'Ellis': [2133, 4140], 'M.J.': [2134, 4141], 'Endocrine-therapy-resistant': [2135], 'ESR1': [2136], 'variants': [2137], 'revealed': [2138], 'genomic': [2140], 'characterization': [2141], 'breast-cancer-derived': [2143], 'xenografts.Cell': [2144], 'Rep.': [2145], '2013;': [2146], '4:': [2147], '1116-1130Abstract': [2148], '(451)': [2156], 'Cells,': [2159], 'murine': [2162], 'liver': [2163], 'lysed': [2166], '8': [2168, 2546, 3022], 'm': [2169, 2310, 2550], 'urea': [2170, 2311], '40': [2172, 2313, 3716], 'Tris-HCl,': [2174, 2315, 2322], '7.6': [2176, 2317], '(Hela),': [2177], '75': [2179, 2992, 3050], 'NaCl': [2181], '50': [2183, 2285, 2320, 2477, 2717, 3176, 3211], 'Tris,': [2185, 2551], '8.0': [2187, 2324], '(Jurkat,': [2188, 2270, 2299, 2325, 2373], 'liver,': [2189, 2272, 2301, 2327, 2375], 'tissue),': [2191], 'containing': [2192, 3764], 'protease': [2193], 'phosphatase': [2196], 'cocktails.': [2198], 'Lysates': [2199, 2304], 'incubated': [2201, 2517, 2750], 'ice': [2203], '15': [2205, 2219, 2557], '30': [2207, 2254, 2257, 2289, 3257], 'min': [2208, 2220, 2258, 2290, 2298, 2558], 'centrifugation': [2211], '20,000': [2213], '×': [2214, 2842, 3052], 'g': [2215], '4': [2222, 3123], '°C': [2223, 2255, 2266, 2348, 2361, 2424, 2523, 2561, 2586, 2756], 'remove': [2225], 'insoluble': [2226, 2393], 'debris.': [2227], 'Protein': [2228, 2241, 2446, 4185], 'supernatant': [2232], 'determined': [2234, 2441, 4404], 'PierceTM': [2237, 2444], 'Coomassie': [2238], 'BCA': [2240, 2445], 'Assay': [2242, 2447], 'Kit': [2243], '(ThermoScientific).': [2244], 'Disulfide': [2245], 'bridges': [2246], 'DTT': [2252, 2263], '(HeLa)': [2259, 2291, 2352], '5': [2261, 2767, 3110, 3173], '37': [2265, 2347], '1': [2268, 2519, 2549, 2752], 'h': [2269, 2368, 2520, 2753], 'mouse': [2271, 2300, 2326, 2374, 3580, 3761, 3769, 4035, 4383], 'tissue).': [2274, 2303, 2329, 2377], 'Alkylation': [2275], 'room': [2279], 'temperature': [2280], 'dark': [2283], 'chloroacetamide': [2287], 'iodoacetamide': [2295], '45': [2297, 2995], 'diluted': [2306], '<': [2308, 4434], '(HeLa),': [2318], 'Digestion': [2330, 4186], 'either': [2334, 2536, 3650], 'adding': [2335], 'trypsin': [2336, 2371], '(Promega)': [2337], '1:50': [2340, 2363, 2370], 'enzyme-to-substrate': [2341], 'ratio': [2342], 'incubating': [2344], 'overnight': [2345, 2372], '600': [2350], 'rpm': [2351], 'performing': [2355], 'double': [2357], '25': [2360, 2522, 2560, 2755, 2774], 'LysC': [2364], '(Wako)': [2365], 'Digests': [2378], 'acidified': [2380, 2568], 'addition': [2382, 2534, 2729], 'neat': [2384], 'formic': [2385], 'acid': [2386, 2885, 3875], '(FA)': [2387], '1%,': [2389], 'centrifuged': [2390], 'pellet': [2392], 'matter,': [2394], 'desalted': [2396, 2795, 2898], 'tC18': [2398], 'extraction': [2401, 2800], 'cartridges': [2402, 2801], '(Waters': [2403, 2802], 'Corp.;': [2404, 2803], 'wash': [2405, 