Publication Information

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'https://openalex.org/W2217908275', 'https://openalex.org/W2232234141', 'https://openalex.org/W2410873647', 'https://openalex.org/W2505802419'], 'related_works': ['https://openalex.org/W4239724675', 'https://openalex.org/W2899211828', 'https://openalex.org/W2564946823', 'https://openalex.org/W2471443024', 'https://openalex.org/W2415139107', 'https://openalex.org/W2351542508', 'https://openalex.org/W2135353249', 'https://openalex.org/W2036891548', 'https://openalex.org/W1560235021', 'https://openalex.org/W10839406'], 'abstract_inverted_index': {'In': [0, 168, 1021, 2347], 'recent': [1, 169, 2091], 'years,': [2, 170], 'cross-linking': [3, 25, 47, 75, 146, 171, 193, 215, 243, 314, 585, 877, 957, 1175, 1219, 1393, 1444, 1487, 1560, 1641, 2107, 2151, 2471, 2550, 3400], 'mass': [4, 26, 172, 194, 388, 413, 436, 501, 587, 628, 959, 1177, 1220, 1395, 1488, 1528, 1642, 1731, 1754, 1805, 1827, 1834, 1900, 2153, 2211, 2264, 3580, 4008, 4128], 'spectrometry': [5, 27, 173, 195, 502, 564, 588, 960, 1221, 1396, 1489, 1606, 1828, 1835, 3581], 'has': [6, 174, 534, 1085], 'proven': [7, 175], 'to': [8, 96, 125, 143, 176, 264, 293, 311, 435, 589, 651, 961, 1059, 1078, 1223, 1257, 1397, 1423, 1491, 1658, 1660, 1684, 1686, 1753, 2078, 2098, 2169, 2384, 2444, 2455, 2567, 2594, 2667, 2692, 2743, 3043, 3202, 3208, 3229, 3254, 3520, 3557, 3624, 3663, 3744, 3788, 3824, 3908, 3952], 'be': [9, 177, 1706], 'a': [10, 50, 155, 178, 218, 323, 362, 537, 560, 834, 968, 1026, 1090, 1168, 1404, 1681, 1712, 1869, 1878, 1965, 2158, 2165, 2230, 2370, 2403, 2427, 2476, 2507, 2745, 2778, 2828, 2870, 2900, 2961, 3236, 3293, 3468, 3620, 3659, 3692, 3748, 3766, 3828, 3851, 3912, 3930, 4069, 4105], 'robust': [11, 179], 'and': [12, 40, 53, 73, 103, 106, 111, 117, 141, 158, 180, 208, 221, 241, 271, 274, 279, 285, 309, 326, 343, 355, 372, 385, 440, 467, 565, 569, 586, 594, 630, 661, 721, 729, 746, 878, 913, 919, 958, 1055, 1118, 1124, 1176, 1248, 1319, 1327, 1394, 1568, 1612, 1676, 1758, 1854, 1865, 2035, 2191, 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4154], 'interrogating': [16, 163, 184, 331], 'macromolecular': [17, 185, 2137], 'protein': [18, 60, 165, 186, 228, 333, 345, 374, 410, 477, 490, 498, 542, 592, 623, 1002, 1014, 1071, 1169, 1259, 1530, 1613, 1638, 1728, 1799, 1821, 1863, 1894, 1971, 2009, 2076, 2173, 2576, 2879, 2898, 2967, 3005, 3140, 4012, 4122], 'complex': [19, 166, 187, 334, 346, 478, 543, 683, 775, 921, 994, 1126, 1281, 1362, 1822, 2174, 2336, 2398, 2459, 2578, 2842, 2854, 2880], 'topologies': [20, 188], 'at': [21, 189, 551, 1877, 3106, 3119, 3242, 3431, 3436, 3450, 3458, 3509, 3514, 3533, 3538, 3554, 3633, 3672, 3802, 3890, 3967], 'peptide': [22, 190, 553, 2287, 2356, 2367, 2373, 4003, 4044], 'resolution.': [23, 191], 'Traditionally,': [24, 192], 'workflows': [28, 196, 756, 1043, 1058, 1679, 1859, 2238], 'have': [29, 197, 360, 750, 1044, 1252, 1655, 1856, 2062], 'utilized': [30, 198, 1045], 'homogenous': [31, 199, 1046], 'complexes': [32, 61, 200, 229, 375, 411, 491, 659, 749, 1047, 1077, 1729, 1800, 1895, 2077, 2408, 4123], 'obtained': [33, 201, 1048], 'through': [34, 202, 545, 1049], 'time-limiting': [35, 203, 1050], 'reconstitution,': [36, 204, 1051], 'tandem': [37, 205, 1052, 1082], 'affinity': [38, 71, 206, 239, 1053, 1825, 1832, 3150, 3344, 3356, 3367, 3422], 'purification,': [39, 72, 207, 240, 1054, 3368], 'conventional': [41, 209, 1056], 'chromatography': [42, 210, 1057, 1431, 1435, 3584], 'workflows.': [43, 211], 'Here,': [44, 212, 2148], 'we': [45, 107, 122, 213, 275, 290, 2149, 2349, 2564, 2664, 2865], 'present': [46, 214, 2150, 2800, 2866, 4146], 'immunoprecipitation-MS': [48, 216], '(xIP-MS),': [49, 217], 'simple,': [51, 219, 2059, 2159, 2871], 'rapid,': [52, 220], 'efficient': [54, 142, 222, 310, 2160], 'for': [56, 162, 224, 330, 458, 540, 1527, 1690, 1776, 1860, 1968, 2105, 2131, 2194, 2259, 2369, 2402, 2478, 2599, 2685, 2780, 2803, 2877, 2964, 3108, 3116, 3239, 3300, 3346, 3353, 3428, 3453, 3480, 3506, 3530, 3579, 3628, 3639, 3667, 3678, 3698, 3709, 3723], 'structurally': [57, 86, 225, 254, 2395], 'probing': [58, 226, 1166, 2878], 'chromatin-associated': [59, 98, 164, 227, 266, 332, 748, 1798, 1893, 2446, 4121], 'using': [62, 84, 230, 252, 412, 753, 923, 1081, 1089, 1128, 1730, 1868, 3307, 3847, 3983, 4104], 'small': [63, 231, 1027, 2176], 'volumes': [64, 232, 2177, 3067], 'mammalian': [66, 234], 'whole': [67, 235, 2180, 3197, 3212, 3374], 'cell': [68, 130, 236, 298, 2181, 3065, 3198, 3213, 3375], 'lysates,': [69, 237], 'single': [70, 238], 'on-bead': [74, 242, 2106, 2189], 'followed': [76, 244, 2163], 'by': [77, 245, 387, 625, 876, 922, 1127, 1173, 1562, 1570, 1640, 1802, 1824, 1897, 2042, 2164, 2263, 2549, 3060, 3340, 3396, 3403, 3442, 3618, 3657, 3690, 4039, 4125], 'LC-MS/MS': [78, 246], 'analysis.': [79, 247, 1039, 2196, 3302, 3582], 'We': [80, 92, 248, 260, 2390, 2440, 2452, 2611, 2799, 2844], 'first': [81, 249], 'benchmarked': [82, 250], 