DIA-NN 1.8.2 beta 17 (Data-Independent Acquisition by Neural Networks) Compiled on Apr 5 2023 14:56:11 Current date and time: Mon Oct 9 22:59:25 2023 CPU: GenuineIntel Intel(R) Xeon(R) W-3225 CPU @ 3.70GHz SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 Logical CPU cores: 16 diann.exe --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-33_1_1366.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-34_1_1367.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-35_1_1368.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-36_1_1369.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-37_1_1370.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-38_1_1371.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-39_1_1372.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-40_1_1373.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-42_1_1378.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-43_1_1379.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-44_1_1380.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-45_1_1381.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-46_1_1382.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-47_1_1388.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-48_1_1389.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-81_1_1390.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-82_1_1391.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-83_1_1392.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-84_1_1393.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-85_1_1394.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-86_1_1395.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-87_1_1396.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-88_1_1397.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-89_1_1398.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-90_1_1399.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-91_1_1400.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-92_1_1401.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-93_1_1402.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-94_1_1403.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-95_1_1404.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-96_1_1405.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-97_1_1406.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-98_1_1407.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-99_1_1408.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-100_1_1409.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-101_1_1410.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-102_1_1411.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-103_1_1412.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-104_1_1413.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-105_1_1414.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-106_1_1415.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-107_1_1416.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-108_1_1417.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-109_1_1418.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-110_1_1419.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-111_1_1420.d --f D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-112_1_1421.d --lib G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\appnote\libgen\library_TPM.tsv --threads 8 --verbose 1 --out G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\appnote\Searched_DDM\report.tsv --qvalue 0.01 --matrices --reannotate --fasta G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\LK\FASTA\swissprot_human_CanIso_02142022_synYeast.fasta --met-excision --cut K*,R*,!*P --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --window 6 --mass-acc 15 --mass-acc-ms1 10 --relaxed-prot-inf --smart-profiling --peak-center --no-ifs-removal --fixed-mod mTRAQ, 140.0949630177, nK --channels mTRAQ,0,nK,0:0; mTRAQ,4,nK,4.0070994:4.0070994;mTRAQ,8,nK,8.0141988132:8.0141988132 --peak-translation --original-mods --report-lib-info --peak-height --mass-acc-quant 5.0 --ms1-subtract 2 --ms1-base-profile --tr-ref-profile Thread number set to 8 Output will be filtered at 0.01 FDR Precursor/protein x samples expression level matrices will be saved along with the main report Library precursors will be reannotated using the FASTA database N-terminal methionine excision enabled In silico digest will involve cuts at K*,R* But excluding cuts at *P Maximum number of missed cleavages set to 1 Min peptide length set to 7 Max peptide length set to 30 Min precursor m/z set to 300 Max precursor m/z set to 1800 Min precursor charge set to 1 Max precursor charge set to 4 Scan window radius set to 6 Highly heuristic protein grouping will be used, to reduce the number of protein groups obtained; this mode is recommended for benchmarking protein ID numbers; use with caution for anything else When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones Fixed-width center of each elution peak will be used for quantification Interference removal from fragment elution curves disabled Modification mTRAQ with mass delta 140.095 at nK will be considered as fixed Translation of retention times between peptides within the same elution group enabled DIA-NN will not attempt to convert library modifications to the UniMod format Peak height will be used for quantification Ms1 deconvolution set to level 2 Peak extraction optimised for high-quality MS1 data Elution profile of the best channel will be used as the reference for other channels Mass accuracy will be fixed to 1.5e-05 (MS2) and 1e-05 (MS1) Registered mTRAQ channel 0 with following masses: n[0] K[0] Registered mTRAQ channel 4 with following masses: n[4.0071] K[4.0071] Registered mTRAQ channel 8 with following masses: n[8.0142] K[8.0142] Registered mTRAQ channel decoy with following masses: n[12.0213] K[12.0213] 47 files will be processed [0:00] Loading spectral library G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\appnote\libgen\library_TPM.tsv [0:22] Spectral library loaded: 15258 protein isoforms, 10394 protein groups and 118898 precursors in 51971 elution groups. [0:22] Loading FASTA G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\LK\FASTA\swissprot_human_CanIso_02142022_synYeast.fasta [1:09] Reannotating library precursors with information from the FASTA database [1:09] 118898 precursors generated [1:09] Gene names missing for some isoforms [1:09] Library contains 7219 proteins, and 7207 genes [1:10] Splitting library entries across channels [1:11] Assembling elution groups [1:11] Initialising library [1:12] Saving the library to G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\appnote\libgen\library_TPM.tsv.speclib [1:15] File #1/47 [1:15] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-33_1_1366.d [3:29] 473298 library precursors are potentially detectable [3:29] Processing... [4:25] RT window set to 0.469974 [4:25] Ion mobility window set to 0.0266599 [4:25] Recommended MS1 mass accuracy setting: 9.67247 ppm [5:13] Removing low confidence identifications [5:14] Removing interfering precursors [5:22] Training neural networks: 97047 targets, 102905 decoys [5:38] Number of IDs at 0.01 FDR: 31970 [5:39] Translating peaks within elution groups [5:45] Number of IDs at 0.01 FDR: 78007 [5:49] Precursors at 1% channel FDR: 30814 out of 78007 [5:49] Calculating protein q-values [5:49] Number of genes identified at 1% FDR: 3151 (precursor-level), 2863 (protein-level) (inference performed using proteotypic peptides only) [5:49] Quantification [5:50] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-33_1_1366.d.quant. [5:53] File #2/47 [5:53] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-34_1_1367.d [8:11] 473298 library precursors are potentially detectable [8:11] Processing... [9:20] RT window set to 0.461492 [9:20] Ion mobility window set to 0.0250347 [9:20] Recommended MS1 mass accuracy setting: 9.28215 ppm [10:08] Removing low confidence identifications [10:09] Removing interfering precursors [10:17] Training neural networks: 97118 targets, 103028 decoys [10:34] Number of IDs at 0.01 FDR: 28176 [10:34] Translating peaks within elution groups [10:40] Number of IDs at 0.01 FDR: 82094 [10:44] Precursors at 1% channel FDR: 26308 out of 82094 [10:44] Calculating protein q-values [10:44] Number of genes identified at 1% FDR: 3296 (precursor-level), 2781 (protein-level) (inference performed using proteotypic peptides only) [10:45] Quantification [10:46] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-34_1_1367.d.quant. [10:49] File #3/47 [10:49] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-35_1_1368.d [13:12] 473298 library precursors are potentially detectable [13:12] Processing... [13:58] RT window set to 0.45975 [13:58] Ion mobility window set to 0.0269884 [13:58] Recommended MS1 mass accuracy setting: 9.47702 ppm [14:50] Removing low confidence identifications [14:50] Removing interfering precursors [15:00] Training neural networks: 99220 targets, 106375 decoys [15:17] Number of IDs at 0.01 FDR: 44951 [15:18] Translating peaks within elution groups [15:24] Number of IDs at 0.01 FDR: 106648 [15:30] Precursors at 1% channel FDR: 41882 out of 106648 [15:30] Calculating protein q-values [15:30] Number of genes identified at 1% FDR: 3732 (precursor-level), 3748 (protein-level) (inference performed using proteotypic peptides only) [15:30] Quantification [15:32] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-35_1_1368.d.quant. [15:35] File #4/47 [15:35] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-36_1_1369.d [17:49] 473298 library precursors are potentially detectable [17:49] Processing... [18:45] RT window set to 0.464866 [18:45] Ion mobility window set to 0.025609 [18:45] Recommended MS1 mass accuracy setting: 9.75134 ppm [19:35] Removing low confidence identifications [19:35] Removing interfering precursors [19:44] Training neural networks: 97887 targets, 104116 decoys [20:01] Number of IDs at 0.01 FDR: 35951 [20:02] Translating peaks within elution groups [20:08] Number of IDs at 0.01 FDR: 88634 [20:12] Precursors at 1% channel FDR: 33732 out of 88634 [20:12] Calculating protein q-values [20:12] Number of genes identified at 1% FDR: 3388 (precursor-level), 3276 (protein-level) (inference performed using proteotypic peptides only) [20:12] Quantification [20:14] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-36_1_1369.d.quant. [20:17] File #5/47 [20:17] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-37_1_1370.d [22:25] 473298 library precursors are potentially detectable [22:25] Processing... [23:32] RT window set to 0.461324 [23:32] Ion mobility window set to 0.0260967 [23:32] Recommended MS1 mass accuracy setting: 10.0677 ppm [24:18] Removing low confidence identifications [24:18] Removing interfering precursors [24:25] Training neural networks: 96137 targets, 101689 decoys [24:41] Number of IDs at 0.01 FDR: 28266 [24:42] Translating peaks within elution groups [24:47] Number of IDs at 0.01 FDR: 70679 [24:51] Precursors at 1% channel FDR: 27761 out of 70679 [24:51] Calculating protein q-values [24:51] Number of genes identified at 1% FDR: 2947 (precursor-level), 2393 (protein-level) (inference performed using proteotypic peptides only) [24:51] Quantification [24:52] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-37_1_1370.d.quant. [24:55] File #6/47 [24:55] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-38_1_1371.d [27:13] 473298 library precursors are potentially detectable [27:13] Processing... [28:01] RT window set to 0.459302 [28:01] Ion mobility window set to 0.0264641 [28:01] Recommended MS1 mass accuracy setting: 10.0171 ppm [28:51] Removing low confidence identifications [28:51] Removing interfering precursors [29:00] Training neural networks: 97316 targets, 103830 decoys [29:16] Number of IDs at 0.01 FDR: 36556 [29:18] Translating peaks within elution groups [29:23] Number of IDs at 0.01 FDR: 87817 [29:28] Precursors at 1% channel FDR: 35494 out of 87817 [29:28] Calculating protein q-values [29:28] Number of genes identified at 1% FDR: 3285 (precursor-level), 2750 (protein-level) (inference performed using proteotypic peptides only) [29:28] Quantification [29:30] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-38_1_1371.d.quant. [29:33] File #7/47 [29:33] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-39_1_1372.d [31:52] 473298 library precursors are potentially detectable [31:52] Processing... [32:47] RT window set to 0.460295 [32:47] Ion mobility window set to 0.0249896 [32:47] Recommended MS1 mass accuracy setting: 9.76538 ppm [33:33] Removing low confidence identifications [33:33] Removing interfering precursors [33:41] Training neural networks: 96570 targets, 101785 decoys [33:57] Number of IDs at 0.01 FDR: 31281 [33:58] Translating peaks within elution groups [34:03] Number of IDs at 0.01 FDR: 78588 [34:07] Precursors at 1% channel FDR: 30164 out of 78588 [34:07] Calculating protein q-values [34:07] Number of genes identified at 1% FDR: 3132 (precursor-level), 2843 (protein-level) (inference performed using proteotypic peptides only) [34:07] Quantification [34:09] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-39_1_1372.d.quant. [34:12] File #8/47 [34:12] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-40_1_1373.d [36:34] 473298 library precursors are potentially detectable [36:34] Processing... [37:43] RT