2804], 'solvent:': [2406, 2412, 2805, 2809, 2903, 2907], '0.1%': [2407, 2413, 2435, 2806, 2810, 2904, 2908, 2956, 3097, 3103], 'FA': [2408, 2414, 2436, 2574, 2811, 2909, 3039], 'TFA;': [2410, 2807], 'elution': [2411, 2808, 2906], '50%': [2416, 2813, 2911], 'acetonitrile': [2417], '(ACN)).': [2418], 'Eluates': [2419], 'frozen': [2421, 2464, 2583, 2782, 2815, 2913], '−80': [2423, 2466, 2585, 2784, 2817, 2915], 'dried': [2426, 2469, 2588, 2787, 2820, 2856, 2918], 'vacuum': [2428, 2471, 2590, 2789, 2822, 2920], 'centrifugation.': [2429, 2472, 2591, 2790, 2823, 2921], 'Desalted': [2430], 'reconstituted': [2433, 2475], 'Kit.': [2448], 'For': [2449, 2592, 3482, 3605, 3622, 3657, 3708, 3898, 3951, 3980, 4162, 4257, 4271, 4365], 'aliquoted': [2457], 'accordingly': [2458], 'peptides),': [2463], '°C,': [2467, 2785, 2818, 2916], 'Peptides': [2473, 2846, 3306, 4300, 4340], 'HEPES': [2479, 2719], '(pH': [2480, 2720], '8.5)': [2481], 'TMTzero': [2483, 3608, 3625], 'mix': [2487], '(ThermoFisher)': [2491], 'added': [2493], 'stocks': [2495, 2743], 'dissolved': [2496, 2712], '100%': [2498, 2745], 'anhydrous': [2499, 2746], 'ACN.': [2500], 'Respective': [2501], 'specified': [2506, 3612, 3629, 3681, 3938], 'section': [2510], 'peptide–TMT': [2514], 'mixture': [2515], 'rpm,': [2526, 2759], 'stopped': [2532], '5%': [2537, 2770, 2854, 3030, 3041], 'hydroxylamine': [2538, 2771], 'final': [2541], '0.4%': [2544], 'μl': [2547, 2715, 2736, 2768], '8,': [2553], 'incubation': [2555], 'rpm.': [2564], 'solutions': [2566, 2779], '45%': [2570], '(v/v)': [2571], 'ACN': [2577], 'prior': [2578], 'drying': [2580], 'directly': [2582], 'analyses,': [2595, 4261], 'Lys-C/trypsin': [2599], 'tumors': [2606], 'et': [2613], 'al.': [2614], 'following': [2701, 3229, 3271], '300': [2708, 2731, 2836, 3014], '60': [2714], '8.5),': [2721], 'started': [2727], '(15': [2735, 2772], '56.7': [2738], '(20': [2740], 'μg/μl)': [2741], 'ACN).': [2747], 'Samples': [2748], '1,000': [2758, 2776], 'quenched': [2765], 'min;': [2773], '°C;': [2775], 'rpm).': [2777], 'pooled,': [2781], 'TMT-labeled': [2792, 2824], 'tC18,': [2797], 'ACN),': [2814, 2912], 'Zorbax': [2835], 'Extend-C18': [2837], 'column': [2838, 2998, 3057, 3436], '(3.5': [2839], 'μm,': [2840], '4.6': [2841], '250': [2843, 3079], 'mm;': [2844], 'Agilent).': [2845], 'into': [2849, 2869, 3522], 'down': [2857], 'measurements,': [2861], 'residual': [2864], '95%': [2865], 'enrichment': [2874], 'immobilized': [2876], 'metal': [2877], 'affinity': [2878], 'Enrichment': [2880], 'Ni-nitrilotriacetic': [2884], 'superflow': [2886], 'agarose': [2887], 'beads': [2888], '(Qiagen)': [2889], 'loaded': [2890], 'iron': [2892], '(III)': [2893], 'phosphopeptides': [2896], 'self-packed': [2900], 'StageTips': [2901], '(wash': [2902], 'FA;': [2905], 'Tryptic': [2922], 'one-shot': [2925], 'EASY-nLC': [2931, 3044, 3403], '1200': [2932], 