'xIP-MS': [83, 95, 124, 136, 153, 251, 263, 292, 304, 321, 2183, 2392, 2443, 2454, 2566, 2666, 2819, 2851, 2868, 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482, 995, 2404, 2836, 2855], 'biological': [112, 280, 2848], 'insights': [113, 281], 'into': [114, 282], 'their': [115, 283, 2623], 'architectures': [116, 284, 544, 654, 2134, 2861], 'molecular': [118, 286, 354, 879, 1692, 2552], 'function.': [119, 287], 'Of': [120, 288], 'note,': [121, 289], 'use': [123, 291, 1438, 1564, 2350, 2453, 2665], 'perform': [126, 294], 'topological': [127, 295, 474], 'studies': [128, 296, 648, 2108], 'under': [129, 297, 2862, 3037], 'cycle': [131, 299], 'perturbations,': [132, 300], 'showing': [133, 301], 'that': [134, 152, 302, 320, 2810, 4142], 'protocol': [137, 305, 3315], 'is': [138, 154, 306, 322, 2073, 2229, 2741], 'sufficiently': [139, 307, 2074], 'straightforward': [140, 308, 2351], 'allow': [144, 312], 'comparative': [145, 313], 'experiments.': [147, 315, 2069], 'This': [148, 316, 3131], 'work,': [149, 317], 'therefore,': [150, 318, 533], 'demonstrates': [151, 319], 'robust,': [156, 324], 'flexible,': [157, 325], 'widely': [159, 327, 2065, 2233], 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1368, 1415, 1509, 1539, 1586, 1623, 1649, 1741, 1764, 1782, 1848, 1980, 2017, 2052, 2144, 2271, 2307, 2343, 2436, 2520, 2559, 2607, 2659, 2701, 2729, 2762, 2795, 2976, 3013, 4019, 4060], '(932)': [397], 'Google': [398, 425, 448, 580, 605, 645, 696, 744, 783, 809, 849, 888, 934, 981, 1139, 1185, 1243, 1294, 1342, 1370, 1417, 1511, 1541, 1588, 1625, 1651, 1743, 1766, 1784, 1850, 1982, 2019, 2054, 2146, 2273, 2309, 2345, 2438, 2522, 2561, 2609, 2661, 2703, 2731, 2764, 2797, 2978, 3015, 4021, 4062], 'Scholar,': [399, 426, 581, 606, 697, 784, 810, 850, 889, 935, 1140, 1186, 1295, 1343, 1371, 1512, 1542, 1589, 1626, 1744, 1767, 1785, 1813, 1908, 1983, 2020, 2274, 2310, 2523, 2704, 2732, 2765, 2979, 4022], '2.Gingras': [400], 'A.C.': [401, 432, 1719, 1750], 'Gstaiger': [402, 1720], 'Raught': [404, 1722], 'B.': [405, 1723, 1926, 1991, 2312, 2416, 2922, 2987], 'Aebersold': [406, 619, 671, 714, 765, 828, 1163, 1269, 1312, 1352, 1555, 1602, 1724, 2253, 2501], 'R.': [407, 620, 672, 715, 717, 766, 819, 829, 1148, 1164, 1270, 1313, 1315, 1353, 1514, 1546, 1556, 1603, 1725, 1932, 1936, 1954, 2112, 2254, 2492, 2502, 2928, 2932, 2950], 'spectrometry.Nat.': [414, 1732], 'Mol.': [416, 1734], 'Cell': [417, 1735, 2011, 2046, 2695, 2882, 3007, 3017, 3056, 3102], 'Biol.': [418, 573, 881, 1736, 2012, 2554, 2718, 2751, 3008], '2007;': [419, 1737, 2432, 2655], '8:': [420, 1738, 2656], '645-654Crossref': [421, 1739], '(558)': [424, 1742], '3.Dunham': [427, 1745], 'W.H.': [428, 1746], 'Mullin': [429, 1747], 'Gingras': [431, 1749], 'Affinity-purification': [433, 1751], 'coupled': [434, 1752], 'spectrometry:': [437, 1755], 'basic': [438, 1756], 'principles': [439, 1757], 'strategies.Proteomics.': [441, 1759], '2012;': [442, 777, 1179, 1364, 1535, 1576, 1760, 1810, 1905, 2267, 2339, 4133], '12:': [443, 1646, 1761, 1779, 2141], '1576-1590Crossref': [444, 1762], '(205)': [447, 1765], 'Scholar).': [449, 646, 982, 1244, 1418, 1652, 1851, 2055, 2147, 2346, 2439, 2562, 2610, 2662, 2798, 3016, 4063, 4136], 'However,': [450, 1674, 2056], 'although': [451], 'quantitative': [452, 924, 1129, 1804, 1899, 4127], 'AP-MS/MS': [453, 3301, 3341, 3397, 3975], 'experiments': [454, 2379, 2472, 3319, 3385], 'identify': [455], 'interactors': [457, 469, 1704, 1864], 'any': [459], 'given': [460], 'bait,': [461, 3050], 'they': [462], 'cannot': [463], 'differentiate': [464], 'between': [465, 2805, 4086], 'direct': [466, 546], 'indirect': [468], 'or': [470, 473, 488, 495, 1442, 1451, 2155, 2580, 2859, 3486], 'information': [475, 2837], 'on': [476, 2355, 3235, 3334, 3576, 3587, 3612, 3650, 3733, 3812, 3898, 4149], 'assemblies.': [479], 'Furthermore,': [480, 2223], 'traditional': [481, 754, 1041], 'methodologies': [483, 2061], 'often': [484, 1421], 'fail': [485], 'with': [486, 2003, 2188, 2622, 2689, 2747, 2999, 3039, 3085, 3160, 3180, 3211, 3250, 3260, 3274, 3277, 3285, 3292, 3312, 3434, 3456, 3467, 3512, 3536, 3571, 3703, 3747, 3765, 3827, 3850, 3911, 3929, 3979], 'large': [487], 'dynamic': [489, 3798, 3886, 3963], 'including': [492, 1446], 'chromatin': [493, 496, 657, 727, 1325, 1700, 2713], 'remodeling': [494, 658, 918, 1123], 'associated': [497], 'complexes.': [499, 2451], 'Cross-linking': [500, 983, 986, 3424], '(XL-MS),': [503], '1The': [504], 'abbreviations': [505], 'used': [506, 649, 1255, 1422, 2066, 2093, 2565, 3148, 3365, 3378, 4067, 4079], 'are:XL-MSCross-linking': [507], 'Mass': [508, 511, 984, 988, 1533, 2038], 'SpectrometryxIP-MSCross-linking': [509], 'Immunoprecipitation': [510, 987], 'SpectrometrycoIPCo-immunoprecipitationPRPPphosphoribosyl': [512], 'complexSMCstructural': [515], 'maintenance': [516, 996, 1004, 2671], 'chromosomesXRCCX-ray': [518], 'repair': [519, 1000, 2574, 2631], 'cross-complementing': [520, 1001, 2575], 'proteinMCMmini-chromosome': [521], 'maintenanceLFQlabel': [522], 