window set to 0.442107 [37:43] Ion mobility window set to 0.026166 [37:43] Recommended MS1 mass accuracy setting: 9.62238 ppm [38:33] Removing low confidence identifications [38:33] Removing interfering precursors [38:41] Training neural networks: 97123 targets, 103378 decoys [38:58] Number of IDs at 0.01 FDR: 27641 [38:58] Translating peaks within elution groups [39:04] Number of IDs at 0.01 FDR: 71879 [39:07] Precursors at 1% channel FDR: 26631 out of 71879 [39:08] Calculating protein q-values [39:08] Number of genes identified at 1% FDR: 2916 (precursor-level), 2765 (protein-level) (inference performed using proteotypic peptides only) [39:08] Quantification [39:09] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-40_1_1373.d.quant. [39:12] File #9/47 [39:12] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-42_1_1378.d [43:13] 474700 library precursors are potentially detectable [43:13] Processing... [51:34] RT window set to 0.499807 [51:34] Ion mobility window set to 0.0214595 [51:34] Recommended MS1 mass accuracy setting: 7.31852 ppm [54:59] Removing low confidence identifications [54:59] Removing interfering precursors [55:01] Training neural networks: 25302 targets, 16571 decoys [55:04] Number of IDs at 0.01 FDR: 16546 [55:05] Translating peaks within elution groups [55:09] Number of IDs at 0.01 FDR: 45143 [55:11] Precursors at 1% channel FDR: 19390 out of 45143 [55:11] Calculating protein q-values [55:11] Number of genes identified at 1% FDR: 2346 (precursor-level), 2312 (protein-level) (inference performed using proteotypic peptides only) [55:11] Quantification [55:12] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-42_1_1378.d.quant. [55:19] File #10/47 [55:19] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-43_1_1379.d [59:18] 474700 library precursors are potentially detectable [59:18] Processing... [68:46] RT window set to 0.470207 [68:46] Ion mobility window set to 0.0204713 [68:46] Recommended MS1 mass accuracy setting: 7.9493 ppm [71:55] Removing low confidence identifications [71:55] Removing interfering precursors [71:57] Training neural networks: 23742 targets, 15444 decoys [72:00] Number of IDs at 0.01 FDR: 14545 [72:01] Translating peaks within elution groups [72:04] Number of IDs at 0.01 FDR: 41801 [72:06] Precursors at 1% channel FDR: 15898 out of 41801 [72:06] Calculating protein q-values [72:06] Number of genes identified at 1% FDR: 2282 (precursor-level), 2188 (protein-level) (inference performed using proteotypic peptides only) [72:06] Quantification [72:08] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-43_1_1379.d.quant. [72:15] File #11/47 [72:15] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-44_1_1380.d [76:10] 474700 library precursors are potentially detectable [76:10] Processing... [87:37] RT window set to 0.498253 [87:37] Ion mobility window set to 0.0230859 [87:37] Recommended MS1 mass accuracy setting: 7.3571 ppm [91:09] Removing low confidence identifications [91:09] Removing interfering precursors [91:10] Training neural networks: 22588 targets, 14514 decoys [91:14] Number of IDs at 0.01 FDR: 13219 [91:14] Translating peaks within elution groups [91:17] Number of IDs at 0.01 FDR: 39745 [91:20] Precursors at 1% channel FDR: 13768 out of 39745 [91:20] Calculating protein q-values [91:20] Number of genes identified at 1% FDR: 2188 (precursor-level), 2076 (protein-level) (inference performed using proteotypic peptides only) [91:20] Quantification [91:21] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-44_1_1380.d.quant. [91:28] File #12/47 [91:28] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-45_1_1381.d [95:25] 474700 library precursors are potentially detectable [95:25] Processing... [102:13] RT window set to 0.501903 [102:13] Ion mobility window set to 0.0218235 [102:13] Recommended MS1 mass accuracy setting: 7.66973 ppm [105:36] Removing low confidence identifications [105:36] Removing interfering precursors [105:38] Training neural networks: 20131 targets, 12184 decoys [105:41] Number of IDs at 0.01 FDR: 16449 [105:41] Translating peaks within elution groups [105:44] Number of IDs at 0.01 FDR: 43678 [105:47] Precursors at 1% channel FDR: 19339 out of 43678 [105:47] Calculating protein q-values [105:47] Number of genes identified at 1% FDR: 2326 (precursor-level), 2316 (protein-level) (inference performed using proteotypic peptides only) [105:47] Quantification [105:48] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-45_1_1381.d.quant. [105:55] File #13/47 [105:55] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-46_1_1382.d [109:43] 474700 library precursors are potentially detectable [109:43] Processing... [119:22] RT window set to 0.501075 [119:22] Ion mobility window set to 0.0213039 [119:22] Recommended MS1 mass accuracy setting: 7.74419 ppm [122:45] Removing low confidence identifications [122:45] Removing interfering precursors [122:46] Training neural networks: 23710 targets, 15581 decoys [122:50] Number of IDs at 0.01 FDR: 14385 [122:50] Translating peaks within elution groups [122:54] Number of IDs at 0.01 FDR: 39603 [122:56] Precursors at 1% channel FDR: 16204 out of 39603 [122:56] Calculating protein q-values [122:56] Number of genes identified at 1% FDR: 2142 (precursor-level), 2116 (protein-level) (inference performed using proteotypic peptides only) [122:56] Quantification [122:57] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-46_1_1382.d.quant. [123:04] File #14/47 [123:04] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-47_1_1388.d [125:20] 473298 library precursors are potentially detectable [125:20] Processing... [126:06] RT window set to 0.466303 [126:06] Ion mobility window set to 0.024156 [126:06] Recommended MS1 mass accuracy setting: 9.13011 ppm [126:56] Removing low confidence identifications [126:56] Removing interfering precursors [127:05] Training neural networks: 97254 targets, 104248 decoys [127:21] Number of IDs at 0.01 FDR: 39155 [127:22] Translating peaks within elution groups [127:28] Number of IDs at 0.01 FDR: 91709 [127:33] Precursors at 1% channel FDR: 39189 out of 91709 [127:33] Calculating protein q-values [127:33] Number of genes identified at 1% FDR: 3459 (precursor-level), 3393 (protein-level) (inference performed using proteotypic peptides only) [127:33] Quantification [127:35] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-47_1_1388.d.quant. [127:39] File #15/47 [127:39] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-48_1_1389.d [129:49] 473298 library precursors are potentially detectable [129:49] Processing... [130:36] RT window set to 0.462264 [130:36] Ion mobility window set to 0.0266855 [130:36] Recommended MS1 mass accuracy setting: 10.4118 