'Ultimate': [2934], '3000': [2935], 'RSLCnano': [2936], 'system': [2937, 3045], 'coupled': [2938, 3404], 'Q-Exactive': [2941, 2943], 'Plus,': [2942, 3144], 'HF-X': [2944, 3221, 3268], 'Fusion': [2946, 3260, 3407], 'Lumos': [2947, 3261], 'Tribrid': [2948], 'spectrometer': [2950], '(ThermoFisher': [2951], 'Scientific).': [2952], 'reconstitution': [2954], 'FA,': [2957, 3029], 'corresponding': [2960], '500': [2962], 'ng': [2963], 'injected.': [2966], 'Supplemental': [2967], 'Table': [2968], 'I': [2969], 'provides': [2970], 'experiments.': [2980], 'brief,': [2982], 'Ultimate3000': [2985], 'system,': [2986], 'separated': [2989, 3412], 'μm': [2993, 3051], 'x': [2994], 'cm': [2996, 3056], 'analytical': [2997], '(packed': [2999], 'in-house': [3000, 3063], '3-μm': [3002], 'C18': [3003, 3066], 'resin;': [3004, 3067], 'Reprosil': [3005, 3068], 'Gold,': [3006, 3069], 'Dr.': [3007, 3070], 'Maisch)': [3008, 3071], 'flow': [3011, 3076, 3428], 'rate': [3012, 3077, 3429, 3735, 4018], 'nl/min': [3015, 3082, 3432], '20-min': [3018, 3086], 'linear': [3019, 3087, 3416], 'gradient': [3020, 3088, 3108, 3121, 3417], '34%': [3024], 'LC': [3025, 3035], 'solvent': [3026, 3036, 3093, 3113, 3126, 3422], 'B1': [3027], '(0.1%': [3028, 3038], 'DMSO': [3031], 'ACN)': [3033], 'A1': [3037], 'DMSO).': [3042], 'equipped': [3047], '20': [3053, 3290], '22': [3055, 3304], '(Picofrit,': [3058], 'Objective,': [3060], 'Inc.;': [3061], 'packed': [3062], '1.9-μm': [3065], 'operated': [3073, 3133, 3263], '3': [3090], '55%': [3092], 'B2': [3094, 3114, 3127, 3423], '(90%': [3095], 'ACN,': [3096, 3102], 'FA)': [3098], 'A2': [3100, 3425], '(3%': [3101], 'FA),': [3104], '17-min': [3106], 'three-step': [3107, 3120], '60%': [3112, 3125], 'A2,': [3116], '97-min': [3119], 'A2.': [3129], 'Mass': [3130], 'spectrometers': [3131], 'data-dependent': [3135], 'positive': [3137], 'ionization': [3138], 'mode.': [3139], 'On': [3140], 'Q': [3142, 3219, 3266], 'Exactive': [3143, 3220, 3267], 'spectra': [3146, 3187, 3232, 3247, 3274, 3286, 3441, 3455, 3562], 'recorded': [3148, 3234, 3296, 3443], 'resolution': [3151, 3199, 3237, 3252, 3299, 3446, 3460], '70k': [3153, 3198], 'automatic': [3156], 'gain': [3157], 'control': [3158], '(AGC)': [3159], 'target': [3160, 3203, 3280, 3450, 3464], 'value': [3161, 3204, 3281, 3451, 3465], '3e6': [3163], '1e6': [3165], 'charges': [3166], 'maximum': [3168, 4221], 'injection': [3169], '(maxIT)': [3171], 'ms': [3174], 'ms.': [3177, 3214, 3245, 3258, 3305, 3473], 'fragmentation': [3180], 'higher': [3182], 'collisional': [3184], 'dissociation,': [3185], 'precursors': [3192, 3292], 'acquired': [3194, 3249, 3276, 3457], '17.5k': [3196], 'AGC': [3202, 3279, 3449, 3463], '5e4': [3206], 'maxIT': [3209, 3242, 3255, 3302, 3470], '120': [3213], 'MS': [3215, 4259], 'above': [3226], 'modifications:': [3230, 3272], '60k': [3239, 3445], 