DIA-NN 1.7.16 (Data-Independent Acquisition by Neural Networks) Compiled on Mar 27 2021 21:34:06 Current date and time: Tue Jun 13 13:15:03 2023 CPU: GenuineIntel Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 Logical CPU cores: 32 diann.exe --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample7_S1r.wiff --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample7_S2r.wiff --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample7_S3r.wiff --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample8_S1r.wiff --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample8_S2r.wiff --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample8_S3r.wiff --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample9_S1r.wiff --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample9_S2r.wiff --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample9_S3r.wiff --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample10_S1r.wiff --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample10_S2r.wiff --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample10_S3r.wiff --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample11_S1.wiff --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample11_S2.wiff --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample11_S3.wiff --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample12_S1.wiff --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample12_S2.wiff --f D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample12_S3.wiff --lib D:\Data\niwa_DIANN\SWATHatlas\EC2020\Ecoli_consensus_peakview.txt --threads 16 --verbose 1 --out D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\230608CY_EC_SWATH6_rep2.tsv --qvalue 0.01 --matrices --min-corr 1.0 --corr-diff 1.0 --time-corr-only --smart-profiling Thread number set to 16 Output will be filtered at 0.01 FDR Precursor/protein x samples expression level matrices will be saved along with the main report Only peaks with correlation sum exceeding 1 will be considered Peaks with correlation sum below 1 from maximum will not be considered A single score will be used until RT alignment to save memory; this can potentially lead to slower search When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones DIA-NN will optimise the mass accuracy automatically using the first run in the experiment. This is useful primarily for quick initial analyses, when it is not yet known which mass accuracy setting works best for a particular acquisition scheme. 18 files will be processed [0:00] Loading spectral library D:\Data\niwa_DIANN\SWATHatlas\EC2020\Ecoli_consensus_peakview.txt WARNING: no neutral loss information found in the library - assuming fragments without losses [0:02] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete) [0:02] Spectral library loaded: 4152 protein isoforms, 4152 protein groups and 68959 precursors in 56883 elution groups. [0:02] Initialising library [0:02] Saving the library to D:\Data\niwa_DIANN\SWATHatlas\EC2020\Ecoli_consensus_peakview.txt.speclib [0:02] File #1/18 [0:02] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample7_S1r.wiff [5:21] 68709 library precursors are potentially detectable [5:21] Processing... [5:41] RT window set to 2.9522 [5:41] Peak width: 3 [5:41] Scan window radius set to 6 [5:41] Recommended MS1 mass accuracy setting: 29.3246 ppm [6:41] Optimised mass accuracy: 31.8247 ppm [7:07] Removing low confidence identifications [7:07] Removing interfering precursors [7:10] Training the neural network: 30784 targets, 59054 decoys [7:13] Number of IDs at 0.01 FDR: 15986 [7:13] Calculating protein q-values [7:13] Number of protein isoforms identified at 1% FDR: 1726 (precursor-level), 1578 (protein-level) (inference performed using proteotypic peptides only) [7:13] Quantification [7:15] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample7_S1r.wiff.quant. [7:15] File #2/18 [7:15] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample7_S2r.wiff [11:38] 68709 library precursors are potentially detectable [11:38] Processing... [11:50] RT window set to 2.30523 [11:50] Recommended MS1 mass accuracy setting: 43.0625 ppm [12:15] Removing low confidence identifications [12:15] Removing interfering precursors [12:18] Training the neural network: 30191 targets, 56472 decoys [12:21] Number of IDs at 0.01 FDR: 15435 [12:22] Calculating protein q-values [12:22] Number of protein isoforms identified at 1% FDR: 1717 (precursor-level), 1547 (protein-level) (inference performed using