ppm [131:25] Removing low confidence identifications [131:25] Removing interfering precursors [131:34] Training neural networks: 96783 targets, 103600 decoys [131:51] Number of IDs at 0.01 FDR: 35385 [131:52] Translating peaks within elution groups [131:57] Number of IDs at 0.01 FDR: 85836 [132:02] Precursors at 1% channel FDR: 32923 out of 85836 [132:02] Calculating protein q-values [132:02] Number of genes identified at 1% FDR: 3285 (precursor-level), 2672 (protein-level) (inference performed using proteotypic peptides only) [132:02] Quantification [132:03] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-48_1_1389.d.quant. [132:07] File #16/47 [132:07] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-81_1_1390.d [134:23] 473298 library precursors are potentially detectable [134:23] Processing... [135:11] RT window set to 0.468097 [135:11] Ion mobility window set to 0.0239454 [135:11] Recommended MS1 mass accuracy setting: 9.94961 ppm [136:01] Removing low confidence identifications [136:02] Removing interfering precursors [136:11] Training neural networks: 97147 targets, 103982 decoys [136:28] Number of IDs at 0.01 FDR: 37657 [136:29] Translating peaks within elution groups [136:35] Number of IDs at 0.01 FDR: 93901 [136:40] Precursors at 1% channel FDR: 36232 out of 93901 [136:40] Calculating protein q-values [136:40] Number of genes identified at 1% FDR: 3508 (precursor-level), 2960 (protein-level) (inference performed using proteotypic peptides only) [136:40] Quantification [136:41] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-81_1_1390.d.quant. [136:45] File #17/47 [136:45] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-82_1_1391.d [139:03] 473298 library precursors are potentially detectable [139:03] Processing... [139:59] RT window set to 0.450432 [139:59] Ion mobility window set to 0.0239883 [139:59] Recommended MS1 mass accuracy setting: 10.5975 ppm [140:49] Removing low confidence identifications [140:49] Removing interfering precursors [140:58] Training neural networks: 96701 targets, 103177 decoys [141:15] Number of IDs at 0.01 FDR: 33247 [141:16] Translating peaks within elution groups [141:22] Number of IDs at 0.01 FDR: 80020 [141:26] Precursors at 1% channel FDR: 32145 out of 80020 [141:26] Calculating protein q-values [141:26] Number of genes identified at 1% FDR: 3124 (precursor-level), 2870 (protein-level) (inference performed using proteotypic peptides only) [141:26] Quantification [141:27] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-82_1_1391.d.quant. [141:31] File #18/47 [141:31] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-83_1_1392.d [143:45] 473298 library precursors are potentially detectable [143:45] Processing... [144:31] RT window set to 0.452977 [144:31] Ion mobility window set to 0.0245002 [144:31] Recommended MS1 mass accuracy setting: 9.15893 ppm [145:20] Removing low confidence identifications [145:20] Removing interfering precursors [145:28] Training neural networks: 97150 targets, 103295 decoys [145:44] Number of IDs at 0.01 FDR: 36365 [145:45] Translating peaks within elution groups [145:51] Number of IDs at 0.01 FDR: 90361 [145:56] Precursors at 1% channel FDR: 33813 out of 90361 [145:56] Calculating protein q-values [145:56] Number of genes identified at 1% FDR: 3394 (precursor-level), 2848 (protein-level) (inference performed using proteotypic peptides only) [145:56] Quantification [145:58] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-83_1_1392.d.quant. [146:02] File #19/47 [146:02] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-84_1_1393.d [148:13] 473298 library precursors are potentially detectable [148:13] Processing... [149:34] RT window set to 0.464449 [149:34] Ion mobility window set to 0.0253716 [149:35] Recommended MS1 mass accuracy setting: 9.08415 ppm [150:22] Removing low confidence identifications [150:22] Removing interfering precursors [150:29] Training neural networks: 95390 targets, 100965 decoys [150:46] Number of IDs at 0.01 FDR: 23289 [150:46] Translating peaks within elution groups [150:52] Number of IDs at 0.01 FDR: 70263 [150:55] Precursors at 1% channel FDR: 21854 out of 70263 [150:56] Calculating protein q-values [150:56] Number of genes identified at 1% FDR: 2943 (precursor-level), 2742 (protein-level) (inference performed using proteotypic peptides only) [150:56] Quantification [150:57] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-84_1_1393.d.quant. [151:01] File #20/47 [151:01] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-85_1_1394.d [153:11] 473298 library precursors are potentially detectable [153:11] Processing... [153:58] RT window set to 0.455811 [153:58] Ion mobility window set to 0.0243802 [153:58] Recommended MS1 mass accuracy setting: 9.52911 ppm [154:47] Removing low confidence identifications [154:47] Removing interfering precursors [154:56] Training neural networks: 96286 targets, 103062 decoys [155:12] Number of IDs at 0.01 FDR: 38617 [155:13] Translating peaks within elution groups [155:19] Number of IDs at 0.01 FDR: 92100 [155:24] Precursors at 1% channel FDR: 37125 out of 92100 [155:24] Calculating protein q-values [155:24] Number of genes identified at 1% FDR: 3473 (precursor-level), 3281 (protein-level) (inference performed using proteotypic peptides only) [155:24] Quantification [155:25] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-85_1_1394.d.quant. [155:29] File #21/47 [155:29] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-86_1_1395.d [157:40] 473298 library precursors are potentially detectable [157:41] Processing... [159:04] RT window set to 0.464546 [159:04] Ion mobility window set to 0.027385 [159:04] Recommended MS1 mass accuracy setting: 10.5953 ppm [159:54] Removing low confidence identifications [159:54] Removing interfering precursors [160:02] Training neural networks: 95201 targets, 101742 decoys [160:18] Number of IDs at 0.01 FDR: 26216 [160:19] Translating peaks within elution groups [160:24] Number of IDs at 0.01 FDR: 66645 [160:28] Precursors at 1% channel FDR: 25328 out of 66645 [160:28] Calculating protein q-values [160:28] Number of genes identified at 1% FDR: 2822 (precursor-level), 2241 (protein-level) (inference performed using proteotypic peptides only) [160:28] Quantification [160:29] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-86_1_1395.d.quant. [160:33] File #22/47 [160:33] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-87_1_1396.d [162:44] 473298 library precursors are potentially detectable [162:45] Processing... [163:41] RT window set to 0.4774 [163:41] Ion mobility window set to 0.0243827 [163:41] Recommended MS1 mass accuracy setting: 9.53307 ppm [164:31] Removing low confidence identifications [164:31] Removing interfering precursors [164:40] Training neural networks: 95151 targets, 101956 decoys [164:56] Number of IDs at 0.01 FDR: 33739 [164:57] Translating peaks within elution groups [165:03] Number of IDs at 0.01 FDR: 81222 [165:07] Precursors at 1% channel FDR: 32532 out of 81222 [165:07] Calculating protein q-values [165:07] Number of genes identified at 1% FDR: 3229 (precursor-level), 2624 (protein-level) (inference performed using proteotypic peptides only) [165:07] Quantification [165:09] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-87_1_1396.d.quant. [165:12] File #23/47 [165:12] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-88_1_1397.d [167:25] 473298 library precursors are potentially detectable [167:25] Processing... [168:22] RT window set to 0.454463 [168:22] Ion mobility window set to 0.0272251 [168:22] Recommended MS1 mass accuracy setting: 9.9428 ppm [169:11] Removing low confidence identifications [169:11] Removing interfering precursors [169:19] Training neural networks: 95561 targets, 102290 decoys [169:36] Number of IDs at 0.01 FDR: 32810 [169:37] Translating peaks within elution groups [169:42] Number of IDs at 0.01 FDR: 77723 [169:47] Precursors at 1% channel FDR: 31641 out of 77723 [169:47] Calculating protein q-values [169:47] Number of genes identified at 1% FDR: 3080 (precursor-level), 3027 (protein-level) (inference performed using proteotypic peptides only) [169:47] Quantification [169:48] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-88_1_1397.d.quant. [169:52] File #24/47 [169:52] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-89_1_1398.d [172:04] 473298 library precursors are potentially detectable [172:04] Processing... [173:14] RT window set to 0.475977 [173:14] Ion mobility window set to 0.0257716 [173:14] Recommended MS1 mass accuracy setting: 9.47711 ppm [174:05] Removing low confidence identifications [174:05] Removing interfering precursors [174:13] Training neural networks: 94886 targets, 100893 decoys [174:30] Number of IDs at 0.01 FDR: 25385 [174:30] Translating peaks within elution groups [174:35] Number of IDs at 0.01 FDR: 69844 [174:39] Precursors at 1% channel FDR: 23034 out of 69844 [174:39] Calculating protein q-values [174:39] Number of genes identified at 1% FDR: 2911 (precursor-level), 2404 (protein-level) (inference performed using proteotypic peptides only) [174:39] Quantification [174:40] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-89_1_1398.d.quant. [174:44] File #25/47 [174:44] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-90_1_1399.d [176:55] 473298 library precursors are potentially detectable [176:55] Processing... [177:51] RT window set to 0.449405 [177:51] Ion mobility window set to 0.025577 [177:51] Recommended MS1 mass accuracy setting: 10.3286 ppm [178:38] Removing low confidence identifications [178:39] Removing interfering precursors [178:46] Training neural networks: 95919 targets, 102214 decoys [179:03] Number of IDs at 0.01 FDR: 34706 [179:04] Translating peaks within elution groups [179:09] Number of IDs at 0.01 FDR: 85433 [179:14] Precursors at 1% channel FDR: 33828 out of 85433 [179:14] Calculating protein q-values [179:14] Number of genes identified at 1% FDR: 3288 (precursor-level), 3083 (protein-level) (inference performed using proteotypic peptides only) [179:14] Quantification [179:15] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-90_1_1399.d.quant. [179:19] File #26/47 [179:19] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-91_1_1400.d [181:32] 473298 library precursors are potentially detectable [181:32] Processing... [182:17] RT window set to 0.455139 [182:17] Ion mobility window set to 0.0252536 [182:17] Recommended MS1 mass accuracy setting: 9.66808 ppm [183:08] Removing low confidence identifications [183:08] Removing interfering precursors [183:18] Training neural networks: 98269 targets, 105379 decoys [183:34] Number of IDs at 0.01 FDR: 39907 [183:36] Translating peaks within elution groups [183:42] Number of IDs at 0.01 FDR: 100247 [183:47] Precursors at 1% channel FDR: 36417 out of 100247 [183:47] Calculating protein q-values [183:47] Number of genes identified at 1% FDR: 3620 (precursor-level), 3361 (protein-level) (inference performed using proteotypic peptides only) [183:47] Quantification [183:49] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-91_1_1400.d.quant. [183:53] File #27/47 [183:53] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-92_1_1401.d [186:02] 473298 library precursors are potentially detectable [186:02] Processing... [187:00] RT window set to 0.46809 [187:00] Ion mobility window set to 0.0254346 [187:00] Recommended MS1 mass accuracy setting: 9.77066 ppm [187:49] Removing low confidence identifications [187:49] Removing interfering precursors [187:58] Training neural networks: 94700 targets, 101588 decoys [188:14] Number of IDs at 0.01 FDR: 32638 [188:15] Translating peaks within elution groups [188:21] Number of IDs at 0.01 FDR: 80762 [188:25] Precursors at 1% channel FDR: 30370 out of 80762 [188:25] Calculating protein q-values [188:25] Number of genes identified at 1% FDR: 3214 (precursor-level), 2892 (protein-level) (inference performed using proteotypic peptides only) [188:25] Quantification [188:26] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-92_1_1401.d.quant. [188:30] File #28/47 [188:30] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-93_1_1402.d [190:40] 473298 library precursors are potentially detectable [190:40] Processing... [191:35] RT window set to 0.450703 [191:35] Ion mobility window set to 0.0264225 [191:35] Recommended MS1 mass accuracy setting: 10.4504 ppm [192:24] Removing low confidence identifications [192:24] Removing interfering precursors [192:33] Training neural networks: 94451 targets, 101188 decoys [192:49] Number of IDs at 0.01 FDR: 31006 [192:50] Translating peaks within elution groups [192:55] Number of IDs at 0.01 FDR: 74102 [192:59] Precursors at 1% channel FDR: 31062 out of 74102 [192:59] Calculating protein q-values [192:59] Number of genes identified at 1% FDR: 2984 (precursor-level), 2390 (protein-level) (inference performed using proteotypic peptides only) [192:59] Quantification [193:00] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-93_1_1402.d.quant. [193:04] File #29/47 [193:04] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-94_1_1403.d [195:13] 473298 library precursors are potentially detectable [195:13] Processing... [196:21] RT window set to 0.462582 [196:21] Ion mobility window set to 0.0258609 [196:21] Recommended MS1 mass accuracy setting: 9.85868 ppm [197:09] Removing low confidence identifications [197:09] Removing interfering precursors [197:17] Training