DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks) Compiled on Apr 14 2022 15:31:19 Current date and time: Wed Dec 18 10:03:44 2024 CPU: GenuineIntel Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 Logical CPU cores: 32 diann.exe --f C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_1_SWATH.wiff.dia --f C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_2_SWATH.wiff.dia --f C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_3_SWATH.wiff.dia --f C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_4_SWATH.wiff.dia --f C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_5_SWATH.wiff.dia --f C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_6_SWATH.wiff.dia --f C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_7_SWATH.wiff.dia --f C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_8_SWATH.wiff.dia --f C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_9_SWATH.wiff.dia --lib --threads 16 --verbose 1 --out C:\DIA-NN\1.8.1\report.tsv --qvalue 0.01 --matrices --out-lib C:\DIA-NN\1.8.1\report-lib.tsv --gen-spec-lib --predictor --fasta C:\DIA-NN\1.8.1\fasta\UniProt_Mouse.fasta --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --met-excision --cut K*,R* --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 --unimod4 --reanalyse --relaxed-prot-inf --smart-profiling --peak-center --no-ifs-removal 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 A spectral library will be generated Deep learning will be used to generate a new in silico spectral library from peptides provided Library-free search enabled Min fragment m/z set to 200 Max fragment m/z set to 1800 N-terminal methionine excision enabled In silico digest will involve cuts at K*,R* 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 Cysteine carbamidomethylation enabled as a fixed modification 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 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. Exclusion of fragments shared between heavy and light peptides from quantification is not supported in FASTA digest mode - disabled; to enable, generate an in silico predicted spectral library and analyse with this library 9 files will be processed [0:00] Loading FASTA C:\DIA-NN\1.8.1\fasta\UniProt_Mouse.fasta [0:03] Processing FASTA [0:10] Assembling elution groups [0:15] 3733749 precursors generated [0:15] Gene names missing for some isoforms [0:15] Library contains 17105 proteins, and 16744 genes [0:15] [0:22] [36:27] [39:00] [39:07] [39:10] Saving the library to C:\DIA-NN\1.8.1\report-lib.predicted.speclib [39:15] Initialising library [39:18] First pass: generating a spectral library from DIA data [39:18] File #1/9 [39:18] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_1_SWATH.wiff.dia [39:53] 2689068 library precursors are potentially detectable [39:54] Processing... [40:08] Cannot perform MS1 mass calibration, too few confidently identified precursors [41:15] RT window set to 8.29243 [41:15] Peak width: 2.752 [41:15] Scan window radius set to 6 [41:15] Cannot perform MS1 mass calibration, too few confidently identified precursors [41:15] Recommended MS1 mass accuracy setting: 74.2784 ppm [44:07] Optimised mass accuracy: 22.8684 ppm [51:36] Removing low confidence identifications [51:37] Removing interfering precursors [51:41] Training neural networks: 96577 targets, 61506 decoys [51:48] Number of IDs at 0.01 FDR: 39733 [51:48] Calculating protein q-values [51:49] Number of genes identified at 1% FDR: 4495 (precursor-level), 3883 (protein-level) (inference performed using proteotypic peptides only) [51:49] Quantification [51:51] Quantification information saved to C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_1_SWATH.wiff.dia.quant. [51:52] File #2/9 [51:52] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_2_SWATH.wiff.dia [52:12] 2689068 library precursors are potentially detectable [52:12] Processing... [52:26] Cannot perform MS1 mass calibration, too few confidently identified precursors [53:31] RT window set to 8.23074 [53:31] Cannot perform MS1 mass calibration, too few confidently identified precursors [53:31] Recommended MS1 mass accuracy setting: 68.7252 ppm [60:16] Removing low confidence identifications [60:16] Removing interfering precursors [60:20] Training neural networks: 83111 targets, 52995 decoys [60:25] Number