proteotypic peptides only) [12:22] Quantification [12:23] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample7_S2r.wiff.quant. [12:24] File #3/18 [12:24] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample7_S3r.wiff [17:47] 68709 library precursors are potentially detectable [17:47] Processing... [17:59] RT window set to 2.35859 [17:59] Recommended MS1 mass accuracy setting: 38.4932 ppm [18:24] Removing low confidence identifications [18:24] Removing interfering precursors [18:27] Training the neural network: 28008 targets, 56738 decoys [18:30] Number of IDs at 0.01 FDR: 15124 [18:30] Calculating protein q-values [18:30] Number of protein isoforms identified at 1% FDR: 1711 (precursor-level), 1544 (protein-level) (inference performed using proteotypic peptides only) [18:30] Quantification [18:32] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample7_S3r.wiff.quant. [18:32] File #4/18 [18:32] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample8_S1r.wiff [23:23] 68709 library precursors are potentially detectable [23:23] Processing... [23:35] RT window set to 2.26324 [23:35] Recommended MS1 mass accuracy setting: 28.3083 ppm [24:02] Removing low confidence identifications [24:02] Removing interfering precursors [24:05] Training the neural network: 31369 targets, 56503 decoys [24:08] Number of IDs at 0.01 FDR: 16488 [24:09] Calculating protein q-values [24:09] Number of protein isoforms identified at 1% FDR: 1780 (precursor-level), 1642 (protein-level) (inference performed using proteotypic peptides only) [24:09] Quantification [24:11] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample8_S1r.wiff.quant. [24:11] File #5/18 [24:11] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample8_S2r.wiff [29:12] 68709 library precursors are potentially detectable [29:12] Processing... [29:25] RT window set to 2.22166 [29:25] Recommended MS1 mass accuracy setting: 22.9032 ppm [29:51] Removing low confidence identifications [29:51] Removing interfering precursors [29:54] Training the neural network: 30765 targets, 56367 decoys [29:57] Number of IDs at 0.01 FDR: 15990 [29:57] Calculating protein q-values [29:57] Number of protein isoforms identified at 1% FDR: 1760 (precursor-level), 1605 (protein-level) (inference performed using proteotypic peptides only) [29:57] Quantification [29:59] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample8_S2r.wiff.quant. [29:59] File #6/18 [29:59] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample8_S3r.wiff [34:54] 68709 library precursors are potentially detectable [34:54] Processing... [35:06] RT window set to 2.4613 [35:06] Recommended MS1 mass accuracy setting: 26.5199 ppm [35:32] Removing low confidence identifications [35:32] Removing interfering precursors [35:36] Training the neural network: 30944 targets, 56885 decoys [35:39] Number of IDs at 0.01 FDR: 16242 [35:39] Calculating protein q-values [35:39] Number of protein isoforms identified at 1% FDR: 1783 (precursor-level), 1652 (protein-level) (inference performed using proteotypic peptides only) [35:39] Quantification [35:41] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample8_S3r.wiff.quant. [35:41] File #7/18 [35:41] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample9_S1r.wiff [40:54] 68709 library precursors are potentially detectable [40:54] Processing... [41:06] RT window set to 2.6486 [41:06] Recommended MS1 mass accuracy setting: 29.1373 ppm [41:32] Removing low confidence identifications [41:32] Removing interfering precursors [41:34] Training the neural network: 29381 targets, 57222 decoys [41:38] Number of IDs at 0.01 FDR: 14808 [41:38] Calculating protein q-values [41:38] Number of protein isoforms identified at 1% FDR: 1682 (precursor-level), 1550 (protein-level) (inference performed using proteotypic peptides only) [41:38] Quantification [41:40] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample9_S1r.wiff.quant. [41:40] File #8/18 [41:40] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample9_S2r.wiff [46:12] 68709 library precursors are potentially detectable [46:12] Processing... [46:24] RT window set to 2.25082 [46:24] Recommended MS1 mass accuracy setting: 27.2988 ppm [46:49] Removing low confidence identifications [46:49] Removing interfering precursors [46:52] Training the neural network: 30078 targets, 55821 decoys [46:55] Number of IDs at 0.01 FDR: 15060 [46:56] Calculating protein q-values [46:56] Number of protein isoforms identified at 1% FDR: 1698 (precursor-level), 1562 (protein-level) (inference performed using proteotypic peptides only) [46:56] Quantification [46:57] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample9_S2r.wiff.quant. [46:58] File #9/18 [46:58] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample9_S3r.wiff [52:02] 68709 library precursors are potentially detectable [52:02] Processing... [52:14] RT window set to 2.28587 [52:14] Recommended MS1 mass accuracy setting: 29.6214 ppm [52:39] Removing low confidence identifications [52:39] Removing interfering precursors [52:42] Training the neural network: 29117 targets, 55539 decoys [52:45] Number of IDs at 0.01 FDR: 14536 [52:45] Calculating protein q-values [52:45] Number of protein isoforms identified at 1% FDR: 1669 (precursor-level), 1567 (protein-level) (inference performed using proteotypic peptides only) [52:45] Quantification [52:47] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample9_S3r.wiff.quant. [52:48] File #10/18 [52:48] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample10_S1r.wiff [57:16] 68709 library precursors are potentially detectable [57:16] Processing... [57:28] RT window set to 2.37127 [57:28] Recommended MS1 mass accuracy setting: 30.1423 ppm [57:53] Removing low confidence identifications [57:53] Removing interfering precursors [57:56] Training the neural network: 27646 targets, 56754 decoys [57:59] Number of IDs at 0.01 FDR: 14239 [57:59] Calculating protein q-values [57:59] Number of protein isoforms identified at 1% FDR: 1679 (precursor-level), 1534 (protein-level) (inference performed using proteotypic peptides only) [57:59] Quantification [58:01] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample10_S1r.wiff.quant. [58:01] File #11/18 [58:01] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample10_S2r.wiff [62:29] 68709 library precursors are potentially detectable [62:29] Processing... [62:41] RT window set to 2.48406 [62:41] Recommended MS1 mass accuracy setting: 30.0007 ppm [63:06] Removing low confidence identifications [63:06] Removing interfering precursors [63:09] Training the neural network: 28554 targets, 57206 decoys [63:12] Number of IDs at 0.01 FDR: 13670 [63:13] Calculating protein q-values [63:13] Number of protein isoforms identified at 1% FDR: 1627 (precursor-level), 1477 (protein-level) (inference performed using proteotypic peptides only) [63:13] Quantification [63:14] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample10_S2r.wiff.quant. [63:14] File #12/18 [63:14] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample10_S3r.wiff [67:36] 68709 library precursors are potentially detectable [67:36] Processing... [67:48] RT window set to 2.65854 [67:48] Recommended MS1 mass accuracy setting: 29.3425 ppm [68:13] Removing low confidence identifications [68:13] Removing interfering precursors [68:16] Training the neural network: 28598 targets, 57717 decoys [68:19] Number of IDs at 0.01 FDR: 13710 [68:19] Calculating protein q-values [68:19] Number of protein isoforms identified at 1% FDR: 1616 (precursor-level), 1478 (protein-level) (inference performed using proteotypic peptides only) [68:19] Quantification [68:21] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample10_S3r.wiff.quant. [68:21] File #13/18 [68:21] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample11_S1.wiff [73:44] 68709 library precursors are potentially detectable [73:44] Processing... [73:54] RT window set to 2.74398 [73:54] Recommended MS1 mass accuracy setting: 26.6078 ppm [74:21] Removing low confidence identifications [74:21] Removing interfering precursors [74:24] Training the neural network: 31435 targets, 58257 decoys [74:28] Number of IDs at 0.01 FDR: 17939 [74:28] Calculating protein q-values [74:28] Number of protein isoforms identified at 1% FDR: 1882 (precursor-level), 1727 (protein-level) (inference performed using proteotypic peptides only) [74:28] Quantification [74:30] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample11_S1.wiff.quant. [74:30] File #14/18 [74:30] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample11_S2.wiff [79:42] 68709 library precursors are potentially detectable [79:42] Processing... [79:53] RT window set to 2.67776 [79:53] Recommended MS1 mass accuracy setting: 25.6429 ppm [80:19] Removing low confidence identifications [80:19] Removing interfering precursors [80:22] Training the neural network: 32347 targets, 58286 decoys [80:25] Number of IDs at 0.01 FDR: 17849 [80:26] Calculating protein q-values [80:26] Number of protein isoforms