'free': [523, 1006], 'quantificationDSBdouble-strand': [524], 'breaksPTMpost-translational': [525], 'modificationGFPgreen': [526], 'fluorescent': [527, 1013], 'proteinSCXstrong': [528], 'cation': [529, 1016, 1429], 'exchangeSECsize': [530], 'exclusion': [531, 1019, 1434, 1572, 2198, 2200, 3799, 3887, 3964], 'chromatography.': [532, 1020], 'emerged': [535], 'as': [536, 2290, 2292, 2869, 3351, 4068, 4080, 4101, 4147], 'powerful': [538], 'technique': [539, 2876], 'analyzing': [541], 'observation': [547], 'subcomplex': [549, 870, 2543, 2739, 2860], 'interfaces': [550, 2840], 'level': [554, 1880, 2102], '(4.Rappsilber': [555], 'J.': [556, 788, 790, 802, 860, 927, 1132, 1204, 1472, 1599, 1989, 2116, 2320, 2418, 2431, 2533, 2587, 2985, 3997, 4024], 'beginning': [558], 'beautiful': [561], 'friendship:': [562], 'cross-linking/mass': [563, 1605], 'modelling': [566], 'multi-protein': [570], 'complexes.J.': [571], 'Structural': [572, 1165, 2640], '2011;': [574, 1778], '173:': [575], '530-540Crossref': [576], '(316)': [579], '5.Sinz': [582], 'Chemical': [584, 956, 1392, 1604], 'map': [590], 'three-dimensional': [591], 'structures': [593, 624], 'protein-protein': [595, 1225, 1493], 'interactions.Mass': [596], 'Spectrometry': [597, 985, 989], '2006;': [599, 2791], '25:': [600], '663-682Crossref': [601], '(525)': [604], '6.Leitner': [607], 'Walzthoeni': [609, 1151, 1547, 1596], 'T.': [610, 1152, 1202, 1470, 1548, 1597, 2240], 'Kahraman': [611, 1143], 'Herzog': [613, 702, 763, 816, 1300, 1350, 1549, 2245, 2489], 'F.': [614, 668, 703, 764, 817, 1142, 1266, 1301, 1351, 1550, 1554, 1601, 1628, 1960, 2246, 2250, 2490, 2677, 2956], 'Rinner': [615], 'O.': [616, 707, 1305, 2639], 'Beck': [617, 1155, 2251], 'Probing': [621], 'native': [622, 2136], 'chemical': [626, 1174, 1559], 'cross-linking,': [627], 'spectrometry,': [629, 2154], 'bioinformatics.Mol.': [631], 'Cell.': [632, 1230, 1498, 1574, 1837, 2296, 4049], 'Proteomics.': [633, 1231, 1499, 1575, 1838, 2297, 4050], '2010;': [634, 2013, 3009], '9:': [635, 2268, 2340], '1634-1649Abstract': [636], 'Full': [637, 639, 688, 690, 736, 738, 1235, 1237, 1286, 1288, 1334, 1336, 1503, 1505, 1580, 1582, 1842, 1844, 2301, 2303, 2723, 2725, 2756, 2758, 3737, 3817, 3901, 4054, 4056], 'Text': [638, 640, 689, 691, 737, 739, 1236, 1238, 1287, 1289, 1335, 1337, 1504, 1506, 1581, 1583, 1843, 1845, 2302, 2304, 2724, 2726, 2757, 2759, 4055, 4057], 'PDF': [641, 692, 740, 1239, 1290, 1338, 1507, 1584, 1846, 2305, 2727, 2760, 4058], '(371)': [644], 'Landmark': [647], 'XL-MS': [650, 755, 1042, 1688, 2068, 2237], 'reveal': [652], 'Ino80': [660], 'SWR1': [662], '(7.Nguyen': [663, 1261], 'V.Q.': [664, 1262], 'Ranjan': [665, 1263], 'Stengel': [667, 1265], 'Wei': [669, 1267], 'D.': [670, 1146, 1210, 1268, 1478, 1922, 2679, 2706, 2918], 'Wu': [673, 1271, 2313], 'C.': [674, 701, 709, 758, 941, 1194, 1272, 1299, 1307, 1345, 1377, 1462], 'Leschziner': [675, 1273], 'A.E.': [676, 1274], 'Molecular': [677, 769, 1275, 1356], 'architecture': [678, 770, 914, 1119, 1276, 1357, 2802], 'ATP-dependent': [681, 1279], 'chromatin-remodeling': [682, 1280], 'SWR1.Cell.': [684, 1282], '2013;': [685, 733, 1283, 1331], '154:': [686, 734, 1284, 1332], '1220-1231Abstract': [687, 1285], '(115)': [695, 1293], '8.Tosi': [698, 1296], 'Haas': [700, 1298], 'Gilmozzi': [704, 1302], 'Berninghausen': [706, 1304], 'Ungewickell': [708, 1306], 'Gerhold': [710, 1308], 'C.B.': [711, 1309], 'Lakomek': [712, 1310], 'K.': [713, 1311, 1946, 1952, 2322, 2942, 2948], 'Beckmann': [716, 1314], 'Hopfner': [718, 1316], 'K.P.': [719, 1317, 1948, 2944], 'Structure': [720, 1318, 2588], 'subunit': [722, 964, 1320, 1400, 2839], 'topology': [723, 866, 1321, 2539], 'INO80': [726, 1324], 'remodeler': [728, 1326], 'its': [730, 1328, 2597, 2648], 'nucleosome': [731, 917, 1122, 1329], 'complex.Cell.': [732, 1330], '1207-1219Abstract': [735, 1333], '(173)': [743, 1341], 'Scholar),': [745], 'other': [747], 'interrogated': [752], '(9.Ciferri': [757], 'Lander': [759, 1346], 'G.C.': [760, 1347], 'Maiolica': [761, 1348], 'Nogales': [767, 1354], 'E.': [768, 825, 955, 1355, 1391, 2498], 'human': [772, 840, 970, 1359, 1406, 2179, 2422, 2480, 2513, 2644, 3992], 'polycomb': [773, 1360], 'repressive': [774, 1361], '2.Elife.': [776, 1363], '1:': [778, 1365], 'e00005Crossref': [779, 1366], '(190)': [782, 1369], '10.Han': [785], 'Y.': [786, 1198, 1466, 1918, 1944, 2110, 2120, 2414, 2914, 2940], 'Luo': [787], 'Ranish': [789], 'Hahn': [791], 'S.': [792, 823, 945, 1208, 1381, 1476, 1552, 1934, 1950, 2248, 2324, 2412, 2496, 2681, 2930, 2946], 'Architecture': [793], 'Saccharomyces': [796], 'cerevisiae': [797], 'SAGA': [798, 971, 1407], 'transcription': [799], 'coactivator': [800], 'complex.EMBO': [801], '2014;': [803, 843, 1232, 1500, 1619, 2298, 2516, 4051], '33:': [804], '2534-2546Crossref': [805], '(82)': [808], '11.Huis': [811], "'t": [813, 2486], 'Veld': [814, 2487], 'P.J.': [815, 2280, 2488], 'Ladurner': [818, 2491], 'Davidson': [820, 2493], 'I.F.': [821, 2494], 'Piric': [822, 2495], 