of IDs at 0.01 FDR: 33550 [60:26] Calculating protein q-values [60:26] Number of genes identified at 1% FDR: 3983 (precursor-level), 3497 (protein-level) (inference performed using proteotypic peptides only) [60:26] Quantification [60:28] Quantification information saved to C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_2_SWATH.wiff.dia.quant. [60:29] File #3/9 [60:29] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_3_SWATH.wiff.dia [60:49] 2689068 library precursors are potentially detectable [60:49] Processing... [61:00] Cannot perform MS1 mass calibration, too few confidently identified precursors [62:28] RT window set to 8.1709 [62:28] Cannot perform MS1 mass calibration, too few confidently identified precursors [62:28] Recommended MS1 mass accuracy setting: 73.2675 ppm [69:12] Removing low confidence identifications [69:13] Removing interfering precursors [69:16] Training neural networks: 72343 targets, 44977 decoys [69:21] Number of IDs at 0.01 FDR: 28479 [69:22] Calculating protein q-values [69:22] Number of genes identified at 1% FDR: 3700 (precursor-level), 3242 (protein-level) (inference performed using proteotypic peptides only) [69:22] Quantification [69:24] Quantification information saved to C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_3_SWATH.wiff.dia.quant. [69:25] File #4/9 [69:25] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_4_SWATH.wiff.dia [69:44] 2689068 library precursors are potentially detectable [69:44] Processing... [70:00] Cannot perform MS1 mass calibration, too few confidently identified precursors [71:26] RT window set to 7.82481 [71:26] Cannot perform MS1 mass calibration, too few confidently identified precursors [71:26] Recommended MS1 mass accuracy setting: 65.6698 ppm [77:38] Removing low confidence identifications [77:38] Removing interfering precursors [77:41] Training neural networks: 68549 targets, 42651 decoys [77:46] Number of IDs at 0.01 FDR: 26070 [77:46] Calculating protein q-values [77:47] Number of genes identified at 1% FDR: 3565 (precursor-level), 3163 (protein-level) (inference performed using proteotypic peptides only) [77:47] Quantification [77:49] Quantification information saved to C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_4_SWATH.wiff.dia.quant. [77:50] File #5/9 [77:50] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_5_SWATH.wiff.dia [78:07] 2689068 library precursors are potentially detectable [78:07] Processing... [78:29] Cannot perform MS1 mass calibration, too few confidently identified precursors [79:51] RT window set to 7.91303 [79:51] Cannot perform MS1 mass calibration, too few confidently identified precursors [85:48] Removing low confidence identifications [85:48] Removing interfering precursors [85:51] Training neural networks: 55817 targets, 34973 decoys [85:55] Number of IDs at 0.01 FDR: 22320 [85:55] Calculating protein q-values [85:56] Number of genes identified at 1% FDR: 3159 (precursor-level), 2792 (protein-level) (inference performed using proteotypic peptides only) [85:56] Quantification [85:57] Quantification information saved to C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_5_SWATH.wiff.dia.quant. [85:58] File #6/9 [85:58] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_6_SWATH.wiff.dia [86:13] 2689068 library precursors are potentially detectable [86:14] Processing... [86:31] Cannot perform MS1 mass calibration, too few confidently identified precursors [87:50] RT window set to 8.20452 [87:50] Cannot perform MS1 mass calibration, too few confidently identified precursors [93:44] Removing low confidence identifications [93:44] Removing interfering precursors [93:47] Training neural networks: 56427 targets, 34529 decoys [93:51] Number of IDs at 0.01 FDR: 21288 [93:51] Calculating protein q-values [93:51] Number of genes identified at 1% FDR: 3229 (precursor-level), 2819 (protein-level) (inference performed using proteotypic peptides only) [93:51] Quantification [93:53] Quantification information saved to C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_6_SWATH.wiff.dia.quant. [93:54] File #7/9 [93:54] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_7_SWATH.wiff.dia [94:08] 2689068 library precursors are potentially detectable [94:08] Processing... [94:25] Cannot perform MS1 mass calibration, too few