PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

Name: Work Video:
Duration: 3 min 30 s
Jing Zhang; Lei Xin; Baozhen Shan; Weiwu Chen; Mingjie Xie; Denis Yuen; Weimin Zhang; Zefeng Zhang; Gilles Lajoie; Bin Ma
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3997, 4004, 4023, 4035, 4091, 4095, 4126, 4152, 4156, 4163, 4194, 4216, 4220, 4227, 4243, 4264, 4269, 4277, 4310, 4312, 4323, 4327, 4337, 4346, 4349, 4358, 4370, 4383, 4401, 4408, 4420, 4423, 4426, 4437, 4441, 4453, 4458, 4463, 4472, 4482, 4498, 4502, 4514, 4526, 4538, 4547, 4552, 4575, 4587, 4591], 'automated': [8, 109, 1321], 'identification': [9, 22, 99, 110, 123, 200, 203, 261, 514, 699, 854, 1105, 1250, 1785, 2794, 3139, 3335, 3471, 3805], 'of': [10, 20, 84, 97, 111, 121, 185, 198, 252, 259, 547, 640, 672, 771, 777, 852, 928, 981, 996, 1040, 1134, 1172, 1314, 1323, 1420, 1452, 1596, 1601, 1610, 1634, 1645, 1709, 1717, 1727, 1736, 1759, 1783, 1811, 1819, 1899, 1930, 1933, 2047, 2075, 2088, 2172, 2195, 2216, 2241, 2283, 2295, 2373, 2417, 2440, 2457, 2483, 2487, 2523, 2563, 2809, 2822, 2830, 2866, 2934, 2945, 2948, 2969, 2992, 3012, 3044, 3051, 3095, 3106, 3114, 3170, 3274, 3363, 3375, 3446, 3511, 3552, 3558, 3592, 3611, 3617, 3629, 3657, 3692, 3719, 3728, 3761, 3764, 3780, 3793, 3817, 3873, 3942, 3958, 3975, 3984, 4006, 4026, 4129, 4162, 4165, 4196, 4229, 4263, 4295, 4298, 4326, 4348, 4403, 4422, 4440, 4451, 4465, 4490, 4509, 4529, 4574, 4586], 'peptides': [11, 112, 548, 1222, 1375, 1765, 1932, 2056, 2372, 2517, 2958, 3763, 3881, 3886, 3908, 3944, 4284], 'from': [12, 113, 204, 262, 339, 1766, 2243, 2494, 2588, 3301, 3387, 3585, 3652, 3706, 3866, 3878, 3897, 4022, 4088, 4102, 4125, 4145], 'tandem': [13, 114, 205, 295, 313, 394, 482, 543, 578, 778, 1204, 1378, 1856, 2625, 2748], 'mass': [14, 115, 206, 213, 229, 296, 314, 395, 483, 520, 544, 579, 609, 645, 657, 703, 779, 888, 1205, 1316, 1353, 1379, 1455, 1857, 2189, 2215, 2537, 2548, 2626, 2671, 2694, 2749, 3085], 'spectra.': [15, 116, 2966], 'The': [16, 117, 248, 768, 800, 994, 1023, 1757, 1815, 1830, 1882, 1913, 1991, 2053, 2086, 2097, 2111, 2148, 2170, 2265, 2360, 2583, 2696, 3252, 3305, 3347, 3437, 3485, 3563, 3870, 3973, 4017, 4083, 4113, 4119, 4142, 4209, 4255, 4583], 'accuracy': [17, 59, 118, 160, 249, 1020, 1024, 1073, 1133, 1292, 1810, 3169], 'and': [18, 60, 119, 161, 250, 292, 467, 496, 668, 705, 750, 774, 925, 936, 947, 1021, 1074, 1090, 1102, 1140, 1177, 1223, 1237, 1280, 1291, 1308, 1407, 1548, 1619, 1669, 1679, 1724, 1747, 1797, 1809, 1922, 1998, 2051, 2117, 2274, 2392, 2459, 2540, 2648, 2673, 2719, 2774, 2814, 2833, 2841, 2854, 2939, 3002, 3040, 3102, 3136, 3153, 3176, 3193, 3200, 3210, 3216, 3228, 3371, 3468, 3487, 3500, 3514, 3523, 3575, 3614, 3675, 3683, 3806, 3996, 4029, 4039, 4314, 4331, 4364, 4374, 4443, 4457, 4511, 4517, 4533, 4541, 4572, 4590], 'sensitivity': [19, 61, 120, 162, 251, 1290, 1672], 'via': [24, 125, 418, 476], 'database': [25, 35, 52, 126, 136, 153, 293, 345, 350, 474, 498, 783, 801, 815, 830, 834, 846, 997, 1017, 1141, 1159, 1253, 1262, 1297, 1324, 1769, 1780, 1813, 1904, 2000, 2124, 2276, 2404, 2466, 3177, 3458, 3547, 4111, 4114, 4224, 4239, 4256, 4332, 4375, 4429, 4454, 4534, 4549], 'search': [26, 36, 127, 137, 346, 499, 611, 733, 802, 835, 847, 933, 998, 1018, 1157, 1160, 1254, 1263, 1298, 1325, 1343, 1405, 1435, 1479, 1503, 1534, 1562, 1598, 1612, 1648, 1781, 2125, 2461, 3259, 3339, 3650, 4333, 4376, 4455, 4535], 'are': [27, 128, 1013, 1887, 1905, 1923, 1937, 1960, 2062, 2078, 2091, 2126, 2362, 2406, 2498, 2698, 2721, 2777, 2816, 2972, 3003, 3246, 3254, 3287, 3490, 3526, 3537, 3578, 3584, 3737, 3771, 3826, 3887, 3909, 3915, 3934, 3945, 4066, 4493, 4544], 'critical': [28, 129], 'successful': [30, 131], 'proteomics': [31, 132, 1315, 2423], 'experiments.': [32, 133, 2424], 'A': [33, 134, 449, 731, 879, 976, 1227, 1515, 2026, 2554, 2566, 2897, 2967, 3418, 4191], 'new': [34, 71, 135, 172, 1077, 1743], 'tool,': [37, 138], 'PEAKS': [38, 54, 139, 155, 370, 1243, 1266, 1760, 1775, 1788, 1821, 1831, 2098, 2145, 2149, 2173, 2484, 2598, 3007, 3405, 3519, 3684, 3734, 3781, 4007, 4355, 4362, 4391], 'DB,': [39, 140, 3520, 3782], 'has': [40, 77, 141, 178, 1000, 1426, 2453, 2659, 2682], 'by': [43, 144, 393, 481, 515, 1028, 1055, 1138, 1333, 1352, 1377, 1402, 1587, 1855, 2120, 2144, 2180, 2187, 2205, 2280, 2364, 2370, 2389, 2518, 2624, 2747, 2851, 2920, 3032, 3174, 3289, 3404, 3497, 3505, 3580, 3920, 4155, 4226, 4274, 4390, 4398, 4448, 4578], 'incorporating': [44, 145], 'de': [46, 147, 289, 364, 390, 454, 477, 1272, 1791, 1800, 1852, 1874, 1883, 1995, 2104, 2130, 2139, 2161, 2232, 2270, 2323, 2591, 2599, 2621, 2744, 3017, 4328, 4350, 4371, 4385, 4409, 4467, 4530, 4553], 'novo': [47, 148, 290, 332, 365, 391, 415, 455, 478, 1273, 1792, 1801, 1828, 1853, 1875, 1884, 1996, 2105, 2131, 2140, 2162, 2233, 2271, 2324, 2592, 2600, 2622, 2745, 3018, 4329, 4351, 4372, 4386, 4410, 4468, 4531, 4554], 'sequencing': [48, 149, 291, 333, 366, 392, 417, 480, 1274, 1793, 1802, 1854, 1876, 2106, 2141, 2593, 2601, 2623, 2746, 4330, 4352, 4373, 4387, 4469, 4532, 4555], 'results': [49, 150, 1275, 1286, 1650, 1803, 4353, 4470], 'into': [50, 151, 286, 736, 3828], 'search.': [53, 154, 294, 824, 1814, 4112, 4240], 'DB': [55, 156, 1244, 1267, 1761, 1776, 1789, 1822, 3406, 3685], 'achieves': [56, 157, 3340], 'significantly': [57, 158, 1288], 'improved': [58, 159, 1289, 1749], 'over': [62, 163], 'two': [63, 164, 287, 1305, 1706, 2377, 2645], 'other': [64, 165, 268, 2970, 3841, 3998], 