'Kreidl': [824, 2497], 'Bhaskara': [826, 2499], 'V.': [827, 897, 949, 1102, 1385, 2500], 'Peters': [830, 1957, 2503, 2953], 'J.M.': [831, 1958, 2504, 2954], 'Characterization': [832, 2505], 'DNA': [835, 2508, 2595, 2626, 2651, 2783], 'exit': [836, 2509], 'gate': [837, 2510], 'ring.Science.': [842, 2515], '346:': [844, 2517], '968-972Crossref': [845, 2518], '(128)': [848, 2521], '12.Barysz': [851, 2524], 'H.': [852, 903, 1108, 1632, 1942, 2326, 2525, 2938], 'Kim': [853, 2526], 'J.H.': [854, 2527], 'Chen': [855, 2329, 2528], 'Z.A.': [856, 2529], 'Hudson': [857, 2530], 'D.F.': [858, 2531], 'Rappsilber': [859, 2532], 'Gerloff': [861, 2534], 'D.L.': [862, 2535], 'Earnshaw': [863, 2536], 'W.C.': [864, 2537], 'Three-dimensional': [865, 2538], 'SMC2/SMC4': [869, 2542], 'from': [871, 1068, 1670, 2175, 2335, 2544, 2886, 2899, 3328, 3564, 3622, 3661, 3742, 3822, 3906, 3973], 'chicken': [872, 2545], 'condensin': [873, 2546], 'I': [874, 2547], 'revealed': [875, 1801, 1896, 2548, 4124], 'modelling.Open': [880, 2553], '2015;': [882, 928, 975, 1133, 1411, 1645, 1839, 2140, 2555], '5:': [883, 1977, 2556, 2973], '150005Crossref': [884, 2557], '(41)': [887, 2560], '13.Kloet': [890], 'S.L.': [891, 1096], 'Baymaz': [892, 1097], 'H.I.': [893, 1098, 2022], 'Makowski': [894, 1099], 'Groenewold': [896, 1101], 'Jansen': [898, 1103, 1788, 1883, 4111], 'P.W.': [899, 1104, 1789, 1884, 2769, 4112], 'Berendsen': [900, 1105], 'Niazi': [902, 1107], 'Kops': [904, 1109], 'G.J.': [905, 1110], 'Vermeulen': [906, 1111, 1772, 1794, 1889, 2025, 4117], 'Towards': [908, 1113], 'elucidating': [909, 1114], 'stability,': [911, 1116], 'dynamics': [912, 1117], 'deacetylase': [920, 1125], 'interaction': [925, 965, 1130, 1401, 1866, 2483], 'proteomics.FEBS': [926, 1131], '282:': [929, 1134], '1774-1785Crossref': [930, 1135], '(70)': [933, 1138], '14.Nguyen-Huynh': [936, 1372], 'N.T.': [937, 1373], 'Sharov': [938, 1374], 'G.': [939, 1375], 'Potel': [940, 1376], 'Fichter': [942, 1378], 'P.': [943, 951, 1379, 1387, 1595, 1993, 2989], 'Trowitzsch': [944, 1380], 'Berger': [946, 1382], 'I.': [947, 1383, 1791, 1886, 1910, 1995, 2906, 2991, 4030, 4114], 'Lamour': [948, 1384], 'Schultz': [950, 1386], 'Potier': [952, 1388], 'N.': [953, 1160, 1389, 4032], 'Leize-Wagner': [954, 1390], 'determine': [962, 1398], 'network': [966, 1172, 1402], 'recombinant': [969, 1249, 1405], 'HAT': [972, 1408], 'subcomplex.Protein': [973, 1409], 'Sci.': [974, 1410, 2789], '24:': [976, 1412], '1232-1246Crossref': [977, 1413], '(16)': [980, 1416], 'Co-immunoprecipitation': [990], 'chromosomes': [998], 'X-ray': [999], 'mini-chromosome': [1003, 2670], 'label': [1005], 'quantification': [1007, 4038], 'double-strand': [1008, 2600], 'breaks': [1009], 'post-translational': [1010], 'modification': [1011], 'green': [1012], 'strong': [1015, 1428], 'exchange': [1017, 1430], 'size': [1018, 1433, 1571], 'general,': [1022], 'cross-linked': [1023, 1066, 1525, 1668, 2085, 2221, 2227, 2260, 2286, 2333, 3487], 'peptides': [1024, 1034, 1067, 1669, 2086, 2228, 2261, 2334, 3563, 3568], 'represent': [1025], 'fraction': [1028], 'total': [1031, 3373, 3643, 3682, 3713], 'pool': [1032], 'measured': [1035, 3395, 3617, 3656, 3689, 3732, 3811, 3897], 'an': [1037, 1661, 2801, 3588, 3734, 3753, 3770, 3775, 3780, 3813, 3833, 3855, 3865, 3899, 3917, 3934, 3939, 3944], 'MS/MS': [1038, 2195, 3758, 3838, 3922], 'Therefore,': [1040], 'facilitate': [1060, 2079, 2213], 'detection': [1062], 'low': [1064, 2219], 'abundance': [1065, 2220], 'target': [1070, 1672, 3755, 3772, 3835, 3857, 3919, 3936], 'For': [1073, 3031, 4158], 'example,': [1074], 'reconstitution': [1075], 'near': [1079], 'homogeneity': [1080], 'tagging': [1083, 1093], 'systems': [1084, 1251, 1873], 'previously': [1087, 1857], 'reported,': [1088], 'variety': [1091], 'combinations': [1094], '(13.Kloet': [1095], '15.Herzog': [1141], 'Boehringer': [1145], 'Mak': [1147], 'Bracher': [1149], 'Leitner': [1153, 2243], 'Hartl': [1157], 'F.U.': [1158], 'Ban': [1159], 'Malmstrom': [1161], 'L.': [1162, 1214, 1482, 1930, 2635, 2926], 'phosphatase': [1170], '2A': [1171], 'spectrometry,.Science.': [1178], '337:': [1180], '1348-1352Crossref': [1181], '(311)': [1184], '16.Kaake': [1187], 'R.M.': [1188, 1456], 'Wang': [1189, 1457, 2121], 'X.': [1190, 1458], 'Burke': [1191, 1459], 'Yu': [1193, 1461], 'Kandur': [1195, 1463], 'W.': [1196, 1464], 'Yang': [1197, 1465], 'Novtisky': [1199, 1467], 'E.J.': [1200, 1468], 'Second': [1201, 1469], 'Duan': [1203, 1471], 'Kao': [1205, 1473], 'Guan': [1207, 1475], 'Vellucci': [1209, 1477], 'Rychnovsky': [1211, 1479], 'S.D.': [1212, 1480], 'Huang': [1213, 1481], 'A': [1215, 1483, 2089, 2129, 3594], 'new': [1216, 1484], 'vivo': [1218, 1486, 2008, 2410, 3004], 'platform': [1222, 1490], 'define': [1224, 1492], 'living': [1228, 1496], 'cells.Mol.': [1229, 1497], '13:': [1233, 1501, 2299, 4052], '3533-3543Abstract': [1234, 1502], '(130)': [1242, 1510], 'Similarly,': [1245], 'baculovirus': [1246], 'over-expression': [1247], 'yeast': [1250], 'also': [1253], 'effectively': [1256], 