confidently identified precursors [95:45] RT window set to 7.88332 [95:45] Cannot perform MS1 mass calibration, too few confidently identified precursors [101:17] Removing low confidence identifications [101:18] Removing interfering precursors [101:21] Training neural networks: 64317 targets, 38890 decoys [101:25] Number of IDs at 0.01 FDR: 24761 [101:25] Calculating protein q-values [101:26] Number of genes identified at 1% FDR: 3388 (precursor-level), 2967 (protein-level) (inference performed using proteotypic peptides only) [101:26] Quantification [101:27] Quantification information saved to C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_7_SWATH.wiff.dia.quant. [101:28] File #8/9 [101:28] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_8_SWATH.wiff.dia [101:40] 2689068 library precursors are potentially detectable [101:40] Processing... [101:52] Cannot perform MS1 mass calibration, too few confidently identified precursors [103:10] RT window set to 7.82317 [103:10] Cannot perform MS1 mass calibration, too few confidently identified precursors [108:28] Removing low confidence identifications [108:29] Removing interfering precursors [108:32] Training neural networks: 58301 targets, 35626 decoys [108:36] Number of IDs at 0.01 FDR: 23308 [108:36] Calculating protein q-values [108:36] Number of genes identified at 1% FDR: 3335 (precursor-level), 2897 (protein-level) (inference performed using proteotypic peptides only) [108:36] Quantification [108:38] Quantification information saved to C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_8_SWATH.wiff.dia.quant. [108:39] File #9/9 [108:39] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_9_SWATH.wiff.dia [108:50] 2689068 library precursors are potentially detectable [108:50] Processing... [109:10] Cannot perform MS1 mass calibration, too few confidently identified precursors [110:41] RT window set to 7.55342 [110:41] Cannot perform MS1 mass calibration, too few confidently identified precursors [115:55] Removing low confidence identifications [115:55] Removing interfering precursors [115:58] Training neural networks: 54777 targets, 34369 decoys [116:01] Number of IDs at 0.01 FDR: 21857 [116:01] Calculating protein q-values [116:02] Number of genes identified at 1% FDR: 3162 (precursor-level), 2827 (protein-level) (inference performed using proteotypic peptides only) [116:02] Quantification [116:03] Quantification information saved to C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_9_SWATH.wiff.dia.quant. [116:04] Cross-run analysis [116:04] Reading quantification information: 9 files [116:05] Quantifying peptides [116:09] Assembling protein groups [116:11] Quantifying proteins [116:12] Calculating q-values for protein and gene groups [116:12] Calculating global q-values for protein and gene groups [116:12] Writing report [116:28] Report saved to C:\DIA-NN\1.8.1\report-first-pass.tsv. [116:28] Saving precursor levels matrix [116:28] Precursor levels matrix (1% precursor and protein group FDR) saved to C:\DIA-NN\1.8.1\report-first-pass.pr_matrix.tsv. [116:28] Saving protein group levels matrix [116:28] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to C:\DIA-NN\1.8.1\report-first-pass.pg_matrix.tsv. [116:28] Saving gene group levels matrix [116:28] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to C:\DIA-NN\1.8.1\report-first-pass.gg_matrix.tsv. [116:28] Saving unique genes levels matrix [116:28] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to C:\DIA-NN\1.8.1\report-first-pass.unique_genes_matrix.tsv. [116:28] Stats report saved to C:\DIA-NN\1.8.1\report-first-pass.stats.tsv [116:28] Generating spectral library: [116:28] 44086 precursors passing the FDR threshold are to be extracted [116:28] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_1_SWATH.wiff.dia [116:56] 2689068 library precursors are potentially detectable [116:57] 5988 spectra added to the library [116:57] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_2_SWATH.wiff.dia [117:13] 2689068 library precursors are potentially detectable [117:15] 7318 spectra added to the library [117:15] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_3_SWATH.wiff.dia [117:30] 2689068 library precursors are potentially detectable [117:31] 847 spectra added to the library [117:31] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_4_SWATH.wiff.dia [117:45] 2689068 library precursors are potentially detectable [117:46] 840 spectra added to the library [117:46] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_5_SWATH.wiff.dia [117:59] 2689068 library precursors are potentially detectable [118:00] 2000 spectra added to the library [118:00] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_6_SWATH.wiff.dia [118:12] 2689068 library precursors are potentially detectable [118:13] 1600 spectra added to the library [118:13] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_7_SWATH.wiff.dia [118:25] 2689068 library precursors are potentially detectable [118:25] 2435 spectra added to the library [118:26] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_8_SWATH.wiff.dia [118:37] 2689068 library precursors are potentially detectable [118:38] 3064 spectra added to the library [118:38] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_9_SWATH.wiff.dia [118:48] 2689068 library precursors are potentially detectable [118:49] 4356 spectra added to the library [118:50] Saving spectral library to C:\DIA-NN\1.8.1\report-lib.tsv [118:54] 44086 precursors saved [118:54] Loading the generated library and saving it in the .speclib format [118:54] Loading spectral library C:\DIA-NN\1.8.1\report-lib.tsv [118:57] Spectral library loaded: 5255 protein isoforms, 5609 protein groups and 44086 precursors in 35339 elution groups. [118:57] Loading protein annotations from FASTA C:\DIA-NN\1.8.1\fasta\UniProt_Mouse.fasta [118:57] Gene names missing for some isoforms [118:57] Library contains 5255 proteins, and 5211 genes [118:57] Saving the library to C:\DIA-NN\1.8.1\report-lib.tsv.speclib [119:00] Second pass: using the newly created spectral library to reanalyse the data [119:00] File #1/9 [119:00] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_1_SWATH.wiff.dia [119:17] 44086 library precursors are potentially detectable [119:17] Processing... [119:17] RT window set to 2.35087 [119:17] Recommended MS1 mass accuracy setting: 50.817 ppm [119:20] Removing low confidence identifications [119:20] Removing interfering precursors [119:21] Training neural networks: 43358 targets, 43500 decoys [119:24] Number of IDs at 0.01 FDR: 41154 [119:25] Calculating protein q-values [119:25] Number of genes identified at 1% FDR: 4437 (precursor-level), 3723 (protein-level) (inference performed using proteotypic peptides only) [119:25] Quantification [119:27] File #2/9 [119:27] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_2_SWATH.wiff.dia [119:41] 44086 library precursors are potentially detectable [119:41] Processing... [119:42] RT window set to 2.34845 [119:42] Cannot perform MS1 mass calibration, too few confidently identified precursors [119:42] Recommended MS1 mass accuracy setting: 52.9418 ppm [119:44] Removing low confidence identifications [119:44] Removing interfering precursors [119:45] Training neural networks: 43235 targets, 42909 decoys [119:48] Number of IDs at 0.01 FDR: 39845 [119:49] Calculating protein q-values [119:49] Number of genes identified at 1% FDR: 4361 (precursor-level), 3675 (protein-level) (inference performed using proteotypic peptides only) [119:49] Quantification [119:50] File #3/9 [119:50] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_3_SWATH.wiff.dia [120:04] 44086 library precursors are potentially detectable [120:04] Processing... [120:04] RT window set to 2.29867 [120:04] Cannot perform MS1 mass calibration, too few confidently identified precursors [120:04] Recommended MS1 mass accuracy setting: 32.99 ppm [120:07] Removing low confidence identifications [120:07] Removing interfering precursors [120:08] Training neural networks: 43080 targets, 42495 decoys [120:11] Number of IDs at 0.01 FDR: 37864 [120:11] Calculating protein q-values [120:11] Number of genes identified at 1% FDR: 4256 (precursor-level), 3554 (protein-level) (inference performed using proteotypic peptides only) [120:11] Quantification [120:13] File #4/9 [120:13] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_4_SWATH.wiff.dia [120:25] 44086 library precursors are potentially detectable [120:25] Processing... [120:26] Cannot perform MS1 mass calibration, too few confidently identified precursors [120:26] RT window set to 2.35878 [120:26] Cannot perform MS1 mass calibration, too