'commonly': [65, 166], 'used': [66, 167, 211, 227, 1429, 1656, 1871, 1888, 1924, 1938, 1982, 2032, 2063, 2101, 2128, 2558, 2572, 2596, 2722, 2778, 2903, 2973, 3123, 3196, 3203, 3213, 3223, 3230, 3427, 4001, 4032, 4109, 4150, 4213, 4237, 4307, 4545], 'packages.': [68, 169], 'Additionally,': [69, 170], 'a': [70, 171, 243, 344, 348, 554, 641, 650, 808, 817, 827, 833, 1076, 1164, 1170, 1184, 1433, 1626, 1647, 1695, 1733, 1767, 1795, 1945, 1977, 2082, 2153, 2167, 2177, 2206, 2238, 2269, 2275, 2318, 2342, 2415, 2454, 2464, 2640, 2660, 2683, 2706, 2823, 2867, 2993, 3030, 3045, 3217, 3249, 3261, 3293, 3312, 3320, 3333, 3384, 3447, 3641, 3665, 3725, 3745, 3749, 3767, 3790, 3803, 3836, 3843, 3976, 4130, 4302, 4449, 4480, 4524], 'result': [72, 173], 'validation': [73, 174, 1322, 1329], 'method,': [74, 175, 1752], 'decoy': [75, 92, 176, 193, 1336, 1382, 1397, 1414, 1590, 1603, 1638, 1701, 1712, 1725, 1751, 1753, 2029, 3421, 3424, 3441, 3448, 3488, 3513, 3524, 3576, 3612, 3642, 3676, 4267, 4270, 4296, 4304, 4315, 4444, 4589, 4592], 'fusion,': [76, 177, 1754, 3425], 'introduced': [79, 180, 1605], 'to': [80, 181, 355, 541, 782, 806, 823, 1081, 1130, 1153, 1167, 1233, 1259, 1276, 1295, 1302, 1374, 1399, 1416, 1427, 1698, 1763, 1778, 1804, 1872, 1889, 1908, 1939, 1983, 2016, 2033, 2042, 2064, 2102, 2176, 2212, 2236, 2259, 2445, 2504, 2559, 2573, 2644, 2904, 2961, 2976, 2998, 3166, 3208, 3220, 3267, 3303, 3311, 3351, 3428, 3644, 3740, 3754, 3786, 3789, 3810, 3852, 3963, 3981, 4002, 4033, 4140, 4308, 4477, 4506, 4558], 'solve': [81, 182, 1704, 3662], 'issue': [83, 184], 'overconfidence': [85, 186], 'that': [86, 187, 1084, 1576, 1641, 1694, 2070, 2209, 2302, 2655, 2678, 3332, 3379, 3702, 3832, 4436], 'exists': [87, 188], 'in': [88, 189, 246, 359, 553, 662, 887, 1007, 1015, 1044, 1287, 1293, 1348, 1520, 1657, 1893, 1902, 1925, 1972, 2006, 2093, 2159, 2249, 2303, 2314, 2331, 2336, 2421, 2434, 2479, 2492, 2597, 2856, 2890, 2974, 3006, 3069, 3079, 3124, 3197, 3204, 3214, 3224, 3281, 3336, 3456, 3518, 3532, 3671, 3698, 3733, 3774, 3842, 4105, 4151, 4280, 4354, 4471], 'conventional': [90, 191, 3439], 'target': [91, 192, 1335, 1637, 1700, 1723, 1750, 2028, 3420, 3440, 3453, 3486, 3515, 3522, 3574, 3618, 3631, 3659, 3674, 3708, 4299, 4303, 4313, 4442, 4588], 'method': [93, 194, 840, 1166, 1337, 1395, 1425, 1639, 1702, 4305], 'certain': [95, 196], 'types': [96, 197], 'peptide': [98, 199, 263, 278, 306, 324, 336, 354, 389, 416, 456, 479, 698, 732, 842, 1104, 1135, 1175, 1249, 1659, 1784, 1851, 1954, 1974, 1987, 2001, 2037, 2076, 2142, 2277, 2339, 2489, 2506, 2511, 2530, 2536, 2620, 2658, 2681, 2743, 2793, 2824, 2865, 2994, 3037, 3046, 3059, 3138, 3171, 3397, 3470, 3656, 3705, 3892, 3904, 4137, 4388, 4396, 4473], 'software.': [100, 201, 1299, 1786], 'Peptide': [202], 'spectrometry': [207, 297, 315, 521, 610, 646, 1317, 1380], '(MS/MS)': [208], '1The': [209, 225], 'abbreviations': [210, 226], 'are:MS/MStandem': [212, 228], 'spectrometryPTMpost-translational': [214, 230], 'modificationETDelectron': [215, 231], 'transfer': [216, 232, 301, 319], 'dissociationFDRfalse': [217, 233], 'discovery': [218, 234, 304, 322, 950, 1031], 'ratePSMpeptide': [219, 235], 'spectrum': [220, 236, 307, 325, 2038, 2507, 2641, 2870, 4484], 'matchiPRGProteome': [221, 237], 'Informatics': [222, 238, 310, 328, 4158], 'Research': [223, 239, 311, 329, 4159], 'Group.': [224, 240, 312, 330], 'data': [241, 546, 1318, 2569, 3265, 3990, 4010, 4019, 4084, 4093, 4121, 4144, 4211, 4218, 4339, 4360, 4500], 'is': [242, 803, 831, 836, 1025, 1035, 1231, 1246, 1330, 1625, 1640, 1655, 1745, 1755, 1762, 1870, 1981, 2002, 2014, 2031, 2100, 2146, 2166, 2174, 2203, 2210, 2278, 2299, 2310, 2387, 2428, 2462, 2538, 2549, 2557, 2571, 2586, 2642, 2825, 2879, 2902, 2918, 2959, 3047, 3309, 3327, 3383, 3393, 3407, 3411, 3426, 3503, 3561, 3603, 3633, 3669, 3710, 3715, 3724, 3752, 3784, 3801, 3807, 3819, 3876, 3893, 3905, 3961, 3979, 4212, 4415, 4430, 4446, 4486], 'central': [244], 'task': [245, 254], 'proteomics.': [247], 'this': [253, 1008, 1061, 1216, 1240, 1328, 1690, 1740, 1742, 2164, 2226, 2256, 2304, 2399, 2859, 2895, 3055, 3566, 3663, 3720], 'directly': [255, 338], 'impacts': [256], 'performance': [258, 999, 4005, 4325, 4528], 'protein': [260, 513, 555, 663, 707, 813, 828, 1173, 1350, 1653, 1730, 1895, 1920, 1935, 2245, 2305, 2410, 2496, 3025, 3028, 3042, 3449, 3454, 3553, 3560, 3632, 3709, 3713, 3730, 3750, 3757, 3875, 3960, 3977, 4038, 4099, 4117, 4222, 4259], 'hits,': [264], 'as': [265, 267, 1037, 1257, 1714, 1732, 1794, 1825, 2222, 2408, 2468, 2827, 3279, 3329, 3529, 3605, 3678, 3882, 3947], 'well': [266], 'downstream': [269], 'analyses.': [270], 'identification;': [279], 'these': [280, 1705, 2089, 3115], 'can': [282, 1052, 1437, 2019, 2326, 2345, 2476, 2847, 3687, 3850, 4433], 'be': [283, 807, 1053, 1082, 1400, 1428, 2020, 2414, 2446, 2477, 2848, 2873, 2999, 3835, 4434], 'broadly': [284], 'divided': [285], 'categories:': [288], 'post-translational': [298, 316], 'modification': [299, 317, 2312, 2354], 'electron': [300, 318], 'dissociation': [302, 320, 2709], 'false': [303, 321, 949, 1030, 1042, 1091, 1421, 3334, 3354, 3364, 3376, 3380], 'rate': [305, 323, 1032, 3382], 'match': [308, 326, 1940, 2327, 2347, 2820, 2915, 2980, 3244], 'Proteome': [309, 327, 613, 740, 1109, 1384, 1457, 1481, 1505, 1536, 1564, 3143, 3475, 4157], 'De': [331, 414], 'derives': [334], 'sequence': [337, 349, 517, 814, 829, 1768, 1885, 1896, 1910, 1997, 2178, 2234, 2272, 2316, 2325, 2333, 2512, 