DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks) Compiled on Apr 14 2022 15:31:19 Current date and time: Mon Apr 24 17:16:03 2023 CPU: GenuineIntel Intel(R) Xeon(R) Gold 6248R CPU @ 3.00GHz SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 Logical CPU cores: 48 diann.exe --f E:\2_Proteo_Jutaku\KK2094\KK2094-1_Dish-1.raw --f E:\2_Proteo_Jutaku\KK2094\KK2094-2_Dish-2.raw --f E:\2_Proteo_Jutaku\KK2094\KK2094-3_Dish-3.raw --f E:\2_Proteo_Jutaku\KK2094\KK2094-4_Dish-4.raw --f E:\2_Proteo_Jutaku\KK2094\KK2094-5_Dish-5.raw --f E:\2_Proteo_Jutaku\KK2094\KK2094-6_Dish-6.raw --f E:\2_Proteo_Jutaku\KK2094\KK2094-7_Dish-7.raw --lib E:\9_DIA_NN\Database\230307_GC_Human\DIA-NN\230307_Human_UP000005640_E20591_pep7-45_z2-4_mz490-750_Car_Trypsin_miss1_Contami.predicted.speclib --threads 20 --verbose 1 --out E:\2_Proteo_Jutaku\KK2094\Result\KK2094.tsv --qvalue 0.01 --matrices --out-lib E:\2_Proteo_Jutaku\KK2094\Result\KK2094_SL.tsv --gen-spec-lib --fasta E:\9_DIA_NN\Database\230307_GC_Human\230307_Human_UP000005640_E20591_Contami.fasta --met-excision --cut K*,R*,!*P --mass-acc 10 --mass-acc-ms1 10 --individual-mass-acc --individual-windows --reanalyse --relaxed-prot-inf --smart-profiling --peak-center --no-ifs-removal --protein-qvalue 0.01 --peak-translation --mass-acc-cal 10 --matrix-qvalue 0.01 --matrix-spec-q Thread number set to 20 Output will be filtered at 0.01 FDR Precursor/protein x samples expression level matrices will be saved along with the main report A spectral library will be generated N-terminal methionine excision enabled In silico digest will involve cuts at K*,R* But excluding cuts at *P Mass accuracy will be determined separately for different runs Scan windows will be inferred separately for different runs A spectral library will be created from the DIA runs and used to reanalyse them; .quant files will only be saved to disk during the first step 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 Output will be filtered at 0.01 protein-level FDR Translation of retention times between peptides within the same elution group enabled Calibration mass accuracy set to 1e-05 Precursor/protein x sample matrices will be filtered at 0.01 precursor & protein-level FDR Protein x sample matrices will be also filtered using run-specific protein q-value Mass accuracy will be fixed to 1e-05 (MS2) and 1e-05 (MS1) 7 files will be processed [0:00] Loading spectral library E:\9_DIA_NN\Database\230307_GC_Human\DIA-NN\230307_Human_UP000005640_E20591_pep7-45_z2-4_mz490-750_Car_Trypsin_miss1_Contami.predicted.speclib [0:01] Library annotated with sequence database(s): I:\3_ScaffoldDIA\Prosit\220915_New_comtaminats_fasta_HaoGroup\New\Protein-Contaminant-Libraries-for-DDA-and-DIA-Proteomics-main\Universal protein contaminant FASTA\0602_Universal Contaminants_trans.fasta; I:\3_ScaffoldDIA\Prosit\230307_GC_Human\230307_Human_UP000005640_E20591.fasta [0:01] Spectral library loaded: 20874 protein isoforms, 27330 protein groups and 1143798 precursors in 1001177 elution groups. [0:01] Loading protein annotations from FASTA E:\9_DIA_NN\Database\230307_GC_Human\230307_Human_UP000005640_E20591_Contami.fasta [0:02] Annotating library proteins with information from the FASTA database [0:02] Gene names missing for some isoforms [0:02] Library contains 20744 proteins, and 20366 genes [0:02] Initialising library [0:03] First pass: generating a spectral library from DIA data [0:03] File #1/7 [0:03] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-1_Dish-1.raw [0:38] 1054319 library precursors are potentially detectable [0:38] Processing... [0:44] RT window set to 2.63793 [0:44] Peak width: 2.796 [0:44] Scan window radius set to 6 [0:44] Recommended MS1 mass accuracy setting: 17.449 ppm [1:02] Removing low confidence identifications [1:02] Removing interfering precursors [1:15] Training neural networks: 337859 targets, 595099 decoys [1:40] Number of IDs at 0.01 FDR: 75702 [1:41] Translating peaks within elution groups [1:41] Number of IDs at 0.01 FDR: 77141 [1:41] Calculating protein q-values [1:42] Number of genes identified at 1% FDR: 8934 (precursor-level), 8496 (protein-level) (inference performed using proteotypic peptides only) [1:42] Quantification [1:43] Quantification information saved to E:\2_Proteo_Jutaku\KK2094\KK2094-1_Dish-1.raw.quant. [1:44] File #2/7 [1:44] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-2_Dish-2.raw [2:18] 1054319 library precursors are potentially detectable [2:19] Processing... [2:24] RT window set to 2.67804 [2:24] Peak width: 2.752 [2:24] Scan window radius set to 6 [2:24] Recommended MS1 mass accuracy setting: 21.3544 ppm [2:43] Removing low confidence identifications [2:43] Removing interfering precursors [2:55] Training neural networks: 340486 targets, 603904 decoys [3:20] Number of IDs at 0.01 FDR: 75951 [3:21] Translating peaks within elution groups [3:22] Number of IDs at 0.01 FDR: 77352 [3:22] Calculating protein q-values [3:22] Number of genes identified at 1% FDR: 8872 (precursor-level), 8475 (protein-level) (inference performed using proteotypic peptides only) [3:22] Quantification [3:24] Quantification information saved to E:\2_Proteo_Jutaku\KK2094\KK2094-2_Dish-2.raw.quant. [3:25] File #3/7 [3:25] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-3_Dish-3.raw [3:59] 1054319 library precursors are potentially detectable [4:00] Processing... [4:05] RT window set to 2.5869 [4:05] Peak width: 2.808 [4:05] Scan window radius set to 6 [4:05] Recommended MS1 mass accuracy setting: 22.5032 ppm [4:24] Removing low confidence identifications [4:24] Removing interfering precursors [4:37] Training neural networks: 353873 targets, 603596 decoys [5:03] Number of IDs at 0.01 FDR: 76535 [5:04] Translating peaks within elution groups [5:04] Number of IDs at 0.01 FDR: 77975 [5:04] Calculating protein q-values [5:05] Number of genes identified at 1% FDR: 8951 (precursor-level), 8476 (protein-level) (inference performed using proteotypic peptides only) [5:05] Quantification [5:07] Quantification information saved to E:\2_Proteo_Jutaku\KK2094\KK2094-3_Dish-3.raw.quant. [5:07] File #4/7 [5:07] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-4_Dish-4.raw [5:40] 1054319 library precursors are potentially detectable [5:40] Processing... [5:45] RT window set to 2.59224 [5:45] Peak width: 2.796 [5:45] Scan window radius set to 6 [5:45] Recommended MS1 mass accuracy setting: 19.2696 ppm [6:04] Removing low confidence identifications [6:04] Removing interfering precursors [6:16] Training neural networks: 334255 targets, 583314 decoys [6:40] Number of IDs at 0.01 FDR: 73349 [6:41] Translating peaks within elution groups [6:42] Number of IDs at 0.01 FDR: 74717 [6:42] Calculating protein q-values [6:42] Number of genes identified at 1% FDR: 8701 (precursor-level), 8266 (protein-level) (inference performed using proteotypic peptides only) [6:42] Quantification [6:44] Quantification information saved to E:\2_Proteo_Jutaku\KK2094\KK2094-4_Dish-4.raw.quant. [6:44] File #5/7 [6:44] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-5_Dish-5.raw [7:18] 1054319 library precursors are potentially detectable [7:18] Processing... [7:23] RT window set to 2.61245 [7:23] Peak width: 2.796 [7:23] Scan window radius set to 6 [7:23] Recommended MS1 mass accuracy setting: 19.9194 ppm [7:42] Removing low confidence identifications [7:42] Removing interfering precursors [7:55] Training neural networks: 348534 targets, 600106 decoys [8:21] Number of IDs at 0.01 FDR: 74749 [8:21] Translating peaks within elution groups [8:22] Number of IDs at 0.01 FDR: 76161 [8:22] Calculating protein q-values [8:22] Number of genes identified at 1% FDR: 8729 (precursor-level), 8283 (protein-level) (inference performed using proteotypic peptides only) [8:22] Quantification [8:24] Quantification information saved to E:\2_Proteo_Jutaku\KK2094\KK2094-5_Dish-5.raw.quant. [8:25] File #6/7 [8:25] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-6_Dish-6.raw [8:57] 1054319 library precursors are