'maximize': [1258], 'yield': [1260], '9.Ciferri': [1344], 'Further': [1419], 'enrich': [1424, 1659], 'cross-link': [1425, 2388, 4159], 'identifications': [1426], 'include': [1427], '(SCX),': [1432], '(SEC),': [1436], 'multiple': [1440, 1566, 2378], 'proteases,': [1441], 'alternate': [1443], 'acid-acid': [1447], 'cross-linkers,': [1448, 1450], 'CID-cleavable': [1449], 'tagged,': [1452], 'enrichable': [1453], 'cross-linkers': [1454], '(16.Kaake': [1455], '17.Fritzsche': [1513], 'Ihling': [1515], 'C.H.': [1516], 'Gotze': [1517], 'Sinz': [1519], 'Optimizing': [1521], 'enrichment': [1523, 1569, 1826], 'products': [1526], 'spectrometric': [1529], 'analysis.Rapid': [1531], 'Commun.': [1532], 'Spectrom.': [1534], '26:': [1536, 4016], '653-658Crossref': [1537], '(78)': [1540], '18.Leitner': [1543], 'Reischl': [1545], 'Bohn': [1551, 2247], 'Forster': [1553, 1600, 2249], 'Expanding': [1557], 'toolbox': [1561], 'proteases': [1567], 'chromatography.Mol.': [1573], '11': [1577], '(M111': [1578], '014126)Abstract': [1579], '(212)': [1587], '19.Leitner': [1590], 'Joachimiak': [1592], 'L.A.': [1593], 'Unverdorben': [1594], 'Frydman': [1598], 'targeting': [1607], 'acidic': [1608], 'residues': [1609], 'complexes.Proc': [1614], 'Natl': [1615], 'Acad': [1616], 'Sci': [1617], 'U.S.A.': [1618, 2790], '111:': [1620], '9455-9460Crossref': [1621], '(153)': [1624], '20.Liu': [1627], 'Rijkers': [1629], 'D.T.': [1630], 'Post': [1631], 'Heck': [1633], 'A.J.': [1634], 'Proteome-wide': [1635], 'profiling': [1636], 'assemblies': [1639], 'spectrometry.Nature': [1643, 2265], 'Methods.': [1644, 1975, 2139, 2266, 2338, 2971], '1179-1184Crossref': [1647], '(303)': [1650], 'These': [1653], 'steps': [1654, 2353], 'necessary': [1657], 'appreciable': [1662], 'degree': [1663], 'number': [1665], 'measurable': [1667], 'implementing': [1675], 'optimizing': [1677], 'these': [1678], 'represents': [1680], 'considerable': [1682], 'barrier': [1683], 'entry': [1685], 'field': [1689], 'biologists.': [1693], 'Single-AP-MS': [1694], 'are': [1696, 2814], 'commonly': [1697], 'biology,': [1701], 'where': [1702, 2362], 'can': [1705, 2833], 'identified': [1707, 2262], 'presence': [1710], 'vast': [1713], 'amount': [1714], 'background': [1716], '(2.Gingras': [1718], '21.Eberl': [1768], 'H.C.': [1769], 'Mann': [1770, 1818, 1998, 2994, 3998, 4033], 'Quantitative': [1774, 2000, 2037, 2996], 'proteomics': [1775, 2001, 2997], 'epigenetics.Chembiochem.': [1777], '224-234Crossref': [1780], '(52)': [1783], '22.Smits': [1786], 'A.H.': [1787, 1882, 4110], 'Poser': [1790, 1885, 1994, 2990, 4113], 'Hyman': [1792, 1887, 1961, 1996, 2957, 2992, 4115], 'A.A.': [1793, 1888, 1962, 2958, 4116], 'Stoichiometry': [1796, 1891, 4093, 4119], 'label-free': [1803, 1898, 4037, 4126], 'spectrometry-based': [1806, 1901, 4129], 'proteomics.Nucleic': [1807, 1902, 4130], 'Acids': [1808, 1903, 2044, 4131], 'Res.': [1809, 1904, 2696, 4132], ':': [1811, 1906, 4134], 'gks941Google': [1812, 1907, 4135], '23.Keilhauer': [1814], 'E.C.': [1815], 'Hein': [1816, 4025], 'M.Y.': [1817, 4026], 'Accurate': [1820, 4035], 'retrieval': [1823], '(AE-MS)': [1829], 'rather': [1830], 'than': [1831], 'purification': [1833, 2187, 3151], '(AP-MS).Mol.': [1836], '14:': [1840], '120-135Abstract': [1841], '(155)': [1849], 'Our': [1852], 'group': [1853], 'others': [1855], 'established': [1858], 'identifying': [1861], 'stoichiometries': [1867], 'GFP-tagging': [1870], 'BAC': [1871, 1963, 2004, 2902, 2959, 3000], 'transgene': [1872, 2903], 'expressing': [1874, 2892], 'tagged': [1875, 2103, 3049], 'baits': [1876, 2104], 'near-endogenous': [1879, 2893], '(22.Smits': [1881, 4109], '24.Poser': [1909], 'Sarov': [1911, 2907], 'Hutchins': [1913, 2909], 'J.R.': [1914, 2583, 2910], 'Hériché': [1915, 2911], 'J.-K.': [1916, 2912], 'Toyoda': [1917, 2913], 'Pozniakovsky': [1919, 2915], 'Weigl': [1921, 2917], 'Nitzsche': [1923, 2919], 'Hegemann': [1925, 2921], 'Bird': [1927, 1986, 2923, 2982], 'A.W.': [1928, 1987, 2924, 2983], 'Pelletier': [1929, 2925], 'Kittler': [1931, 2927], 'Hua': [1933, 2929], 'Naumann': [1935, 2931], 'Augsburg': [1937, 2933], 'Sykora': [1939, 2935], 'M.M.': [1940, 2936], 'Hofemeister': [1941, 2937], 'Zhang': [1943, 2321, 2939], 'Nasmyth': [1945, 2941], 'White': [1947, 2943], 'Dietzel': [1949, 2945], 'Mechtler': [1951, 2947], 'Durbin': [1953, 2949], 'Stewart': [1955, 2951], 'A.F.': [1956, 2952], 'Buchholz': [1959, 2955], 'TransgeneOmics:': [1964, 2960], 'high-throughput': [1966, 2962], 'exploration': [1969, 2965], 'function': [1972, 2968], 'mammals.Nature': [1974, 2970], '2008;': [1976, 2972, 4015], '409-415Crossref': [1978, 2974], '(477)': [1981, 2977], '25.Hubner': [1984, 2980], 'N.C.': [1985, 2981], 'Cox': [1988, 2984], 'Splettstoesser': [1990, 2986], 'Bandilla': [1992, 2988], 'combined': [2002, 2998], 'TransgeneOmics': [2005, 3001], 'reveals': [2006, 2426, 3002], 'interactions.J.': [2010, 3006], '189:': [2014, 3010], '739-754Crossref': [2015, 3011], '(333)': [2018, 3014], '26.Baymaz': [2021], 'Spruijt': [2023], 'C.G.': [2024], 