2531, 2578, 2877, 2887, 2907, 3019, 3064, 3075, 3450, 3455, 3643, 3931, 4223, 4411], 'MS/MS': [341, 361, 932, 1139, 1771, 1942, 1964, 2542, 2797, 2869, 3175], 'spectrum,': [342, 2135, 2711, 2767, 4381], 'whereas': [343], 'queries': [347], 'best': [353, 1986, 4438], 'explain': [356], 'peaks': [358], 'spectrum.': [362, 1990, 2110, 2582, 2896, 2911], 'Representative': [363], 'packages': [368, 501], 'include': [369, 502], '(1Ma': [371, 1833, 2602], 'B.': [372, 433, 1834, 2603, 2726, 2784, 2788], 'Zhang': [373, 1835, 2604, 2727], 'K.': [374, 1836, 2605, 2728, 4055], 'Hendrie': [375, 1837, 2606, 2729], 'C.': [376, 378, 1470, 1525, 1838, 1840, 2607, 2609, 2730, 2732, 4045], 'Liang': [377, 1839, 2608, 2731], 'Li': [379, 1841, 2610, 2733], 'M.': [380, 599, 635, 694, 729, 955, 1094, 1446, 1492, 1551, 1842, 2611, 2734, 3128, 3460, 4059, 4170], 'Doherty-Kirby': [381, 1843, 2612, 2735], 'A.': [382, 410, 723, 1120, 1844, 2613, 2736, 3156], 'Lajoie': [383, 1845, 2614, 2737], 'G.': [384, 1846, 2615, 2738], 'PEAKS:': [385, 1847, 2616, 2739], 'powerful': [386, 1848, 2617, 2740], 'spectrometry.Rapid': [396, 484, 1858, 2627, 2750], 'Commun.': [397, 485, 1859, 2628, 2751], 'Mass': [398, 486, 559, 986, 1860, 2629, 2752, 4201], 'Spectrom.': [399, 487, 560, 1861, 2630, 2753], '2003;': [400, 1862, 2631, 2754], '17:': [401, 1863, 2632, 2755], '2337-2342Crossref': [402, 1864, 2633, 2756], 'PubMed': [403, 426, 462, 491, 526, 564, 584, 618, 685, 713, 745, 795, 895, 942, 1114, 1147, 1210, 1359, 1389, 1462, 1486, 1510, 1541, 1569, 1865, 2634, 2757, 3148, 3183, 3480, 4078], 'Scopus': [404, 427, 463, 492, 527, 565, 585, 619, 686, 714, 746, 796, 896, 943, 1115, 1148, 1211, 1360, 1390, 1463, 1487, 1511, 1542, 1570, 1866, 2635, 2758, 2803, 3149, 3184, 3481, 4079], '(966)': [405, 1867, 2636, 2759], 'Google': [406, 429, 465, 494, 529, 567, 587, 621, 688, 716, 748, 798, 898, 945, 1117, 1150, 1213, 1362, 1392, 1465, 1489, 1513, 1544, 1572, 1868, 2637, 2760, 2805, 3151, 3186, 3483, 4081], 'Scholar),': [407, 430, 466, 495, 530, 568, 588, 622, 689], 'PepNovo': [408], '(2Frank': [409], 'Pevzner': [411, 766], 'P.': [412, 443, 4096, 4427, 4515, 4539], 'PepNovo:': [413], 'probabilistic': [419], 'network': [420], 'modeling.Anal.': [421], 'Chem.': [422, 458, 1143, 3179], '2005;': [423, 459, 677, 939], '77:': [424, 460], '964-973Crossref': [425], '(526)': [428], 'NovoHMM': [431], '(3Fischer': [432], 'Roth': [434], 'V.': [435], 'Roos': [436], 'F.': [437, 903], 'Grossmann': [438], 'J.': [439, 533, 692, 719, 1100, 3134, 3466], 'Baginsky': [440], 'S.': [441, 753, 763, 869], 'Widmayer': [442], 'Gruissem': [444], 'W.': [445, 605], 'Buhmann': [446], 'J.M.': [447, 4043], 'NovoHMM:': [448], 'hidden': [450], 'Markov': [451], 'model': [452, 1129, 3165], 'sequencing.Anal.': [457], '7265-7273Crossref': [461], '(138)': [464], 'Lutefisk': [468], '(4Taylor': [469], 'J.A.': [470, 595, 907], 'Johnson': [471], 'R.S.': [472], 'Sequence': [473], 'searches': [475, 3565], '1997;': [488], '11:': [489, 2801], '1067-1075Crossref': [490], '(339)': [493], 'representative': [497], 'Mascot': [503, 1107, 3141, 3473, 3682, 4365, 4399, 4476, 4507, 4548, 4579], '(5Perkins': [504], 'D.N.': [505], 'Pappin': [506], 'D.J.': [507], 'Creasy': [508], 'D.M.': [509, 601], 'Cottrell': [510], 'J.S.': [511], 'Probability-based': [512], 'searching': [516], 'databases': [518, 3489, 4316, 4489, 4519, 4543], 'using': [519, 1251, 1381, 4466], 'data.Electrophoresis.': [522], '1999;': [523], '20:': [524, 582, 1208], '3551-3567Crossref': [525], '(6763)': [528], 'SEQUEST': [531], '(6Eng': [532], 'McCormack': [534], 'A.L.': [535, 637], 'Yates': [536], '3rd,': [537], 'J.R.': [538], 'An': [539, 922], 'approach': [540, 810, 2030, 3442], 'correlate': [542], 'spectral': [545], 'with': [549, 577, 1106, 1183, 1203, 1430, 1673, 1770, 1944, 1958, 2200, 2351, 2544, 2551, 2668, 2691, 2700, 2795, 3140, 3240, 3248, 3256, 3415, 3472, 3766, 3994, 4014, 4249, 4407, 4580], 'amino': [550, 2157, 2185, 2197, 2285, 3013, 3627, 3929, 4278, 4405, 4564], 'acid': [551, 2158, 2198, 3628, 3930], 'sequences': [552, 1726, 2490, 3525, 3677, 4271], 'database.J.': [556], 'Am.': [557], 'Soc.': [558], '1994;': [561], '5:': [562, 940], '976-989Crossref': [563], '(5420)': [566], 'X!Tandem': [569], '(7Craig': [570], 'R.': [571, 867, 1126, 1197, 3162], 'Beavis': [572, 866, 1198], 'R.C.': [573, 1199], 'TANDEM:': [574, 1200], 'Matching': [575, 1201], 'proteins': [576, 1202, 1398, 1415, 1591, 1604, 1713, 1901, 1917, 2069, 2242, 2361, 2378, 2405, 2420, 2433, 2442, 2458, 3053, 3818, 3825, 3838, 3865, 4253], 'spectra.Bioinformatics.': [580, 1206], '2004;': [581, 615, 1207], '1466-1467Crossref': [583, 1209], '(1987)': [586, 1212], 'OMSSA': [589], '(8Geer': [590], 'L.Y.': [591], 'Markey': [592], 'S.P.': [593, 1341], 'Kowalak': [594], 'Wagner': [596], 'L.': [597, 629, 761, 973, 1096, 1365, 2786, 3130, 3462, 4188], 'Xu': [598], 'Maynard': [600], 'Yang': [602], 'X.': [603, 2782, 3775], 'Shi': [604], 'Bryant': [606], 'S.H.': [607], 'Open': [608], 'algorithm.J.': [612], 'Res.': [614, 741, 1110, 1385, 1458, 1482, 1506, 1537, 1565, 3144, 3476], '3:': [616], '958-964Crossref': [617], '(1164)': [620], 'ProteinProspector': [623], '(9Chalkley': [624], 'R.J.': [625, 921, 959, 4174], 'Baker': [626], 'P.R.': [627], 'Huang': [628], 'Hansen': [630], 'K.C.': [631], 'Allen': [632], 'N.P.': [633], 'Rexach': [634], 'Burlingame': [636], 'Comprehensive': [638], 'analysis': [639, 671, 1475, 1499, 1530, 1558], 'multidimensional': [642], 'liquid': [643], 