potentially detectable [8:57] Processing... [9:02] RT window set to 2.65865 [9:02] Peak width: 2.812 [9:02] Scan window radius set to 6 [9:02] Recommended MS1 mass accuracy setting: 19.3351 ppm [9:21] Removing low confidence identifications [9:21] Removing interfering precursors [9:33] Training neural networks: 334413 targets, 590161 decoys [9:58] Number of IDs at 0.01 FDR: 73331 [9:59] Translating peaks within elution groups [9:59] Number of IDs at 0.01 FDR: 74700 [9:59] Calculating protein q-values [9:59] Number of genes identified at 1% FDR: 8630 (precursor-level), 8194 (protein-level) (inference performed using proteotypic peptides only) [9:59] Quantification [10:02] Quantification information saved to E:\2_Proteo_Jutaku\KK2094\KK2094-6_Dish-6.raw.quant. [10:02] File #7/7 [10:02] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-7_Dish-7.raw [10:35] 1054319 library precursors are potentially detectable [10:36] Processing... [10:41] RT window set to 2.60383 [10:41] Peak width: 2.804 [10:41] Scan window radius set to 6 [10:41] Recommended MS1 mass accuracy setting: 18.6666 ppm [11:00] Removing low confidence identifications [11:00] Removing interfering precursors [11:12] Training neural networks: 341895 targets, 589156 decoys [11:37] Number of IDs at 0.01 FDR: 73208 [11:38] Translating peaks within elution groups [11:38] Number of IDs at 0.01 FDR: 74522 [11:38] Calculating protein q-values [11:39] Number of genes identified at 1% FDR: 8662 (precursor-level), 8212 (protein-level) (inference performed using proteotypic peptides only) [11:39] Quantification [11:41] Quantification information saved to E:\2_Proteo_Jutaku\KK2094\KK2094-7_Dish-7.raw.quant. [11:41] Cross-run analysis [11:41] Reading quantification information: 7 files [11:43] Averaged recommended settings for this experiment: Mass accuracy = 10ppm, MS1 accuracy = 10ppm, Scan window = 6 [11:43] Quantifying peptides [11:48] Assembling protein groups [11:49] Quantifying proteins [11:50] Calculating q-values for protein and gene groups [11:50] Calculating global q-values for protein and gene groups [11:50] Writing report [12:24] Report saved to E:\2_Proteo_Jutaku\KK2094\Result\KK2094-first-pass.tsv. [12:24] Saving precursor levels matrix [12:25] Precursor levels matrix (1% precursor and protein group FDR) saved to E:\2_Proteo_Jutaku\KK2094\Result\KK2094-first-pass.pr_matrix.tsv. [12:25] Saving protein group levels matrix [12:25] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to E:\2_Proteo_Jutaku\KK2094\Result\KK2094-first-pass.pg_matrix.tsv. [12:25] Saving gene group levels matrix [12:25] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to E:\2_Proteo_Jutaku\KK2094\Result\KK2094-first-pass.gg_matrix.tsv. [12:25] Saving unique genes levels matrix [12:25] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to E:\2_Proteo_Jutaku\KK2094\Result\KK2094-first-pass.unique_genes_matrix.tsv. [12:25] Stats report saved to E:\2_Proteo_Jutaku\KK2094\Result\KK2094-first-pass.stats.tsv [12:25] Generating spectral library: [12:25] 90897 precursors passing the FDR threshold are to be extracted [12:25] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-1_Dish-1.raw [12:40] 1054319 library precursors are potentially detectable [12:41] 7965 spectra added to the library [12:41] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-2_Dish-2.raw [12:56] 1054319 library precursors are potentially detectable [12:58] 22159 spectra added to the library [12:58] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-3_Dish-3.raw [13:13] 1054319 library precursors are potentially detectable [13:13] 7662 spectra added to the library [13:13] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-4_Dish-4.raw [13:29] 1054319 library precursors are potentially detectable [13:29] 9132 spectra added to the library [13:29] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-5_Dish-5.raw [13:45] 1054319 library precursors are potentially detectable [13:45] 6585 spectra added to the library [13:46] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-6_Dish-6.raw [14:01] 1054319 library precursors are potentially detectable [14:01] 7856 spectra added to the library [14:01] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-7_Dish-7.raw [14:17] 1054319 library precursors are potentially detectable [14:18] 16166 spectra added to the library [14:18] Saving spectral library to E:\2_Proteo_Jutaku\KK2094\Result\KK2094_SL.tsv [14:31] 90897 precursors saved [14:31] Loading the generated library and saving it in the .speclib format [14:31] Loading spectral library E:\2_Proteo_Jutaku\KK2094\Result\KK2094_SL.tsv [14:35] Spectral library loaded: 10731 protein isoforms, 11161 protein groups and 90897 precursors in 86977 elution groups. [14:35] Loading protein annotations from FASTA E:\9_DIA_NN\Database\230307_GC_Human\230307_Human_UP000005640_E20591_Contami.fasta [14:36] Gene names missing for some isoforms [14:36] Library contains 10675 proteins, and 10581 genes [14:36] Saving the library to E:\2_Proteo_Jutaku\KK2094\Result\KK2094_SL.tsv.speclib [14:37] Second pass: using the newly created spectral library to reanalyse the data [14:37] File #1/7 [14:37] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-1_Dish-1.raw [14:52] 90897 library precursors are potentially detectable [14:52] Processing... [14:52] RT window set to 1.29231 [14:52] Peak width: 2.896 [14:52] Scan window radius set to 6 [14:52] Recommended MS1 mass accuracy setting: 20.2609 ppm [14:54] Removing low confidence identifications [14:54] Removing interfering precursors [14:56] Training neural networks: 85706 targets, 48703 decoys [15:00] Number of IDs at 0.01 FDR: 83550 [15:00] Translating peaks within elution groups [15:01] Number of IDs at 0.01 FDR: 84681 [15:01] Calculating protein q-values [15:01] Number of genes identified at 1% FDR: 9259 (precursor-level), 8730 (protein-level) (inference performed using proteotypic peptides only) [15:01] Quantification [15:01] File #2/7 [15:01] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-2_Dish-2.raw [15:17] 90897 library precursors are potentially detectable [15:17] Processing... [15:17] RT window set to 1.29318 [15:17] Peak width: 2.964 [15:17] Scan window radius set to 6 [15:17] Recommended MS1 mass accuracy setting: 20.3402 ppm [15:18] Removing low confidence identifications [15:18] Removing interfering precursors [15:20] Training neural networks: 85878 targets, 48917 decoys [15:24] Number of IDs at 0.01 FDR: 83640 [15:25] Translating peaks within elution groups [15:25] Number of IDs at 0.01 FDR: 84751 [15:25] Calculating protein q-values [15:25] Number of genes identified at 1% FDR: 9247 (precursor-level), 8744 (protein-level) (inference performed using proteotypic peptides only) [15:25] Quantification [15:26] File #3/7 [15:26] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-3_Dish-3.raw [15:41] 90897 library precursors are potentially detectable [15:41] Processing... [15:41] RT window set to 1.30302 [15:41] Peak width: 2.996 [15:41] Scan window radius set to 6 [15:41] Recommended MS1 mass accuracy setting: 20.4686 ppm [15:42] Removing low confidence identifications [15:42] Removing interfering precursors [15:44] Training neural networks: 85932 targets, 50077 decoys [15:48] Number of IDs at 0.01 FDR: 83697 [15:49] Translating peaks within elution groups [15:49] Number of IDs at 0.01 FDR: 84803 [15:49] Calculating protein q-values [15:49] Number of genes identified at 1% FDR: 9250 (precursor-level), 8736 (protein-level) (inference performed using proteotypic peptides only) [15:49] Quantification [15:49] File #4/7 [15:49] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-4_Dish-4.raw [16:04] 90897 library precursors are potentially detectable [16:04] Processing... [16:05] RT window set to 1.29829 [16:05] Peak width: 2.924 [16:05] Scan window radius set to 6 [16:05] Recommended MS1 mass accuracy setting: 21.2314 ppm [16:06] Removing low confidence identifications [16:06] Removing interfering precursors [16:09] Training neural networks: 