neural networks: 94302 targets, 100802 decoys [197:34] Number of IDs at 0.01 FDR: 30439 [197:34] Translating peaks within elution groups [197:40] Number of IDs at 0.01 FDR: 74262 [197:44] Precursors at 1% channel FDR: 28253 out of 74262 [197:44] Calculating protein q-values [197:44] Number of genes identified at 1% FDR: 3052 (precursor-level), 2478 (protein-level) (inference performed using proteotypic peptides only) [197:44] Quantification [197:45] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-94_1_1403.d.quant. [197:49] File #30/47 [197:49] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-95_1_1404.d [199:55] 473298 library precursors are potentially detectable [199:55] Processing... [200:41] RT window set to 0.468453 [200:41] Ion mobility window set to 0.0246268 [200:41] Recommended MS1 mass accuracy setting: 9.41574 ppm [201:32] Removing low confidence identifications [201:32] Removing interfering precursors [201:41] Training neural networks: 95719 targets, 103226 decoys [201:58] Number of IDs at 0.01 FDR: 40984 [201:59] Translating peaks within elution groups [202:05] Number of IDs at 0.01 FDR: 95368 [202:10] Precursors at 1% channel FDR: 40282 out of 95368 [202:10] Calculating protein q-values [202:10] Number of genes identified at 1% FDR: 3516 (precursor-level), 3437 (protein-level) (inference performed using proteotypic peptides only) [202:10] Quantification [202:11] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-95_1_1404.d.quant. [202:15] File #31/47 [202:15] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-96_1_1405.d [204:23] 473298 library precursors are potentially detectable [204:23] Processing... [205:14] RT window set to 0.464583 [205:14] Ion mobility window set to 0.0258071 [205:14] Recommended MS1 mass accuracy setting: 9.88484 ppm [206:03] Removing low confidence identifications [206:03] Removing interfering precursors [206:12] Training neural networks: 95415 targets, 101976 decoys [206:29] Number of IDs at 0.01 FDR: 33265 [206:30] Translating peaks within elution groups [206:36] Number of IDs at 0.01 FDR: 88019 [206:40] Precursors at 1% channel FDR: 29633 out of 88019 [206:40] Calculating protein q-values [206:40] Number of genes identified at 1% FDR: 3319 (precursor-level), 3164 (protein-level) (inference performed using proteotypic peptides only) [206:40] Quantification [206:42] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-96_1_1405.d.quant. [206:45] File #32/47 [206:45] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-97_1_1406.d [208:52] 473298 library precursors are potentially detectable [208:52] Processing... [210:56] RT window set to 0.449086 [210:56] Ion mobility window set to 0.0283888 [210:57] Recommended MS1 mass accuracy setting: 9.13222 ppm [211:49] Removing low confidence identifications [211:49] Removing interfering precursors [211:55] Training neural networks: 95295 targets, 101603 decoys [212:12] Number of IDs at 0.01 FDR: 18853 [212:12] Translating peaks within elution groups [212:17] Number of IDs at 0.01 FDR: 55509 [212:20] Precursors at 1% channel FDR: 17068 out of 55509 [212:20] Calculating protein q-values [212:20] Number of genes identified at 1% FDR: 2490 (precursor-level), 2029 (protein-level) (inference performed using proteotypic peptides only) [212:20] Quantification [212:21] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-97_1_1406.d.quant. [212:25] File #33/47 [212:25] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-98_1_1407.d [214:35] 473298 library precursors are potentially detectable [214:35] Processing... [215:23] RT window set to 0.4671 [215:23] Ion mobility window set to 0.0250376 [215:23] Recommended MS1 mass accuracy setting: 10.1241 ppm [216:15] Removing low confidence identifications [216:15] Removing interfering precursors [216:24] Training neural networks: 95938 targets, 103223 decoys [216:40] Number of IDs at 0.01 FDR: 37140 [216:41] Translating peaks within elution groups [216:47] Number of IDs at 0.01 FDR: 91016 [216:52] Precursors at 1% channel FDR: 35752 out of 91016 [216:52] Calculating protein q-values [216:52] Number of genes identified at 1% FDR: 3453 (precursor-level), 3138 (protein-level) (inference performed using proteotypic peptides only) [216:52] Quantification [216:54] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-98_1_1407.d.quant. [216:58] File #34/47 [216:58] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-99_1_1408.d [219:08] 473298 library precursors are potentially detectable [219:08] Processing... [220:07] RT window set to 0.454193 [220:07] Ion mobility window set to 0.0271279 [220:07] Recommended MS1 mass accuracy setting: 9.47833 ppm [220:56] Removing low confidence identifications [220:56] Removing interfering precursors [221:03] Training neural networks: 96653 targets, 103148 decoys [221:20] Number of IDs at 0.01 FDR: 32283 [221:21] Translating peaks within elution groups [221:27] Number of IDs at 0.01 FDR: 84698 [221:31] Precursors at 1% channel FDR: 30266 out of 84698 [221:31] Calculating protein q-values [221:31] Number of genes identified at 1% FDR: 3268 (precursor-level), 3056 (protein-level) (inference performed using proteotypic peptides only) [221:31] Quantification [221:33] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-99_1_1408.d.quant. [221:37] File #35/47 [221:37] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-100_1_1409.d [223:45] 473298 library precursors are potentially detectable [223:45] Processing... [224:41] RT window set to 0.469971 [224:41] Ion mobility window set to 0.0257481 [224:41] Recommended MS1 mass accuracy setting: 8.85612 ppm [225:32] Removing low confidence identifications [225:32] Removing interfering precursors [225:41] Training neural networks: 95875 targets, 103115 decoys [225:57] Number of IDs at 0.01 FDR: 34500 [225:59] Translating peaks within elution groups [226:04] Number of IDs at 0.01 FDR: 84984 [226:09] Precursors at 1% channel FDR: 33533 out of 84984 [226:09] Calculating protein q-values [226:09] Number of genes identified at 1% FDR: 3264 (precursor-level), 3179 (protein-level) (inference performed using proteotypic peptides only) [226:09] Quantification [226:10] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-100_1_1409.d.quant. [226:14] File #36/47 [226:14] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-101_1_1410.d [228:22] 473298 library precursors are potentially detectable [228:22] Processing... [229:20] RT window set to 0.465351 [229:20] Ion mobility window set to 0.0261071 [229:21] Recommended MS1 mass accuracy setting: 9.52218 ppm [230:11] Removing low confidence identifications [230:11] Removing interfering precursors [230:20] Training neural networks: 95778 targets, 102817 decoys [230:36] Number of IDs at 0.01 FDR: 32618 [230:37] Translating peaks within elution groups [230:43] Number of IDs at 0.01 FDR: 80308 [230:47] Precursors at 1% channel FDR: 31237 out of 80308 [230:47] Calculating protein q-values [230:47] Number of genes identified at 1% FDR: 3188 (precursor-level), 3056 (protein-level) (inference performed using proteotypic peptides only) [230:47] Quantification [230:49] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-101_1_1410.d.quant. [230:53] File #37/47 [230:53] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-102_1_1411.d [232:53] 473298 library precursors are potentially detectable [232:53] Processing... [234:02] RT window set to 0.46608 [234:02] Ion mobility window set to 0.0248081 [234:02] Recommended MS1 mass accuracy setting: 9.77632 ppm [234:50] Removing low confidence identifications [234:51] Removing interfering precursors [234:59] Training neural networks: 94144 targets, 100696 decoys [235:15] Number of IDs at 0.01 FDR: 28778 [235:15] Translating peaks within elution groups [235:21] Number of IDs at 0.01 FDR: 70418 [235:24] Precursors at 1% channel FDR: 27747 out of 70418 [235:24] Calculating protein q-values [235:24] Number of genes identified at 1% FDR: 2953 (precursor-level), 2679 (protein-level) (inference performed using proteotypic peptides only) [235:25] Quantification [235:26] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-102_1_1411.d.quant. [235:29] File #38/47 [235:29] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-103_1_1412.d [237:38] 473298 library precursors are potentially detectable [237:38] Processing... [238:37] RT window set to 0.468305 [238:37] Ion mobility window set to 0.0254584 [238:37] Recommended MS1 mass accuracy setting: 9.92255 ppm [239:26] Removing low confidence identifications [239:26] Removing interfering precursors [239:34] Training neural networks: 96120 targets, 102795 decoys [239:51] Number of IDs at 0.01 FDR: 35120 [239:52] Translating peaks within elution groups [239:58] Number of IDs at 0.01 FDR: 83125 [240:02] Precursors at 1% channel FDR: 35527 out of 83125 [240:02] Calculating protein q-values [240:02] Number of genes identified at 1% FDR: 3250 (precursor-level), 3186 (protein-level) (inference performed using proteotypic peptides only) [240:02] Quantification [240:03] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-103_1_1412.d.quant. [240:07] File #39/47 [240:07] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-104_1_1413.d [242:14] 473298 library precursors are potentially detectable [242:14] Processing... [243:11] RT window set to 0.456754 [243:11] Ion mobility window set to 0.0275696 [243:11] Recommended MS1 mass accuracy setting: 9.88802 ppm [244:02] Removing low confidence identifications [244:02] Removing interfering precursors [244:11] Training neural networks: 95695 targets, 103248 decoys [244:28] Number of IDs at 0.01 FDR: 35821 [244:29] Translating peaks within elution groups [244:34] Number of IDs at 0.01 FDR: 87707 [244:39] Precursors at 1% channel FDR: 34829 out of 87707 [244:39] Calculating protein q-values [244:39] Number of genes identified at 1% FDR: 3339 (precursor-level), 3070 (protein-level) (inference performed using proteotypic peptides only) [244:39] Quantification [244:41] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-104_1_1413.d.quant. [244:44] File #40/47 [244:44] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-105_1_1414.d [246:50] 473298 library precursors are potentially detectable [246:50] Processing... [248:28] RT window set to 0.480948 [248:28] Ion mobility window set to 0.0268312 [248:28] Recommended MS1 mass accuracy setting: 9.45092 ppm [249:19] Removing low confidence identifications [249:19] Removing interfering precursors [249:27] Training neural networks: 94150 targets, 100639 decoys [249:43] Number of IDs at 0.01 FDR: 21917 [249:44] Translating peaks within elution groups [249:49] Number of IDs at 0.01 FDR: 66209 [249:52] Precursors at 1% channel FDR: 20765 out of 66209 [249:52] Calculating protein q-values [249:52] Number of genes identified at 1% FDR: 2929 (precursor-level), 2435 (protein-level) (inference performed using proteotypic peptides only) [249:52] Quantification [249:53] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-105_1_1414.d.quant. [249:57] File #41/47 [249:57] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-106_1_1415.d [252:04] 473298 library precursors are potentially detectable [252:04] Processing... [253:00] RT window set to 0.452088 [253:00] Ion mobility window set to 0.026051 [253:00] Recommended MS1 mass accuracy setting: 9.46563 ppm [253:48] Removing low confidence identifications [253:48] Removing interfering precursors [253:56] Training neural networks: 95692 targets, 102180 decoys [254:13] Number of IDs at 0.01 FDR: 33285 [254:14] Translating peaks within elution groups [254:19] Number of IDs at 0.01 FDR: 81089 [254:24] Precursors at 1% channel FDR: 31649 out of 81089 [254:24] Calculating protein q-values [254:24] Number of genes identified at 1% FDR: 3148 (precursor-level), 2571 (protein-level) (inference performed using proteotypic peptides only) [254:24] Quantification [254:25] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-106_1_1415.d.quant. [254:29] File #42/47 [254:29] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-107_1_1416.d [256:29] 473298 library precursors are potentially detectable [256:29] Processing... [257:38] RT window set to 0.477855 [257:38] Ion mobility window set to 0.0275775 [257:38] Recommended MS1 mass accuracy setting: 10.0663 ppm [258:29] Removing low confidence identifications [258:30] Removing interfering precursors [258:37] Training neural networks: 95913 targets, 102417 decoys [258:53] Number of IDs at 0.01 FDR: 29659 [258:54] Translating peaks within elution groups [259:00] Number of IDs at 0.01 FDR: 82636 [259:04] Precursors at 1% channel FDR: 27325 out of 82636 [259:04] Calculating protein q-values [259:04] Number of genes identified at 1% FDR: 3270 (precursor-level), 2605 (protein-level) (inference performed using proteotypic peptides only) [259:04] Quantification [259:06] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-107_1_1416.d.quant. [259:09] File #43/47 [259:09] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-108_1_1417.d [261:17] 473298 library precursors are potentially detectable [261:17] Processing... [262:02] RT window set to 0.470231 [262:02] Ion mobility window set to 0.0258286 [262:02] Recommended MS1 mass accuracy setting: 9.84064 ppm [262:54] Removing low confidence identifications [262:54] Removing interfering precursors [263:03] Training neural networks: 95804 targets, 103265 decoys [263:19] Number of IDs at 0.01 FDR: 