'chromatography': [644], 'dataset': [647], 'acquired': [648], 'on': [649, 978, 1412, 1496, 1555, 1599, 2255, 2321, 2430, 2463, 3260, 3271, 4193, 4497, 4570], 'quadrupole': [651, 653], 'selecting': [652], 'collision': [654, 2707], 'cell,': [655], 'time-of-flight': [656], 'spectrometer:': [658], 'II.': [659], 'New': [660], 'developments': [661], 'prospector': [664], 'allow': [665], 'reliable': [667], 'comprehensive': [669], 'automatic': [670], 'large': [673, 2465, 3262], 'datasets.Mol.': [674], 'Cell.': [675, 785], 'Proteomics.': [676, 786], '4:': [678, 1357], '1194-1204Abstract': [679], 'Full': [680, 682, 790, 792], 'Text': [681, 683, 791, 793], 'PDF': [684, 794], '(145)': [687], 'MaxQuant': [690, 695, 738], '(10Cox': [691], 'Mann': [693, 728], 'enables': [696], 'high': [697, 948, 1311, 2054], 'rates,': [700], 'individualized': [701], 'p.p.b.-range': [702], 'accuracies': [704], 'proteome-wide': [706], 'quantification.Nat.': [708], 'Biotechnol.': [709], '2008;': [710, 1386], '26:': [711], '1367-1372Crossref': [712], '(9154)': [715], 'Scholar)': [717, 749, 899, 946, 1573, 1869, 3152, 3187], '(11Cox': [718], 'Neuhauser': [720], 'N.': [721, 755, 757, 957, 4172], 'Michalski': [722], 'Scheltema': [724], 'R.A.': [725], 'Olsen': [726], 'J.V.': [727], 'Andromeda:': [730], 'engine': [734, 1406, 1613, 3651], 'integrated': [735], 'environment.J.': [739], '2011;': [742, 990, 1507, 1566, 2800, 4205], '10:': [743, 1508, 1567, 4076], '1794-1805Crossref': [744], '(3450)': [747], 'MS-GFDB': [751], '(12Kim': [752], 'Mischerikow': [754], 'Bandeira': [756, 956, 4171], 'Navarro': [758], 'J.D.': [759, 1367], 'Wich': [760], 'Mohammed': [762], 'Heck': [764], 'A.J.': [765], 'P.A.': [767, 971, 4186], 'generating': [769], 'function': [770, 1079, 1191, 1661, 1980, 2595, 2791, 2901], 'CID,': [772], 'ETD': [773, 2766, 2796, 4120, 4217], 'CID/ETD': [775], 'pairs': [776], 'spectra:': [780], 'Applications': [781], 'search.Mol.': [784], '2010;': [787, 1483, 1538, 4075], '9:': [788, 1484, 1539], '2840-2852Abstract': [789], '(196)': [797], 'Scholar).': [799, 993, 1151, 1214, 1393, 1514, 1688, 2638, 3484, 4082, 4208], 'generally': [804], 'believed': [805], 'simpler': [809], 'because': [811, 1432, 2308], 'provides': [816], 'limited': [818], 'space': [819], 'Therefore,': [825, 2437], 'when': [826, 4335, 4425, 4488, 4513], 'available,': [832], 'most': [838, 2422, 2880, 3000], 'common': [839, 885, 2284, 3413], 'identification.': [843], 'However,': [844, 1060, 1215, 1256, 1423, 1787, 2335, 2987, 3517], 'existing': [845, 1296], 'still': [849, 1580], 'experience': [850], 'problems': [851, 886], 'low': [853, 2183], 'rates': [855, 951], '(low': [856, 952], 'sensitivity)': [857], '(13Bell': [858], 'A.W.': [859], 'Deutsch': [860, 962, 4177], 'E.W.': [861], 'Au': [862], 'C.E.': [863], 'Kearney': [864], 'R.E.': [865], 'Sechi': [868], 'Nilsson': [870], 'T.': [871, 969, 1098, 3132, 3464, 4047, 4184], 'Bergeron': [872], 'J.J.': [873], 'HUPO': [874, 880], 'Test': [875], 'Sample': [876], 'Working': [877], 'Group:': [878], 'test': [881], 'sample': [882], 'study': [883, 4034, 4154, 4235], 'reveals': [884], 'spectrometry-based': [889], 'proteomics.Nat.': [890], 'Methods.': [891, 1355], '2009;': [892, 1111, 1459, 3145, 3477], '6:': [893], '423-430Crossref': [894], '(274)': [897], '(14Kapp': [900], 'E.A.': [901], 'Schütz': [902], 'Connolly': [904], 'L.M.': [905], 'Chakel': [906], 'Meza': [908], 'J.E.': [909, 1339], 'Miller': [910], 'C.A.': [911], 'Fenyo': [912], 'D.': [913, 1450], 'Eng': [914], 'J.K.': [915], 'Adkins': [916], 'J.N.': [917], 'Omenn': [918], 'G.S.': [919], 'Simpson': [920], 'evaluation,': [923], 'comparison,': [924], 'accurate': [926], 'benchmarking': [927], 'several': [929, 3829], 'publicly': [930], 'available': [931], 'algorithms:': [934], 'Sensitivity': [935], 'specificity': [937], 'analysis.Proteomics.': [938], '3475-3490Crossref': [941], '(311)': [944], 'accuracy)': [953], '(15Askenazi': [954, 4169], 'Chalkley': [958, 4173], 'Clauser': [960, 4175], 'K.R.': [961, 4176], 'E.': [963, 1124, 3160, 4178], 'Lam': [964, 4179], 'H.H.N.': [965, 4180], 'McDonald': [966, 4181], 'W.H.': [967, 4182], 'Neubert': [968, 4183], 'Rudnick': [970, 4185], 'Martens': [972, 4187], 'iPRG': [974, 4189, 4233], '2011:': [975, 4190], 'Study': [977, 4192], 'Identification': [980, 4195], 'Electron': [982, 4197], 'Transfer': [983, 4198], 'Dissociation': [984, 4199], '(ETD)': [985, 4200], 'Spectra.J': [987, 4202], 'Biomol': [988, 4203], 'Tech.': [989, 4204], '22:': [991, 4206], 'S20Google': [992, 4207], 'improvement': [995], 'always': [1001], 'an': [1003, 1155, 1584, 1748, 2003, 2223, 2328, 2765, 3257, 3635], 'active': [1004], 'research': [1005], 'area': [1006, 3270], 'field.': [1009], 'Two': [1010, 3907, 3988], 'competing': [1011], 'objectives': [1012, 1306], 'sought': [1014], 'approach:': [1019], 'sensitivity.': [1022, 1069, 1226], 'usually': [1026, 1188], 'measured': [1027, 2279], '(FDR),': [1033], 'which': [1034, 2412], 'defined': [1036, 3328], 'percentage': [1039, 2168], 'identifications': [1043, 1046, 1092, 1136, 1351, 3172, 3365, 3577], 'all': [1045, 2520, 2836, 3760, 3860, 3864, 3937, 4262], 'above': [1047, 2060, 3366, 3620], 'score': [1049, 1058, 2013, 2040, 2298, 2358, 2368, 2562, 2790, 2821, 2846, 2916, 2933, 3031, 3050, 3308, 3369, 3398, 3435, 3599, 3622, 3746, 3769, 3872, 3957, 3974, 3983, 4456, 4567], 'threshold.': [1050, 1059, 3436, 3623], 'Accuracy': [1051], 'accomplished': [1054], 'increasing': [1056], 'will': [1062, 1178, 1703, 2252, 4344], 'at': [1063, 