identified at 1% FDR: 1884 (precursor-level), 1726 (protein-level) (inference performed using proteotypic peptides only) [80:26] Quantification [80:28] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample11_S2.wiff.quant. [80:28] File #15/18 [80:28] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample11_S3.wiff [85:46] 68709 library precursors are potentially detectable [85:46] Processing... [85:56] RT window set to 2.29726 [85:56] Recommended MS1 mass accuracy setting: 38.1711 ppm [86:21] Removing low confidence identifications [86:21] Removing interfering precursors [86:24] Training the neural network: 32412 targets, 57186 decoys [86:28] Number of IDs at 0.01 FDR: 17584 [86:28] Calculating protein q-values [86:28] Number of protein isoforms identified at 1% FDR: 1843 (precursor-level), 1690 (protein-level) (inference performed using proteotypic peptides only) [86:28] Quantification [86:30] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample11_S3.wiff.quant. [86:31] File #16/18 [86:31] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample12_S1.wiff [91:45] 68709 library precursors are potentially detectable [91:45] Processing... [91:55] RT window set to 2.22249 [91:55] Recommended MS1 mass accuracy setting: 25.9933 ppm [92:20] Removing low confidence identifications [92:20] Removing interfering precursors [92:23] Training the neural network: 32249 targets, 57351 decoys [92:26] Number of IDs at 0.01 FDR: 17149 [92:26] Calculating protein q-values [92:27] Number of protein isoforms identified at 1% FDR: 1833 (precursor-level), 1649 (protein-level) (inference performed using proteotypic peptides only) [92:27] Quantification [92:28] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample12_S1.wiff.quant. [92:29] File #17/18 [92:29] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample12_S2.wiff [97:40] 68709 library precursors are potentially detectable [97:40] Processing... [97:50] RT window set to 2.35835 [97:50] Recommended MS1 mass accuracy setting: 27.7789 ppm [98:16] Removing low confidence identifications [98:16] Removing interfering precursors [98:19] Training the neural network: 31668 targets, 57715 decoys [98:23] Number of IDs at 0.01 FDR: 16563 [98:23] Calculating protein q-values [98:23] Number of protein isoforms identified at 1% FDR: 1779 (precursor-level), 1644 (protein-level) (inference performed using proteotypic peptides only) [98:23] Quantification [98:25] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample12_S2.wiff.quant. [98:26] File #18/18 [98:26] Loading run D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample12_S3.wiff [103:19] 68709 library precursors are potentially detectable [103:19] Processing... [103:32] RT window set to 2.36278 [103:32] Recommended MS1 mass accuracy setting: 24.7699 ppm [103:59] Removing low confidence identifications [103:59] Removing interfering precursors [104:02] Training the neural network: 31827 targets, 57903 decoys [104:06] Number of IDs at 0.01 FDR: 16663 [104:06] Calculating protein q-values [104:06] Number of protein isoforms identified at 1% FDR: 1768 (precursor-level), 1661 (protein-level) (inference performed using proteotypic peptides only) [104:06] Quantification [104:08] Quantification information saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\EC_CY_sample12_S3.wiff.quant. [104:08] Cross-run analysis [104:08] Reading quantification information: 18 files [104:09] Quantifying peptides [104:14] Assembling protein groups [104:14] Quantifying proteins [104:14] Calculating q-values for protein and gene groups [104:14] Writing report [104:28] Report saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\230608CY_EC_SWATH6_rep2.tsv. [104:28] Saving precursor levels matrix [104:28] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\230608CY_EC_SWATH6_rep2.pr_matrix.tsv. [104:28] Saving protein group levels matrix [104:28] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\230608CY_EC_SWATH6_rep2.pg_matrix.tsv. [104:28] Saving gene group levels matrix [104:28] Gene groups levels matrix (1% precursor FDR and gene group FDR) saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\230608CY_EC_SWATH6_rep2.gg_matrix.tsv. [104:28] Saving unique genes levels matrix [104:28] Unique genes levels matrix (1% precursor FDR and unique protein FDR) saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\230608CY_EC_SWATH6_rep2.unique_genes_matrix.tsv. [104:28] Stats report saved to D:\Data\niwa_DIANN\230608CY_EC_SWATH6x2\230608CY_EC_SWATH6_rep2.stats.tsv