'Fragment': [3246], '30k': [3251], '4e5': [3283], 'charges.': [3284], 'per': [3293, 3978, 4002], 'cycle': [3294], '15k': [3298], 'before': [3315], 'Lumos.': [3408], 'over': [3413], '84-min': [3415], '6': [3419, 3718], '30%': [3421], '22-cm': [3435], 'above.': [3439], '4e5.': [3453], '50k': [3459], '6e4': [3467], '105': [3472], 'Cycle': [3474], 'set': [3477, 3663, 3697, 3843, 3894, 4010, 4210, 4225], 's.': [3480], 'MaxQuant:': [3481], 'titration': [3486], 'MaxQuant': [3495, 3524, 3543], '(version': [3496], '1.6.3.3)': [3497], 'its': [3499], 'built-in': [3500], 'search': [3501, 3519, 3791, 4360], 'engine,': [3502], 'Andromeda': [3503, 3722], '(15Cox': [3504], 'Neuhauser': [3506], 'Michalski': [3508], 'Scheltema': [3510], 'Olsen': [3512], 'J.V.': [3513], 'Mann': [3514], 'Andromeda:': [3516], 'engine': [3520], 'integrated': [3521, 3811], 'environment.J.': [3525], '2011;': [3528], '10:': [3529], '1794-1805Crossref': [3530], '(3450)': [3533], '16Tyanova': [3536], 'Temu': [3538], 'Cox': [3540], 'computational': [3544], 'platform': [3545], 'shotgun': [3549], 'proteomics.Nat.': [3550], '11:': [3553], '2301Crossref': [3554], '(1872)': [3557], 'searched': [3564, 3756], 'reference': [3568, 3581, 4179], '(UP000005640,': [3570], '95,936': [3571], 'entries,': [3572, 3585], 'downloaded': [3573, 3586], 'October': [3575, 3588], '12,': [3576, 3589], '2018)': [3577, 3590], 'and/or': [3578], '(UP000000589,': [3583], '62,407': [3584], 'common': [3593, 3773], 'contaminants.': [3594], 'Separate': [3595], 'searches': [3596, 3797], 'conducted': [3598], 'check': [3600], 'under-': [3602], 'overlabeling.': [3604], 'underlabeling': [3606, 4272, 4338], 'evaluation,': [3607], 'TMT10': [3610, 3627], 'variable': [3614, 3647, 3677, 3896, 3911], 'modification': [3615, 3648, 3667], 'lysine': [3617, 4284], 'N': [3620, 3823, 3834, 3920, 4206, 4293], 'termini.': [3621], 'assessment,': [3624], 'fixed': [3632, 3666, 3846], 'ion': [3640, 3703, 4372, 4411, 4432], 'additionally,': [3644], 'histidine': [3651], 'serine,': [3653, 3885, 3903, 4353], 'threonine,': [3654, 3886, 3904, 4354], 'tyrosine.': [3656], 'searches,': [3659], 'carbamidomethylated': [3660], 'cysteine': [3661, 3872], 'oxidation': [3669, 3851], 'methionine': [3671], 'N-terminal': [3673, 3848, 3868, 4330], 'acetylation': [3675], 'modifications.': [3678, 3897], 'Trypsin/P': [3679], 'proteolytic': [3684, 3941], 'enzyme': [3685, 3942], 'missed': [3690, 3947, 4215], 'cleavage': [3691, 3948, 4208, 4216], 'sites': [3692, 3949, 4217, 4402], 'allowed.': [3693, 3933, 3950, 4218], 'Precursor': [3694, 4004], 'tolerance': [3695, 3704], '±4.5': [3699], 'ppm,': [3700], 'fragment': [3702, 4222], '±20': [3706, 4012], 'ppm.': [3707], 'modified': [3709, 4279], 'peptides,': [3710], 'default': [3711], 'cutoffs': [3712], 'score': [3723, 4442], 'delta': [3725, 4440], 'score,': [3726], 'respectively.': [3727], 'Results': [3728], 