1592, 1614, 3432, 3689], 'same': [1065, 1404, 1729, 2073, 2112, 2349, 2353, 2381, 2590, 3342, 3550, 3891, 3912, 4210, 4221, 4338], 'time': [1066], 'reduce': [1067, 2260], 'To': [1070, 3661], 'improve': [1071, 1277, 1805], 'both': [1072, 1806, 3690, 4452], 'sensitivity,': [1075, 1235], 'scoring': [1078, 1190, 1282, 1660, 1947, 1953, 1979, 2008, 2340, 2594, 2876, 2886, 2900, 3903], 'needs': [1080], 'more': [1085, 1185, 1589, 2083, 2898, 3231, 3438, 4067, 4563], 'accurately': [1086], 'separates': [1087], 'true': [1089], '(16Brosch': [1093, 3127, 3459], 'Yu': [1095, 3129, 3461], 'Hubbard': [1097, 3131, 3463], 'Choudhary': [1099, 3133, 3465], 'Accurate': [1101, 3135, 3467], 'sensitive': [1103, 3137, 3469], 'percolator.J.': [1108, 3142, 3474], '8:': [1112, 1460, 3146, 3478], '3176-3181Crossref': [1113, 3147, 3479], '(332)': [1116, 3150, 3482], 'Scholar,': [1118, 1363, 1466, 1490, 1545], '17Keller': [1119], 'Nesvizhskii': [1121, 3157], 'A.I.': [1122, 3158], 'Kolker': [1123, 3159], 'Aebersold': [1125, 3161], 'Empirical': [1127, 3163], 'statistical': [1128, 1474, 1498, 1529, 1557, 3164], 'estimate': [1131, 1417, 3167, 3429, 4309], 'made': [1137, 2429, 3173], 'search.Anal.': [1142, 3178], '2002;': [1144, 3180], '74:': [1145, 3181], '5383-5392Crossref': [1146, 3182], '(3886)': [1149, 3185], 'Meanwhile,': [1152], 'maintain': [1154], 'acceptable': [1156], 'speed,': [1158], 'often': [1162, 1219], 'introduces': [1163, 1396], 'filtration': [1165, 1218, 1229, 1279], 'quickly': [1168], 'select': [1169, 2237], 'shortlist': [1171, 1921, 1936, 2441, 2497], 'or': [1174, 2533, 3117, 3343, 3495, 3588, 3854, 3863, 3917, 3932, 4562], 'candidates': [1176, 1182, 1955, 1970, 2579, 2888, 2908], 'only': [1179, 2136, 2253, 2346, 3856, 3900, 3919, 4382], 'evaluate': [1180, 4003], 'those': [1181, 1957], 'advanced': [1186], '(and': [1187], 'slower)': [1189], '(see': [1192, 2723, 2779], 'example': [1194], 'Ref.': [1195, 1521, 2724, 2780], '7Craig': [1196], 'simple': [1217, 2860], 'excludes': [1220], 'real': [1221], 'causes': [1224], 'reduced': [1225], 'good': [1228], 'technique': [1230], 'required': [1232, 4483], 'balance': [1234], 'accuracy,': [1236], 'speed.': [1238], 'In': [1239, 1300, 1689, 1739, 2010, 2225, 2290, 3189, 3776, 4261], 'paper,': [1241, 1691, 1741, 3721], 'described': [1247], 'approach.': [1255], 'opposed': [1258], 'traditional': [1261], 'approach,': [1264, 3422], 'relies': [1269], 'heavily': [1270], 'upon': [1271], 'function.': [1283, 1948, 2009], 'This': [1284, 1394, 1607, 2475, 2845, 4320], 'combination': [1285, 4450], 'comparison': [1294], 'addition': [1301, 2975], 'aforementioned': [1304], '(accuracy': [1307], 'sensitivity),': [1309], 'throughput': [1312], 'generation': [1313, 3445], 'requires': [1319, 1608, 3443], 'results.': [1326], 'Currently,': [1327], 'typically': [1331], 'achieved': [1332, 2369, 4447], '(18Elias': [1338], 'Gygi': [1340], 'Target-decoy': [1342], 'strategy': [1344, 1744], 'increased': [1346, 2447], 'confidence': [1347, 2055, 2154, 2165, 2184, 2202], 'large-scale': [1349], 'spectrometry.Nat.': [1354], '2007;': [1356], '207-214Crossref': [1358], '(2827)': [1361], '19Käll': [1364], 'Storey': [1366], 'MacCoss': [1368], 'M.J.': [1369], 'Noble': [1370], 'W.S.': [1371], 'Assigning': [1372], 'significance': [1373, 3401, 3768, 3871, 3940], 'identified': [1376, 2057, 3880, 3894, 4577], 'databases.J.': [1383], '7:': [1387], '29-34Crossref': [1388], '(441)': [1391], 'searched': [1401, 3492, 4318], 'uses': [1408, 2230], "engine's": [1410, 1649], 'outcome': [1411], 'number': [1419, 2282, 2439, 2456, 2968, 3011, 3105, 3362, 3374, 3551, 3610, 3616, 4294, 4402], 'positives.': [1422], 'caution': [1431], 'multi-stage': [1434, 1477, 1501, 1532, 1560], 'procedure': [1436, 3732], 'make': [1438], 'it': [1439, 1642, 2018], 'biased': [1440], 'toward': [1441], 'underestimating': [1442], 'FDR': [1444, 1622, 1630, 2045, 3277, 3431, 3502, 3602, 4288, 4292, 4504], '(20Bern': [1445], 'Phinney': [1447], 'B.S.': [1448], 'Goldberg': [1449], 'Reanalysis': [1451], 'Tyrannosaurus': [1453], 'rex': [1454], 'spectra.J.': [1456], '4328-4332Crossref': [1461], '(51)': [1464], '21Everett': [1467, 1522], 'L.J.': [1468, 1523], 'Bierl': [1469, 1524], 'Master': [1471, 1526], 'S.R.': [1472, 1527], 'Unbiased': [1473, 1528], 'proteomic': [1478, 1502, 1533, 1561], 'strategies.J.': [1480, 1535], '700-707Crossref': [1485, 1540], '(41)': [1488, 1543], '22Bern': [1491], 'Kil': [1493, 1549, 1552], 'Y.J.': [1494, 1553], 'Comment': [1495, 1554], '"unbiased': [1497, 1556], 'strategies.".J.': [1504, 1563], '2123-2127Crossref': [1509, 1568], '(27)': [1512, 1571], 'fix': [1516, 1578], 'was': [1517, 1579, 1643, 3222, 4030, 4086, 4108, 4123, 4148, 4236, 4242, 4306, 4392, 4556], 'initially': [1518], 'proposed': [1519, 1583], 'but': [1546, 2878, 3555, 3924], 'Bern': [1547], '(22Bern': [1550], 'pointed': [1574], 'out': [1575], 'biased.': [1581], 'They': [1582], 'alternative': [1585], 'solution': [1586], 'adding': [1588, 1710, 3033], 'second': [1594, 2391, 3590], 'stage': [1595], 'top': [1600, 1915, 2403, 2576, 2875, 2885, 2936, 2950], 'initially.': [1606], 'changes': [1609], 'source': [1616], 'code': [1617], 'level': [1618], 'may': [1620, 2443, 2513, 2871, 3647, 3834], 'cause': [1621], 'overestimation': [1623], '(which': [1624], 'smaller': [1627], 'problem': [1628], 'than': [1629, 3233, 4069], 'underestimation).': [1631], 'Another': [1632], 'drawback': [1633], 'standard': [1636, 2943], 'incapable': [1644], 'validating': [1646], 'if': [1651, 2448, 3759, 