85083 targets, 48284 decoys [16:12] Number of IDs at 0.01 FDR: 82508 [16:13] Translating peaks within elution groups [16:13] Number of IDs at 0.01 FDR: 83628 [16:13] Calculating protein q-values [16:13] Number of genes identified at 1% FDR: 9166 (precursor-level), 8643 (protein-level) (inference performed using proteotypic peptides only) [16:13] Quantification [16:14] File #5/7 [16:14] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-5_Dish-5.raw [16:29] 90897 library precursors are potentially detectable [16:29] Processing... [16:29] RT window set to 1.29459 [16:29] Peak width: 2.956 [16:29] Scan window radius set to 6 [16:29] Recommended MS1 mass accuracy setting: 20.6128 ppm [16:31] Removing low confidence identifications [16:31] Removing interfering precursors [16:33] Training neural networks: 85478 targets, 49373 decoys [16:36] Number of IDs at 0.01 FDR: 83021 [16:37] Translating peaks within elution groups [16:37] Number of IDs at 0.01 FDR: 84143 [16:37] Calculating protein q-values [16:37] Number of genes identified at 1% FDR: 9144 (precursor-level), 8645 (protein-level) (inference performed using proteotypic peptides only) [16:37] Quantification [16:38] File #6/7 [16:38] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-6_Dish-6.raw [16:53] 90897 library precursors are potentially detectable [16:53] Processing... [16:54] RT window set to 1.30637 [16:54] Peak width: 2.952 [16:54] Scan window radius set to 6 [16:54] Recommended MS1 mass accuracy setting: 18.7555 ppm [16:55] Removing low confidence identifications [16:55] Removing interfering precursors [16:57] Training neural networks: 84405 targets, 48277 decoys [17:01] Number of IDs at 0.01 FDR: 81387 [17:01] Translating peaks within elution groups [17:02] Number of IDs at 0.01 FDR: 82459 [17:02] Calculating protein q-values [17:02] Number of genes identified at 1% FDR: 9057 (precursor-level), 8545 (protein-level) (inference performed using proteotypic peptides only) [17:02] Quantification [17:02] File #7/7 [17:02] Loading run E:\2_Proteo_Jutaku\KK2094\KK2094-7_Dish-7.raw [17:17] 90897 library precursors are potentially detectable [17:18] Processing... [17:18] RT window set to 1.29665 [17:18] Peak width: 2.896 [17:18] Scan window radius set to 6 [17:18] Recommended MS1 mass accuracy setting: 17.535 ppm [17:19] Removing low confidence identifications [17:19] Removing interfering precursors [17:21] Training neural networks: 84354 targets, 48395 decoys [17:24] Number of IDs at 0.01 FDR: 81267 [17:25] Translating peaks within elution groups [17:25] Number of IDs at 0.01 FDR: 82285 [17:25] Calculating protein q-values [17:25] Number of genes identified at 1% FDR: 9051 (precursor-level), 8560 (protein-level) (inference performed using proteotypic peptides only) [17:25] Quantification [17:26] Cross-run analysis [17:26] Reading quantification information: 7 files [17:28] Averaged recommended settings for this experiment: Mass accuracy = 10ppm, MS1 accuracy = 10ppm, Scan window = 6 [17:28] Quantifying peptides [17:33] Quantifying proteins [17:33] Calculating q-values for protein and gene groups [17:34] Calculating global q-values for protein and gene groups [17:34] Writing report [18:07] Report saved to E:\2_Proteo_Jutaku\KK2094\Result\KK2094.tsv. [18:07] Saving precursor levels matrix [18:08] Precursor levels matrix (1% precursor and protein group FDR) saved to E:\2_Proteo_Jutaku\KK2094\Result\KK2094.pr_matrix.tsv. [18:08] Saving protein group levels matrix [18:08] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to E:\2_Proteo_Jutaku\KK2094\Result\KK2094.pg_matrix.tsv. [18:08] Saving gene group levels matrix [18:08] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to E:\2_Proteo_Jutaku\KK2094\Result\KK2094.gg_matrix.tsv. [18:08] Saving unique genes levels matrix [18:08] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to E:\2_Proteo_Jutaku\KK2094\Result\KK2094.unique_genes_matrix.tsv. [18:08] Stats report saved to E:\2_Proteo_Jutaku\KK2094\Result\KK2094.stats.tsv Finished