'adjusted': [3730], 'false': [3733, 4016], 'discovery': [3734, 4017], 'employing': [3742, 4020], 'target–decoy': [3744, 4022], 'sequences.': [3749, 4027], 'Raw': [3750], 'files': [3751], '(phospho)proteomes': [3754], 'RefSeq': [3762], 'database': [3763], '37,592': [3765], '27,289': [3768], 'entries': [3770], 'complemented': [3771], 'contaminants': [3774], '(RefSeq.20160914_Human_Mouse_ucsc_hg19_mm10_customProDBnr_mito_150contams)': [3775], 'Spectrum': [3777, 4043], 'Mill': [3778, 4044], 'suite': [3779], 'vB.06.01.202': [3780], '(Broad': [3781], 'Institute': [3782], 'Agilent': [3784], 'Technologies).': [3785], 'four-cycle': [3788], 'fixed/mix': [3789], 'ran': [3794], 'consecutive': [3796], 'sets': [3800], 'round': [3805], 'then': [3807], 'produced': [3808], 'output.': [3812], 'cycles': [3815], 'follows:': [3818], 'unmodified,': [3820], 'both': [3821], 'termini': [3824, 3835, 4294], 'lysines': [3826, 3829], 'labeled,': [3827, 3830], 'only': [3828, 3832, 4274, 4380], 'labeled.': [3836], 'Carbamidomethylation': [3837], 'cysteines': [3839], 'selenocysteines': [3841], 'additional': [3845, 3910, 3973], 'modification.': [3847], 'acetylation,': [3850], 'methionine,': [3853], 'de-amidation': [3854, 3914], 'asparagine,': [3856], 'hydroxylation': [3857, 3928], 'proline': [3859, 3930], '(when': [3860], 'Gly),': [3863], 'cyclization': [3865], 'glutamine': [3869], 'carbamidomethyl': [3871], 'pyroglutamic': [3874], '(pyroGlu)': [3876], 'pyro-carbamidomethyl': [3878], 'cysteine,': [3879], 'tyrosine': [3888, 3906, 4356], '(limited': [3889], 'histidine-containing': [3891], 'peptides)': [3892], 'analysis,': [3900, 3953, 3982, 4273], 'phosphorylation': [3901, 4401, 4422, 4472], 'allowed': [3908, 3955], 'while': [3913], 'asparagine': [3916], 'restricted': [3918], 'glycine,': [3923], 'not': [3932, 4290, 4303, 4322], 'Trypsin': [3934], 'Allow': [3935], 'P': [3936], 'shift': [3958], 'range': [3959, 3984], '-18': [3961, 3988], '262': [3963], 'Da': [3964, 3991], 'allow': [3966, 3993], 'pyroGlu': [3968], 'one': [3972, 4318, 4352], 'Met-ox': [3977, 4001], 'peptide.': [3979, 4003], 'expanded': [3986], '272': [3990], 'phosphorylations': [3998], 'product': [4006], 'tolerances': [4008], 'ppm': [4013], 'PSM-level': [4015], '<1%': [4019], 'better': [4029], 'dissect': [4030], 'origin,': [4036], 'subgroup-specific': [4038], 'grouping': [4040], 'option': [4041], 'enabled,': [4046], '(17Huang': [4053], 'K-l.': [4054], 'Li': [4055], 'Cao': [4059], 'Gunawardena': [4061], 'H.P.': [4062], 'Ruggles': [4063], 'K.V.': [4064], 'Tanioka': [4069], 'Usary': [4071], 'Xie': [4075], 'Yoon': [4077], 'Qiao': [4079], 'J.W.': [4080], 'Wrobel': [4081], 'Wyczalkowski': [4083], 'Erdmann-Gilmore': [4085], 'Snider': [4087], 'Singh': [4091], 'Niu': [4093], 'Guo': [4095], 'Sun': [4097], 'S.Q.': [4098], 'Sanati': [4099], 'Kawaler': [4101], 'Scott': [4105], 