3889, 3913, 3927], 'information': [1654, 2313], '(23Matrix': [1662], 'Science': [1663, 1676], 'Ltd.': [1664], '(2010)': [1665], 'Mind': [1666], 'your': [1667], "P's": [1668], "Q's:": [1670], 'Maximising': [1671], 'percolator.': [1674], 'Matrix': [1675], 'ASMS': [1677], 'Workshop': [1678], 'User': [1680], 'Meeting': [1681], 'Salt': [1682], 'Lake': [1683], 'City,': [1684], 'May': [1685], '23,': [1686], '2010Google': [1687], 'we': [1692, 1720], 'show': [1693], 'slight': [1696], 'change': [1697, 3300], 'problems.': [1707], 'Instead': [1708], 'separate': [1715, 3530], 'entries': [1716, 3531], 'database,': [1719, 2317, 4100], 'concatenate': [1721], 'together': [1731, 2080, 3239, 3496, 3539], 'single': [1734], 'entry': [1735], 'database.': [1738, 1897, 2246, 2334, 2436, 3534, 3569], 'investigated,': [1746], 'presented.': [1756], 'aim': [1758], 'identify': [1764, 4479], 'data.': [1772], 'As': [1773, 4523], 'such,': [1774], 'belongs': [1777], 'category': [1782], 'employs': [1790], 'subroutine': [1796], 'exploits': [1798], 'speed': [1808], 'main': [1816], 'algorithmic': [1817], 'steps': [1818, 2061, 2090, 2248], 'proceed': [1824], 'follows:': [1826], '•De': [1827], 'sequencing:': [1829], 'algorithm': [1832, 2099, 2150, 2229, 3686], 'perform': [1873, 2103], 'each': [1878, 1963, 1989, 2108, 2134, 2156, 2193, 2374, 2529, 2581, 2910, 3027, 3452, 3541, 3559, 3593, 3597, 3815, 3840, 3846, 3874, 4281, 4380, 4395], 'input': [1879, 2109, 2502], 'spectrum.•Protein': [1880], 'shortlisting:': [1881, 1928], 'tags': [1886, 2235], 'find': [1890, 1984, 2505], 'approximate': [1891], 'matches': [1892, 2508, 4445], 'All': [1898, 1929, 2486], 'evaluated': [1906], 'according': [1907, 3739], 'tag': [1911, 2179, 2273, 3020], 'matches.': [1912, 3516], '7,000': [1914, 2402], 'ranked': [1916, 2363], 'form': [1918], 'future': [1926], 'analysis.•Peptide': [1927], 'spectra': [1943, 2503, 2543], 'rapid': [1946], 'Only': [1949], '512': [1951, 1969, 2577, 2884], 'highest': [1952, 2366, 2382, 2395, 3036, 3902], '(including': [1956], 'PTMs)': [1959, 2118], 'kept': [1961, 2889], 'spectrum.•Peptide': [1965], 'scoring:': [1966], 'From': [1967], 'calculated': [1971, 2849, 3504, 3604], 'shortlisting': [1975, 2306], 'step,': [1976, 2227, 2307, 2341], 'precise': [1978], 'similarity': [1992], 'between': [1993, 2268, 3360, 3508, 3608, 3672, 4037], 'important': [2004], 'component': [2005], 'addition,': [2011], 'normalized': [2015, 2919, 2978, 3242], 'ensure': [2017], 'compared': [2021, 2499, 2550], 'across': [2022, 2964, 4072], 'different': [2023, 2965, 3385, 3898, 3926, 4487, 4491], 'spectra.•Result': [2024], 'validation:': [2025], 'modified': [2027, 2319, 2343, 2516, 3419], 'determine': [2034], 'minimum': [2036], 'matching': [2039, 2266, 2546, 3015, 3345], 'threshold': [2041, 3747], 'meet': [2043], 'requirement': [2046], 'user.•Protein': [2049], 'inference': [2050, 3714, 3731], 'grouping:': [2052], 'through': [2058], 'infer': [2065], 'proteins.': [2067], 'Those': [2068], 'share': [2071], 'set': [2074, 3266, 4020, 4122], 'hits': [2077, 3613, 3619], 'grouped': [2079, 3738], 'convenient': [2084], 'report.': [2085], 'details': [2087, 2808], 'discussed': [2092], 'following': [2095, 2989, 3723, 4133], 'sections.': [2096], 'parameters': [2113], '(mass': [2114], 'error': [2115], 'tolerance': [2116], 'specified': [2119], 'user': [2122, 3849, 3868], 'also': [2127, 2151, 3121, 3772], 'sequencing.': [2132], 'For': [2133, 2528, 2705, 2764, 3319, 3596, 3845, 4090, 4215, 4379, 4394, 4475, 4495], 'first': [2138, 3587, 4384], 'reported': [2143, 4389, 4397], 'utilized.': [2147], 'computes': [2152], 'sequence;': [2163], 'value.': [2169], 'output': [2171, 3403], 'converted': [2175, 2643, 3310], 'replacing': [2181], 'acids': [2186, 2286, 3014, 4279, 4406, 4565], 'their': [2188, 3741], 'values.': [2190], 'More': [2191], 'specifically,': [2192], 'stretch': [2194], 'adjacent': [2196], 'residues': [2199], '<30%': [2201], 'replaced': [2204], '"mass': [2207], 'segment"': [2208], 'equal': [2211, 3785, 3962, 3980], 'total': [2214, 2262, 2669, 2692, 3373], 'residues.': [2218], 'See': [2219], 'Fig.': [2220, 2291, 3282, 4417], '1': [2221], 'example.': [2224], 'short': [2239, 2257], 'list': [2240, 2258], 'Future': [2247], 'process': [2251], 'work': [2254], 'computing': [2263], 'time.': [2264], 'quality': [2267, 4485], '(the': [2287, 4412], 'CAA': [2288, 2297, 2357, 2367, 2383, 2396, 3038, 4413, 4459], 'score).': [2289], '2,': [2292], 'computation': [2294], 'illustrated.': [2300], 'Note': [2301, 3378, 3831], 'there': [2309, 3833], 'no': [2311], 'residue': [2320, 2330, 2344, 2350, 2670, 2693], 'unmodified': [2329], 'later': [2338], 'calculation.': [2359, 4289], 'protein.': [2375, 3542, 3660, 3987, 4282], 'If': [2376, 3389, 3624, 3795], 'score,': [2384, 3245, 3322, 4460], 'tie': [2386], 'broken': [2388], 'third': [2394], 'scores.': [2397], 'Within': [2398], 'ranking,': [2400], 'selected': [2407], 'shortlist,': [2411], 'should': [2413], 'superset': [2416], 'identifiable': [2419], 'No': [2425], 'special': [2426, 3666], 'treatment': [2427], 'handling': [2431], 'homologous': [2432], 'need': [2444], 'biological': [2450], 'system': [2451], 'studied': [2452], 'larger': [2455], '(such': [2467], 'NCBInr)': [2469], 'without': [2470], 'specifying': [2471], 'taxonomy': [2473], 'information.': [2474], 'adjusted': [2478], 'configuration': [2481], 'file': [2482, 4085], 'DB.': [2485, 3735, 4008, 4356], 'digested': [2491], 'silico': [2493, 3699], 'against': [2500, 2955], '(PSMs).': [2509], 