36051 [263:21] Translating peaks within elution groups [263:26] Number of IDs at 0.01 FDR: 89521 [263:31] Precursors at 1% channel FDR: 34958 out of 89521 [263:31] Calculating protein q-values [263:31] Number of genes identified at 1% FDR: 3364 (precursor-level), 3121 (protein-level) (inference performed using proteotypic peptides only) [263:31] Quantification [263:33] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-108_1_1417.d.quant. [263:37] File #44/47 [263:37] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-109_1_1418.d [265:43] 473298 library precursors are potentially detectable [265:43] Processing... [266:52] RT window set to 0.471045 [266:52] Ion mobility window set to 0.0269203 [266:52] Recommended MS1 mass accuracy setting: 10.7403 ppm [267:42] Removing low confidence identifications [267:43] Removing interfering precursors [267:51] Training neural networks: 94307 targets, 101511 decoys [268:07] Number of IDs at 0.01 FDR: 29705 [268:08] Translating peaks within elution groups [268:13] Number of IDs at 0.01 FDR: 70315 [268:17] Precursors at 1% channel FDR: 29308 out of 70315 [268:17] Calculating protein q-values [268:17] Number of genes identified at 1% FDR: 2932 (precursor-level), 2287 (protein-level) (inference performed using proteotypic peptides only) [268:17] Quantification [268:19] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-109_1_1418.d.quant. [268:22] File #45/47 [268:22] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-110_1_1419.d [270:29] 473298 library precursors are potentially detectable [270:29] Processing... [271:14] RT window set to 0.477593 [271:14] Ion mobility window set to 0.0259854 [271:14] Recommended MS1 mass accuracy setting: 9.33978 ppm [272:07] Removing low confidence identifications [272:07] Removing interfering precursors [272:16] Training neural networks: 95719 targets, 102880 decoys [272:32] Number of IDs at 0.01 FDR: 37834 [272:33] Translating peaks within elution groups [272:39] Number of IDs at 0.01 FDR: 90424 [272:44] Precursors at 1% channel FDR: 36079 out of 90424 [272:44] Calculating protein q-values [272:44] Number of genes identified at 1% FDR: 3530 (precursor-level), 3537 (protein-level) (inference performed using proteotypic peptides only) [272:44] Quantification [272:45] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-110_1_1419.d.quant. [272:49] File #46/47 [272:49] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-111_1_1420.d [274:56] 473298 library precursors are potentially detectable [274:56] Processing... [276:05] RT window set to 0.471406 [276:05] Ion mobility window set to 0.0271409 [276:05] Recommended MS1 mass accuracy setting: 9.69146 ppm [276:56] Removing low confidence identifications [276:56] Removing interfering precursors [277:05] Training neural networks: 94909 targets, 102017 decoys [277:21] Number of IDs at 0.01 FDR: 29872 [277:22] Translating peaks within elution groups [277:27] Number of IDs at 0.01 FDR: 73674 [277:31] Precursors at 1% channel FDR: 29283 out of 73674 [277:31] Calculating protein q-values [277:31] Number of genes identified at 1% FDR: 3026 (precursor-level), 2955 (protein-level) (inference performed using proteotypic peptides only) [277:31] Quantification [277:33] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-111_1_1420.d.quant. [277:36] File #47/47 [277:36] Loading run D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-112_1_1421.d [279:43] 473298 library precursors are potentially detectable [279:43] Processing... [280:52] RT window set to 0.470506 [280:52] Ion mobility window set to 0.0285508 [280:52] Recommended MS1 mass accuracy setting: 10.5121 ppm [281:45] Removing low confidence identifications [281:45] Removing interfering precursors [281:53] Training neural networks: 95553 targets, 102894 decoys [282:10] Number of IDs at 0.01 FDR: 31582 [282:11] Translating peaks within elution groups [282:17] Number of IDs at 0.01 FDR: 76900 [282:21] Precursors at 1% channel FDR: 30392 out of 76900 [282:21] Calculating protein q-values [282:21] Number of genes identified at 1% FDR: 3013 (precursor-level), 2406 (protein-level) (inference performed using proteotypic peptides only) [282:21] Quantification [282:22] Quantification information saved to D:\Data\protocol_appnote\appnote_transfer\DDM_Slot1-112_1_1421.d.quant. [282:26] Cross-run analysis [282:26] Reading quantification information: 47 files [282:54] Quantifying peptides [283:05] Assembling protein groups [283:07] Quantifying proteins [283:09] Calculating q-values for protein and gene groups [283:10] Calculating global q-values for protein and gene groups [283:10] Writing report [289:16] Report saved to G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\appnote\Searched_DDM\report.tsv. [289:16] Saving precursor levels matrix [289:21] Precursor levels matrix (1% precursor and protein group FDR) saved to G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\appnote\Searched_DDM\report.pr_matrix.tsv. [289:21] Saving precursor levels matrix [289:25] Precursor levels matrix (1% precursor and protein group FDR) saved to G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\appnote\Searched_DDM\report.pr_matrix_channels.tsv. [289:25] Saving precursor levels matrix [289:29] Precursor levels matrix (1% precursor and protein group FDR) saved to G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\appnote\Searched_DDM\report.pr_matrix_channels_translated.tsv. [289:29] Saving precursor levels matrix [289:34] Precursor levels matrix (1% precursor and protein group FDR) saved to G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\appnote\Searched_DDM\report.pr_matrix_channels_ms1.tsv. [289:34] Saving precursor levels matrix [289:38] Precursor levels matrix (1% precursor and protein group FDR) saved to G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\appnote\Searched_DDM\report.pr_matrix_channels_ms1_translated.tsv. [289:38] Saving precursor levels matrix [289:47] Precursor levels matrix (1% precursor and protein group FDR) saved to G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\appnote\Searched_DDM\report.pr_matrix_channels_ms1_extracted.tsv. [289:47] Saving protein group levels matrix [289:47] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\appnote\Searched_DDM\report.pg_matrix.tsv. [289:47] Saving gene group levels matrix [289:47] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\appnote\Searched_DDM\report.gg_matrix.tsv. [289:47] Saving unique genes levels matrix [289:48] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\appnote\Searched_DDM\report.unique_genes_matrix.tsv. [289:48] Stats report saved to G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\appnote\Searched_DDM\report.stats.tsv Finished