'Identifying': [2027], 'Nuclear': [2028], 'Protein–Protein': [2029], 'Interactions': [2030], 'Using': [2031], 'GFP': [2032, 2186, 3144, 3343, 3355, 3361, 3421], 'Affinity': [2033], 'Purification': [2034], 'SILAC-Based': [2036], 'Spectrometry.Stable': [2039], 'Isotope': [2040], 'Labeling': [2041], 'Amino': [2043], 'Culture': [2047], '(SILAC).': [2048], 'Springer,': [2049], '2014:': [2050], '207-226Crossref': [2051], '(22)': [2053, 2702], 'thus': [2057], 'far': [2058], 'single-IP': [2060], 'not': [2063], 'One': [2070], 'main': [2071], 'challenge': [2072], 'purifying': [2075], 'consistent': [2081, 2621], 'identification': [2082, 2217, 4004], 'low-abundance': [2084], 'over': [2087], 'background.': [2088], 'very': [2090], 'study': [2092], 'engineered': [2094], 'high-affinity,': [2095], 'lysine-free': [2096], 'GFP-nanobodies': [2097], 'efficiently': [2099], 'extract': [2100], 'endogenous': [2101], '(27.Shi': [2109], 'Pellarin': [2111], 'Fridy': [2113], 'P.C.': [2114], 'Fernandez-Martinez': [2115], 'Thompson': [2117], 'M.K.': [2118], 'Li': [2119, 2323, 2327], 'Q.J.': [2122], 'Sali': [2123], 'Rout': [2125], 'M.P.': [2126], 'Chait': [2127], 'B.T.': [2128], 'strategy': [2130], 'dissecting': [2132], 'assemblies.Nature': [2138], '1135-1138Crossref': [2142], '(83)': [2145], 'immunoprecipitation': [2152], 'xIP-MS,': [2156, 2348], 'utilizing': [2157], 'GFP-AP': [2161, 3324], 'workflow': [2162, 2820], 'high-stringency': [2166], 'washing': [2167, 3702], 'procedure': [2168], 'obtain': [2170], 'highly': [2171], 'pure': [2172], 'lysates.': [2182], 'couples': [2184], 'single-AP': [2185], 'crosslinking': [2190], 'sample': [2192, 3298], 'prep': [2193, 3299], 'Dynamic': [2197], 'settings,': [2199], 'lower': [2202], 'charge-state': [2203], 'peptides,': [2204], 'high': [2207, 2365, 4002], 'speed': [2208, 3876], 'modern': [2210], 'spectrometers': [2212], 'fragmentation': [2215], 'peptides.': [2222], 'computational': [2224], 'analysis': [2225], 'crucial': [2231], 'discussed': [2234], 'aspect': [2235], '(28.Walzthoeni': [2239], 'Claassen': [2241], 'False': [2255], 'discovery': [2256], 'rate': [2257, 3719], 'estimation': [2258], '901-903Crossref': [2269], '(206)': [2272], '29.Trnka': [2275], 'M.J.': [2276], 'Baker': [2277], 'P.R.': [2278], 'Robinson': [2279], 'Burlingame': [2281], 'Chalkley': [2283], 'R.J.': [2284], 'Matching': [2285], 'spectra:': [2288], 'only': [2289], 'good': [2291], 'worse': [2294], 'identification.Mol.': [2295], '420-434Abstract': [2300], '(127)': [2308], '30.Yang': [2311], 'Y.-J.': [2314], 'Zhu': [2315], 'Fan': [2317], 'S.-B.': [2318], 'Lin': [2319], 'Chi': [2325], 'Y.-X.': [2328], 'H.-F.': [2330], 'Identification': [2331], 'samples,.Nature': [2337], '904-906Crossref': [2341], '(404)': [2344], 'data-filtering': [2352], 'based': [2354], 'length': [2357], '(selectively': [2358], 'removing': [2359], 'those': [2360], 'matches': [2361], 'one': [2363, 3240], 'long,': [2364], 'scoring': [2366], 'compensates': [2368], 'short,': [2371], 'ambiguous': [2372], 'match)': [2374], 'reproducibility': [2376], '(to': [2380], 'remove': [2381], 'spurious': [2382], 'matches)': [2383], 'increase': [2385], 'confidence': [2386], 'identifications.': [2389], 'benchmark': [2391], 'against': [2393, 3988], 'PRPP': [2397, 2407], 'evidence': [2401], 'ensemble': [2405], '(31.Li': [2411], 'Lu': [2413], 'Peng': [2415], 'Ding': [2417], 'Crystal': [2419], 'structure': [2420], 'phosphoribosylpyrophosphate': [2423], '1': [2425, 3032, 3079, 3089, 3220, 3255, 3370, 3413, 3429], 'allosteric': [2429], 'site.Biochem.': [2430], '401:': [2433], '39-47Crossref': [2434], '(79)': [2437], 'apply': [2442], 'cohesin,': [2447], 'XRCC5/6,': [2448], 'analyze': [2456, 2568], 'cohesion': [2458], 'observe': [2461, 2612], 'numerous': [2462], 'cross-links': [2463], 'within': [2464], 'well-ordered': [2466], 'head': [2467, 2482], 'region,': [2468], 'complementing': [2469], 'previous': [2470], 'directly': [2474], 'supporting': [2475], 'model': [2477, 2641], '(11.Huis': [2484], 'Next,': [2563], 'conformational': [2569, 2613, 2857], 'changes': [2570], 'x-ray': [2573], '5/6': [2577], '(XRCC5/6,': [2579], 'Ku70/86)': [2581], '(32.Walker': [2582], 'Corpina': [2584], 'R.A.': [2585], 'Goldberg': [2586], 'Ku': [2591, 2617], 'heterodimer': [2592, 2646], 'bound': [2593], 'implications': [2598], 'break': [2601, 2630], 'repair.Nature.': [2602], '412:': [2604], '607-614Crossref': [2605], '(866)': [2608], 'flexibility': [2614], 'SAP': [2619], 'domains': [2620], 'involvement': [2624], 'binding': [2627, 3308], 'during': [2628], 'double-stranded': [2629], '(33.Rivera-Calzada': [2632], 'Spagnolo': [2634], 'Pearl': [2636], 'L.H.': [2637], 'Llorca': [2638], 'full-length': [2643], 'Ku70-Ku80': [2645], 'recognition': [2649], 'DNA-PKcs.EMBO': [2653], 'Rep.': [2654], '56-62Crossref': [2657], '(96)': [2660], 'Finally,': [2663], 'characterize': [2668], 'soluble': [2669, 2811], '(MCM)': [2672], 'subcomplexes': [2673, 2813], '(34.Coué': [2674], 'Amariglio': [2676], 'Maiorano': [2678], 'Bocquet': [2680], 'Méchali': [2682, 2709], 'Evidence': [2684], 'Different': [2686], 'Subcomplexes': [2688], 'Differential': [2690], 'Binding': [2691], 'Chromatin': [2693], 'inXenopus.Exp.': [2694], '1998;': [2697], '245:': [2698], '282-289Crossref': [2699], '35.Maiorano': [2705], 'Lemaitre': [2707], 'J.