'Each': [2510], 'produce': [2514], 'multiple': [2515, 3895], 'enumerating': [2519], 'possible': [2521], 'combinations': [2522], 'user-specified': [2525, 3598], 'variable': [2526], 'PTMs.': [2527], '(modified': [2532], 'not),': [2534], 'calculated,': [2539, 2817], 'precursor': [2547, 3084], 'sequence.': [2553, 3595], '"quick': [2555], 'scorer"': [2556], 'compute': [2560, 4560], 'PSM.': [2565], 'priority': [2567, 2892], 'queue': [2568, 2893], 'structure': [2570], 'keep': [2574], 'quick': [2584, 2861], 'scorer': [2585], 'derived': [2587], 'Briefly,': [2639], 'functions': [2646], 'fN(m)': [2647, 2651, 2813, 2832, 2853], 'fC(m),': [2649], 'where': [2650, 2928], 'indicates': [2652, 2675], 'odds': [2654, 2677, 2697], 'correct': [2657, 2680, 2864], 'prefix': [2661, 2838], '(a': [2662, 2685], 'subsequence': [2663, 2686], 'containing': [2664, 2687, 3054], 'N': [2666], 'terminus)': [2667, 2690], 'm,': [2672], 'fC(m)': [2674, 2815, 2855], 'suffix': [2684, 2842], 'C': [2689], 'm.': [2695], 'estimated': [2699], 'corresponding': [2702, 3324, 3788], 'fragmentation': [2703], 'ions.': [2704], 'induced': [2708], '(CID)': [2710], 'a,': [2712, 2768], 'b,': [2713, 2769], 'c,': [2714, 2770], 'y,': [2715, 2772], 'z,': [2716, 2773], 'b-H2O,': [2717], 'y-H2O,': [2718], 'y-NH3': [2720], '1Ma': [2725], 'Scholar': [2761, 2806], 'details).': [2763], 'c-H,': [2771], 'z+H': [2775], 'ions': [2776], '24Liu': [2781], 'Shan': [2783], 'Xin': [2785], 'Ma': [2787], 'Better': [2789], 'spectra.BMC': [2798], 'Bioinformatics.': [2799], '4Crossref': [2802], '(23)': [2804], 'calculation).': [2811], 'After': [2812, 3570, 3814], 'ion': [2819, 2914, 2979, 3100, 3243], 'determined': [2826, 3288], 'sum': [2829, 3307], 'fC(m′)': [2834], 'masses': [2839, 2843], 'm': [2840], 'm′.': [2844], 'efficiently': [2850], 'indexing': [2852], 'memory.': [2857], 'With': [2858, 4357], 'scorer,': [2862], 'given': [2868, 3321, 3368, 3434], 'not': [2872, 3299, 3527, 3634, 3716, 3802], 'likely': [2881], 'among': [2882], 'sophisticated': [2899], 'rerank': [2905], 'First,': [2912, 3884], 'sion_match': [2917], 'formula': [2922], 's′ion_match': [2923], '=': [2924, 4293], '(sion_match': [2925], '−': [2926], 'μ)/σ,': [2927], 'μ': [2929], 'represents': [2930, 2941], 'mean': [2932], '10': [2937, 4147], 'candidates,': [2938], 'σ': [2940], 'deviation': [2944], 'scores': [2947, 2963, 3941, 4424, 4508], '150': [2951], 'candidates.': [2952], 'Such': [2953], 'normalization': [2954], 'incorrect': [2957], 'necessary': [2960], 'compare': [2962], 'features': [2971, 2983, 2991, 3116, 3119, 3206, 3232], 'score.': [2981, 3346], 'Several': [2982], 'evaluated.': [2986], 'nine': [2990, 3237], 'candidate': [2995], 'were': [2996, 3120, 3195, 3202, 3212, 4000, 4012, 4272, 4285, 4317, 4367, 4520], 'found': [2997, 3773], 'effective': [3001], 'now': [3004], 'included': [3005], 'DB:': [3008], '1)': [3009], '(CAA': [3021, 4566], 'score);': [3022], '2)': [3023], 'feature:': [3026], 'obtains': [3029], 'its': [3034, 3645, 3879], 'three': [3035], 'scores,': [3039], 'feature': [3043, 3218], 'maximum': [3049, 3093], 'peptide;': [3056, 3071, 3081], '3)': [3057], 'length;': [3060], '4)': [3061, 3209, 3221], 'average': [3063, 3074], 'length': [3065, 3076, 3094, 3557], 'per': [3066, 3077], 'missed': [3067], 'cleavage': [3068, 3637], '5)': [3072, 3211, 4569], 'PTM': [3078, 3922], '6)': [3082, 3199], 'error;': [3086], '7)': [3087], 'charge': [3089], 'state;': [3090], '8)': [3091, 3194], 'consecutively': [3097], 'matched': [3098, 4404], 'fragment': [3099], 'series;': [3101], '9)': [3103, 3201], 'termini': [3107], 'violating': [3108], "enzyme's": [3110], 'digesting': [3111], 'rule.': [3112], 'Some': [3113], 'similar': [3118, 3207, 3219], 'previously': [3122, 4031, 4149], 'Percolator': [3126, 3227], 'PeptideProphet': [3154, 3229], '(17Keller': [3155], 'programs.': [3188], 'particular,': [3190], '6),': [3191], '7),': [3192], 'Percolator;': [3198, 3215], 'PeptideProphet;': [3205], 'PeptideProphet.': [3225], 'Both': [3226, 3681, 4009], 'listed': [3234], 'here.': [3235, 4214], 'These': [3236], 'features,': [3238], 'combined': [3247], 'weighted': [3250, 3306], 'sum.': [3251], 'weights': [3253, 3286], 'trained': [3255], 'iterative': [3258], 'LC-MS/MS': [3263], 'training': [3264, 3291], 'maximize': [3268], 'left': [3273], '1%': [3276, 4503, 4581], 'curve,': [3278], 'shown': [3280], '3.': [3283], 'Once': [3284], 'particular': [3294], 'instrument': [3295], 'type,': [3296], 'they': [3297, 3536, 3583, 3914], 'do': [3298], 'experiment': [3302], 'experiment.': [3304], 'p': [3313, 3325, 3348, 3391, 3791], 'value': [3314, 3326, 3349, 3392, 3792], 'easier': [3316], 'human': [3317], 'interpretation.': [3318], 'probability': [3331], 'current': [3338, 3778], 'better': [3344], 'attempts': [3350], 'predict': [3352], 'positive': [3355, 3381], 'rate,': [3356], 'i.e.': [3357], 'ratio': [3359, 3507, 3607], 'T': [3370, 3783], 'identifications.': [3377], 'concept': [3386], 'FDR.': [3388, 4582], 'P,': [3394], 'final': [3396], '(called': [3399], 'score)': [3402, 4414], '−10lgP.': [3408], 'Here': [3409], 'lg(•)': [3410], 'logarithm': [3414], 'base': [3416], '10.': [3417], 'called': [3423, 3753], 'any': [3433], 'then': [3491, 3639, 3799], 'either': [3493], 'separately': [3494], 'software,': [3499], 'numbers': [3510], 'treated': [3528], 'Instead,': [3535], 'concatenated': [3538, 3594], 'Thus,': [3543], 'newly': [3545, 3567], 'generated': [3546, 3568, 4013], 'contains': [3548, 4115, 4257], 'entries,': [3554], 'doubled.': [3562], 'search,': [3572, 