'Ye': [4107], 'McLellan': [4109], 'M.D.': [4110], 'Wendl': [4111], 'M.C.': [4112], 'Malovannaya': [4113], 'Held': [4115], 'Fenyö': [4119], 'Kinsinger': [4121], 'C.R.': [4122], 'Mesri': [4123], 'Rodriguez': [4125], 'Reid': [4133], 'Proteogenomic': [4144], 'integration': [4145], 'therapeutic': [4147], 'targets': [4148], 'xenografts.Nat.': [4152], 'Commun.': [4153], '8:': [4155], '14864Crossref': [4156], '(87)': [4159], 'estimation': [4163], 'molarities': [4165, 4249], 'functional': [4167], 'groups': [4168], 'digests,': [4171], 'silico': [4174], 'digest': [4175], 'Simulator': [4187], 'released': [4188], 'Pacific': [4191], 'Northwest': [4192], 'National': [4193], 'Laboratory': [4194], '(https://omics.pnl.gov/software/protein-digestion-simulator).': [4195], 'obtain': [4197], 'conservative': [4199], 'estimate': [4200, 4489], 'termini,': [4207], 'trypsin/P': [4212], 'Minimum': [4219], 'masses': [4223, 4244], '6,000': [4229], 'Da,': [4230], 'duplicated': [4232], 'sequences': [4233, 4276], 'given': [4235], 'included.': [4238], 'average': [4240], 'monoisotopic': [4242], 'calculate': [4248], 'acids': [4252], '100': [4254], 'digest.': [4256], 'data': [4260, 4453], 'hits': [4262], 'reverse': [4265], 'contaminant': [4267], 'databases': [4268], 'removed.': [4270], 'side': [4285], 'chains': [4286], 'free': [4288], 'acetylated)': [4291], 'counted': [4296, 4362], '"fully': [4298], 'labeled."': [4299, 4329], 'did': [4302], 'bear': [4304], 'any': [4305], 'annotated': [4308], '"not': [4310], 'labeled,"': [4311], 'whereas': [4312], 'contained': [4315], 'fully': [4323], 'classified': [4326], '"partially': [4328], 'acetylated': [4331], 'arginine': [4332], 'excluded': [4335], 'overlabeled.': [4364], '(phospho)proteomes,': [4370], 'signals': [4373], 'corrected': [4375], 'impurities,': [4378], 'unique': [4390], 'considered': [4393], 'analysis.': [4395], 'Relative': [4396], 'abundances': [4397], 'median': [4407, 4463, 4481, 4484], 'intensity': [4412, 4464], 'PSMs': [4416, 4424], 'matching': [4417], 'site.': [4423], 'lacking': [4425], 'label,': [4428], 'having': [4429, 4437], 'purity': [4433], '50%,': [4435], 'negative': [4439], 'forward–reverse': [4441], '(half': [4443], 'false-positive': [4446], 'identifications)': [4447], 'excluded.': [4449], 'normalize': [4451], 'intensities': [4458], 'divided': [4460], 'channels': [4469], 'site': [4473], 'protein.': [4475], 'Ratios': [4476], 'centering': [4482], 'absolute': [4485], 'deviation': [4486], 'scaling.': [4487]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2937573806', 'counts_by_year': [{'year': 2024, 'cited_by_count': 61}, {'year': 2023, 'cited_by_count': 73}, {'year': 2022, 'cited_by_count': 64}, {'year': 2021, 'cited_by_count': 58}, {'year': 2020, 'cited_by_count': 50}, {'year': 2019, 'cited_by_count': 5}], 'updated_date': '2024-12-27T12:27:13.929416', 'created_date': '2019-04-25'}