-M.': [2708], 'Stepwise': [2711], 'regulated': [2712], 'assembly': [2714, 2740], 'MCM2–7': [2716], 'proteins.J.': [2717], 'Chem.': [2719, 2752], '2000;': [2720, 2753], '275:': [2721, 2754], '8426-8431Abstract': [2722], '(54)': [2730], '36.Prokhorova': [2733], 'T.A.': [2734], 'Blow': [2735], 'J.J.': [2736], 'Sequential': [2737], 'MCM/P1': [2738], 'required': [2742], 'form': [2744], 'heterohexamer': [2746], 'replication': [2748, 2784], 'licensing': [2749], 'activity.J.': [2750], '2491-2498Abstract': [2755], '(91)': [2763], '37.Moyer': [2766], 'S.E.': [2767], 'Lewis': [2768], 'Botchan': [2770], 'M.R.': [2771], 'Isolation': [2772], 'Cdc45/Mcm2–7/GINS': [2775], '(CMG)': [2776], 'complex,': [2777], 'candidate': [2779], 'eukaryotic': [2782], 'fork': [2785], 'helicase.Proc.': [2786], 'Natl.': [2787], 'Acad.': [2788], '103:': [2792], '10236-10241Crossref': [2793], '(544)': [2796], 'subunits': [2807], 'show': [2809], 'generally': [2815], 'cell-cycle': [2816], 'invariant.': [2817], 'requires': [2821], 'approximately': [2822], 'time': [2824], 'resources': [2826], 'standard': [2829], 'coIP': [2830], 'experiment,': [2831], 'yet': [2832], 'additional': [2835], 'about': [2838], 'topologies.': [2843], 'further': [2845], 'demonstrate': [2846], 'usefulness': [2849], 'studying': [2853], 'ensembles,': [2856], 'flexibility,': [2858], 'perturbation.': [2863], 'Thus,': [2864], 'here': [2867], 'efficient,': [2872], 'broadly': [2874], 'lysates': [2883, 3057, 3103, 3136], 'were': [2884, 3019, 3035, 3058, 3104, 3156, 3233, 3247, 3270, 3305, 3320, 3332, 3348, 3386, 3391, 3426, 3440, 3489, 3525, 3551, 3569, 3616, 3655, 3688, 3731, 3740, 3760, 3795, 3810, 3820, 3840, 3871, 3883, 3896, 3904, 3924, 3960, 3977, 4078, 4091, 4098, 4139, 4145], 'collected': [2885, 3059, 3128, 3611, 3649, 3741, 3761, 3821, 3841, 3872, 3905, 3925], 'stably': [2887], 'transgenic': [2888], 'HeLa': [2889], 'Kyoto': [2890], 'cells': [2891, 3034, 3062], 'levels': [2894], 'GFP-tagged': [2896], 'bait': [2897], 'recombined': [2901], 'system': [2904], '(24.Poser': [2905], 'lines': [3018], 'cultured': [3020], 'DMEM': [3022], 'plus': [3023, 3216], '10%': [3024, 3572], 'FBS': [3025], '100U/ml': [3027], 'penicillin': [3028], 'streptomycin.': [3030], 'week,': [3033], 'kept': [3036], 'selection': [3038], '400': [3040, 3209, 3823], 'μg/μl': [3041], 'geneticin': [3042], 'ensure': [3044, 3558], 'stable': [3045], 'integration': [3046], 'expanded': [3052], 'normal': [3054], 'media.': [3055], 'resuspending': [3061, 3405], 'five': [3064], 'pellet': [3066], 'lysis': [3069, 3132, 3214], 'buffer': [3070, 3215, 3495], '(150': [3071], 'mm': [3072, 3075, 3080, 3090, 3164, 3167, 3174, 3177, 3185, 3265, 3409, 3414, 3445, 3500, 3504], 'NaCl,': [3073, 3165], '50': [3074, 3230, 3408, 3521], 'Tris': [3076], 'pH': [3077, 3169], '8.0,': [3078], 'EDTA,': [3081], '20%': [3082, 3171], 'glycerol)': [3083], 'supplemented': [3084, 3179, 3259, 3276], '1%': [3086, 3181, 3217, 3261, 3278], 'Nonidet': [3087, 3182, 3218, 3262, 3279], 'P-40,': [3088, 3183, 3219, 3263, 3280], 'DTT,': [3091, 3186, 3222, 3266], 'Roche': [3093], 'EDTA-free': [3094, 3188], 'complete': [3095, 3189, 3559], 'protease': [3096, 3190], 'inhibitors': [3097, 3191], '(CPIs,': [3098, 3192], 'Roche,': [3099], 'Basel,': [3100], 'Switzerland).': [3101], 'rotated': [3105], '4C': [3107], 'two': [3109], 'hours.': [3110], 'lysate': [3112, 3199, 3376], 'was': [3113, 3127, 3147, 3200, 3227, 3289, 3364, 3377, 3401, 3463, 3474, 3518, 3547, 3585, 3595, 3602, 3720, 3786, 3800, 3888, 3950, 3965, 4066], 'centrifuged': [3115], '30': [3117, 3294, 3469], 'min': [3118, 3508, 3630, 3641, 3669, 3680, 3700, 3711], '4000': [3120], 'rcf': [3121], '4°C,': [3123], 'supernatant': [3126, 3288, 3462], 'snap-frozen.': [3130], 'produced': [3134, 4099], 'high-quality': [3135], '∼10': [3138], 'mg/ml': [3139], 'concentration.': [3141], 'Twenty': [3142], 'microliters': [3143, 3359], 'bead': [3145, 3362], 'slurry': [3146, 3363], 'per': [3149, 3366, 3379], '(Chromotek,': [3152], 'Planegg,': [3153], 'Germany).': [3154], 'Beads': [3155, 3269], 'prewashed': [3157, 3204], 'three': [3158], 'times': [3159], 'Buffer': [3161, 3251, 3593, 3600, 3626, 3637, 3665, 3676, 3696, 3707], 'C': [3162, 3252], '(300': [3163], '20': [3166, 3507, 3803, 3968], 'HEPES': [3168], '7.9,': [3170], 'glycerol,': [3172], '2': [3173], 'MgCl2,': [3175], '0.2': [3176], 'EDTA)': [3178], '0.5': [3184, 3264], 'Roche).': [3193], 'Four': [3194], 'hundred': [3195], 'micrograms': [3196], 'added': [3201, 3228, 3519], 'beads': [3205, 3246, 3311, 3406], 'adjusted': [3207], 'μl': [3210], 'm': [3221, 3256, 3497], 'CPIs.': [3224, 3268], 'Ethidium': [3225], 'bromide': [3226], 'μg/ml.': [3231], 'Reactions': [3232, 3439], 'incubated': [3234, 3449, 3526], 'rotating': [3237], 'wheel': [3238], 