4550], 'separated': [3579], 'checking': [3581], 'whether': [3582], 'half': [3591], 'threshold,': [3600], 'C-terminal': [3626, 3655, 3704], 'enzyme': [3636], 'site,': [3638], 'appending': [3640], 'end': [3646], 'prevent': [3648], 'considering': [3653], 'problem,': [3664], 'letter': [3667, 3694], 'J': [3668, 3695], 'added': [3670, 3809], 'separator.': [3680], 'cleave': [3688], 'sides': [3691], 'digestion,': [3700], 'ensuring': [3701], 'considered.': [3711], 'Although': [3712], 'focus': [3718], 'brief': [3726], 'outline': [3727], 'Proteins': [3736], 'shared': [3742], 'peptides.': [3743], 'Given': [3744], 'T,': [3748], '(X)': [3751], 'dominate': [3755], 'another': [3756], '(Y)': [3758], 'Y': [3765, 3800], '≥T': [3770], 'version': [3779], '15,': [3787], '∼0.03.': [3794], 'X': [3796, 3812], 'dominates': [3797], 'Y,': [3798], 'confident': [3804], 'therefore': [3808], 'group.': [3813, 3844], 'pair': [3816], 'examined': [3820], 'domination': [3822], 'relations,': [3823], 'clustered': [3827], 'groups.': [3830], 'few': [3837], 'dominating': [3839, 3858, 3861, 3986], 'group,': [3847], 'choose': [3851], 'display': [3853], 'export': [3855], 'one': [3857, 3992], 'protein,': [3859], 'proteins,': [3862], 'interface.': [3869], 'computed': [3877], 'follows.': [3883], 'redundant': [3885], 'removed;': [3888], 'times': [3896], 'spectra,': [3899], 'retained.': [3906], 'considered': [3910, 3925], 'identical': [3916], 'differ': [3918], 'location,': [3923], 'PTMs': [3933], 'different.': [3935], 'Second,': [3936], 'nonredundant': [3939], 'sorted': [3946], 's1': [3948, 3950, 3964], '≥': [3949, 3951, 3953, 4568], '…': [3952, 3970], 'sk.': [3954], 'Finally,': [3955], '+': [3965, 3967, 3969, 3971], '(1/2)s2': [3966], '(1/3)s3': [3968], '(1/k)sk.': [3972], 'group': [3978], 'public': [3989], 'sets,': [3991], 'fragmented': [3993], 'CID': [3995, 4018, 4092, 4359, 4499], 'ETD,': [3999], 'sets': [4011], 'LTQ-Orbitrap': [4015], 'instruments.': [4016], 'came': [4021], 'trypsin': [4024], 'digest': [4025, 4128], 'Pseudomonas': [4027], 'aeruginosa': [4028, 4097, 4428, 4516, 4540], 'relation': [4036], 'mRNA': [4040, 4070], 'abundances': [4041, 4065, 4071], '(25Laurent': [4042], 'Vogel': [4044], 'Kwon': [4046], 'Craig': [4048], 'S.A.': [4049], 'Boutz': [4050], 'D.R.': [4051], 'Huse': [4052], 'H.K.': [4053], 'Nozue': [4054], 'Walia': [4056], 'H.': [4057], 'Whiteley': [4058], 'Ronald': [4060], 'P.C.': [4061], 'Marcotte': [4062], 'E.M.': [4063], 'Protein': [4064], 'conserved': [4068], 'diverse': [4073], 'taxa.Proteomics.': [4074], '4209-4212Crossref': [4077], '(101)': [4080], 'downloaded': [4087, 4101], 'http://www.marcottelab.org/MSdata/Data_12/DATA/20090115_SMPA14_2.RAW.gz.': [4089], 'set,': [4094, 4219, 4361, 4501], 'PAO1': [4098], 'PseudoCAP': [4103], '(http://www.pseudomonas.com)': [4104], 'April': [4106], '2011': [4107, 4153, 4234], '5566': [4116], 'entries.': [4118, 4260], 'obtained': [4124], 'Lys-C': [4127], 'yeast': [4131], 'lysate': [4132], 'strong': [4134], 'cation': [4135], 'exchange': [4136], 'fractionation': [4138], 'prior': [4139], 'LC-MS.': [4141], 'raw': [4143], 'fraction': [4146], 'Group': [4160], '(iPRG)': [4161], 'Association': [4164, 4228], 'Biomolecular': [4166, 4230], 'Resource': [4167, 4231], 'Facilities': [4168, 4232], 'provided': [4225], 'It': [4241, 4432], 'complete': [4244], 'proteome': [4245], 'Saccharomyces': [4247], 'cerevisiae': [4248], 'typical': [4250], 'laboratory': [4251], 'contaminant': [4252], 'appended.': [4254], '6666': [4258], 'experiments': [4265], 'involving': [4266], 'sequences,': [4268], 'produced': [4273], 'randomly': [4275], 'shuffling': [4276], 'Decoy': [4283], 'removed': [4286], 'before': [4287], 'That': [4290], 'is,': [4291], 'hits/number': [4297], 'hits.': [4300], 'When': [4301, 4537], 'FDR,': [4311], 'together.': [4319], 'section': [4321], 'demonstrates': [4322], 'relative': [4324, 4527], 'approaches': [4334], 'analyzing': [4336], 'set.': [4340], 'Their': [4341], 'complementary': [4342], 'abilities': [4343], 'justify': [4345], 'utilization': [4347], '5.3': [4363], '2.3': [4366], 'employed': [4368], 'analyses,': [4377], 'respectively.': [4378, 4522], 'selected.': [4393], '2.3,': [4400], 'calculated.': [4416], '4': [4418], 'shows': [4419], 'distribution': [4421], 'used.': [4431, 4494], 'seen': [4435], 'separation': [4439], 'clearly': [4461], 'indicating': [4462], 'effectiveness': [4464], 'scoring.': [4474], 'confidently': [4478], 'peptide,': [4481], 'sizes': [4492], 'example,': [4496], 'corresponds': [4505], '23.6': [4510], '55.1': [4512], 'Swissprot': [4518, 4542], 'employed,': [4521], 'result,': [4525], 'varies.': [4536], 'respectively,': [4551], 'able': [4557], 'correctly': [4559], 'five': [4561], '70': [4571], '88%': [4573], 'PSMs': [4576], 'basic': [4584], 'assumption': [4585]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2135078307', 'counts_by_year': [{'year': 2024, 'cited_by_count': 90}, {'year': 2023, 'cited_by_count': 84}, {'year': 2022, 'cited_by_count': 120}, {'year': 2021, 'cited_by_count': 91}, {'year': 2020, 'cited_by_count': 110}, {'year': 2019, 'cited_by_count': 111}, {'year': 2018, 'cited_by_count': 90}, {'year': 2017, 'cited_by_count': 66}, {'year': 2016, 'cited_by_count': 57}, {'year': 2015, 'cited_by_count': 58}, {'year': 2014, 'cited_by_count': 43}, {'year': 2013, 'cited_by_count': 26}, {'year': 2012, 'cited_by_count': 18}], 'updated_date': '2024-12-23T20:14:56.706404', 'created_date': '2016-06-24'}
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