'hour': [3241], '4°C.': [3243], 'After': [3244], 'IP,': [3245], 'washed': [3248, 3272, 3283], 'twice': [3249, 3273, 3284], 'increased': [3253], 'NaCl': [3257], 'PBS': [3275], 'finally': [3282], 'PBS.': [3286], 'All': [3287, 3317, 3383, 3461, 3583, 3893], 'removed': [3290, 3466], 'carefully': [3291, 3465], 'G': [3295, 3470], 'syringe': [3296], 'before': [3297, 3631, 3670, 3701, 4103], 'Control': [3303], 'samples': [3304, 3327, 3524, 3550, 3610, 3648, 3687, 3730, 3809, 3895], 'prepared': [3306, 3333], 'control': [3309, 3326], 'agarose': [3310], 'same': [3314, 3330, 3336, 3478], '(Chromotek).': [3316], 'LFQ': [3318, 3354, 3481, 3609, 3647, 3729, 3808, 3974], 'performed': [3321, 3349, 3387, 3392, 3402, 3427, 3475, 3586], 'triplicate.': [3323], 'experiment': [3331], 'day': [3337], 'analyzed': [3339, 3978], 'sequentially.': [3342], 'purifications': [3345], 'essentially': [3350, 4100], 'described': [3352, 4102], 'purifications.': [3357], 'Thirty': [3358], 'ml': [3371], 'pulldown': [3380], '(∼10': [3381], 'mg/ml).': [3382], 'duplicate.': [3389], 'Replicates': [3390], 'independently': [3393], 'separately.': [3398], 'On-bead': [3399], 'immediately': [3404], 'borate-buffered': [3410], 'saline': [3411], 'containing': [3412], 'BS3': [3415], '(Thermo': [3416, 3591], 'Scientific,': [3417], 'Waltham,': [3418], 'MA)': [3419], 'following': [3420], 'purification.': [3423], 'reactions': [3425], 'h': [3430], 'room': [3432, 3451, 3510, 3534, 3555], 'temperature': [3433, 3452, 3511, 3535, 3556], 'shaking': [3435, 3457, 3513, 3537], '1000': [3437, 3459, 3515, 3539, 3590], 'rpms.': [3438, 3460, 3516, 3540], 'quenched': [3441], 'adding': [3443], '100': [3444, 3499], 'ammonium': [3446, 3501], 'bicarbonate': [3447], '10': [3454, 3503, 3531], 'mins': [3455, 3532], 'again': [3464], 'syringe.': [3471], 'Sample': [3472], 'preparation': [3473], 'manner': [3479], 'samples.': [3484], 'Purified': [3485], 'denatured': [3490], 'reduced': [3492], 'elution': [3494], '(2': [3496], 'urea,': [3498], 'bicarbonate,': [3502], 'DTT)': [3505], 'Iodoacetimide': [3517], 'mm,': [3522], 'dark': [3529], 'To': [3541], 'this': [3542], '0.25': [3543], 'μg': [3544], 'trypsin': [3546], 'added,': [3548], 'digested': [3552], 'overnight': [3553], 'release': [3560], 'tryptic': [3562], 'beads.': [3566], 'Digested': [3567], 'acidified': [3570], 'TFA': [3573], 'stored': [3575], 'C18': [3577], 'StageTips': [3578], 'Easy-nLC': [3589], 'Scientific).': [3592], '0.1%': [3596, 3606], 'formic': [3597, 3607], 'acid': [3598], 'B': [3601, 3627, 3666, 3697], '80%': [3603], 'acetonitrile': [3604], 'acid.': [3608], 'LTQ-Orbitrap': [3614, 3652, 3735, 3814], 'QExactive': [3615], 'developing': [3619, 3658, 3691], 'gradient': [3621, 3660, 3693], '9': [3623, 3662], '32%': [3625, 3664], '94': [3629], 'washes': [3632, 3671], '50%': [3634, 3673], '95%': [3636, 3675, 3706], 'B,': [3638, 3677, 3708], '120': [3640], 'data': [3644, 3683, 3714], 'collection': [3645, 3684, 3715], 'time.': [3646, 3685, 3716], 'Fusion': [3653, 3815], 'Tribrid': [3654], '114': [3668], '140': [3679], '5–32%': [3695], '214': [3699], '60%': [3704], '240': [3710], 'flow': [3718], '250': [3721], 'nl/min': [3722], 'all': [3724], 'gradients.': [3725], 'SMC1A-GFP': [3726], 'XRCC6-GFP': [3728], 'QExactive.': [3736], 'MS': [3738, 3818, 3902], 'scans': [3739, 3759, 3819, 3839, 3903, 3923], '300': [3743, 3907], '1650': [3745, 3909], 'm/z': [3746, 3826, 3910], 'resolution': [3749, 3767, 3829, 3852, 3913, 3931], '70,000': [3751, 3915], 'AGC': [3754, 3771, 3834, 3856, 3918, 3935], '3e6.': [3757, 3921], 'orbitrap': [3764, 3928], '17,500,': [3769, 3933], '1e5,': [3774, 3938], 'NCE': [3776, 3940], '25,': [3778, 3942], 'intensity': [3781, 3866, 3945], 'threshold': [3782, 3867, 3946], '8.3e2.': [3784], 'TopN': [3785, 3949], 'set': [3787, 3801, 3889, 3951, 3966], '10,': [3789, 3953], 'unassigned': [3790], '1+': [3792], 'charged': [3793, 3958], 'ions': [3794, 3878, 3959], 'excluded,': [3796, 3961], 's.': [3804, 3892, 3969], 'PRPS1-GFP': [3805], 'MCM6-GFP': [3807], 'Tribrid.': [3816], '1500': [3825], '120,000': [3831], '4e5.': [3837], 'linear': [3844], 'ion': [3845], 'trap': [3846], 'CID': [3848], 'activation': [3849], '30,000,': [3854], '1e4,': [3859], 'collision': [3860], 'energy': [3861], '35,': [3863], '5e3.': [3869], 'Scans': [3870], 'data-dependent': [3874], 'top': [3875], 'mode,': [3877], 'charge': [3880], 'state': [3881], '2–7+': [3882], 'considered,': [3884], '60': [3891], 'LTQ-Orbitrap-QExactive.': [3900], '4e2.': [3948], 'unassigned,': [3954], '1+,': [3955], '2+': [3957], 'Thermo': [3970], 'RAW': [3971], 'files': [3972], 'measurements': [3976], 'MaxQuant': [3980, 4000], 'version': [3981], '1.5.1.0': [3982], 'default': [3984], 'settings': [3985], 'searching': [3987], 'Uniprot': [3990], 'curated': [3991], 'proteome': [3993], '(release': [3994], '03/09/2014)': [3995], '(38.Cox': [3996], 'enables': [4001], 'rates,': [4005], 'individualized': [4006], 'ppb-range': [4007], 'accuracies': [4009], 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