few confidently identified precursors [120:29] Removing low confidence identifications [120:29] Removing interfering precursors [120:30] Training neural networks: 42849 targets, 42045 decoys [120:33] Number of IDs at 0.01 FDR: 36896 [120:33] Calculating protein q-values [120:33] Number of genes identified at 1% FDR: 4233 (precursor-level), 3581 (protein-level) (inference performed using proteotypic peptides only) [120:33] Quantification [120:35] File #5/9 [120:35] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_5_SWATH.wiff.dia [120:46] 44086 library precursors are potentially detectable [120:46] Processing... [120:47] Cannot perform MS1 mass calibration, too few confidently identified precursors [120:48] RT window set to 2.29582 [120:48] Cannot perform MS1 mass calibration, too few confidently identified precursors [120:48] Recommended MS1 mass accuracy setting: 54.5371 ppm [120:50] Removing low confidence identifications [120:50] Removing interfering precursors [120:51] Training neural networks: 42466 targets, 41468 decoys [120:55] Number of IDs at 0.01 FDR: 33829 [120:55] Calculating protein q-values [120:55] Number of genes identified at 1% FDR: 4010 (precursor-level), 3453 (protein-level) (inference performed using proteotypic peptides only) [120:55] Quantification [120:56] File #6/9 [120:56] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_6_SWATH.wiff.dia [121:07] 44086 library precursors are potentially detectable [121:07] Processing... [121:08] Cannot perform MS1 mass calibration, too few confidently identified precursors [121:09] RT window set to 2.30141 [121:09] Cannot perform MS1 mass calibration, too few confidently identified precursors [121:11] Removing low confidence identifications [121:11] Removing interfering precursors [121:12] Training neural networks: 42295 targets, 41345 decoys [121:15] Number of IDs at 0.01 FDR: 31729 [121:15] Calculating protein q-values [121:15] Number of genes identified at 1% FDR: 3948 (precursor-level), 3323 (protein-level) (inference performed using proteotypic peptides only) [121:15] Quantification [121:17] File #7/9 [121:17] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_7_SWATH.wiff.dia [121:26] 44086 library precursors are potentially detectable [121:26] Processing... [121:27] Cannot perform MS1 mass calibration, too few confidently identified precursors [121:28] RT window set to 2.3287 [121:28] Cannot perform MS1 mass calibration, too few confidently identified precursors [121:31] Removing low confidence identifications [121:31] Removing interfering precursors [121:32] Training neural networks: 42626 targets, 41425 decoys [121:35] Number of IDs at 0.01 FDR: 35398 [121:35] Calculating protein q-values [121:35] Number of genes identified at 1% FDR: 4113 (precursor-level), 3476 (protein-level) (inference performed using proteotypic peptides only) [121:35] Quantification [121:36] File #8/9 [121:36] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_8_SWATH.wiff.dia [121:46] 44086 library precursors are potentially detectable [121:46] Processing... [121:46] Cannot perform MS1 mass calibration, too few confidently identified precursors [121:47] RT window set to 2.30181 [121:47] Cannot perform MS1 mass calibration, too few confidently identified precursors [121:50] Removing low confidence identifications [121:50] Removing interfering precursors [121:51] Training neural networks: 42417 targets, 41263 decoys [121:54] Number of IDs at 0.01 FDR: 33659 [121:54] Calculating protein q-values [121:54] Number of genes identified at 1% FDR: 4039 (precursor-level), 3409 (protein-level) (inference performed using proteotypic peptides only) [121:54] Quantification [121:55] File #9/9 [121:55] Loading run C:\Data\Ozaki\241213\Brain\241213_Ozaki_Brain_9_SWATH.wiff.dia [122:04] 44086 library precursors are potentially detectable [122:04] Processing... [122:05] Cannot perform MS1 mass calibration, too few confidently identified precursors [122:06] RT window set to 2.27059 [122:06] Cannot perform MS1 mass calibration, too few confidently identified precursors [122:08] Removing low confidence identifications [122:08] Removing interfering precursors [122:09] Training neural networks: 42306 targets, 40904 decoys [122:12] Number of IDs at 0.01 FDR: 31821 [122:12] Calculating protein q-values [122:13] Number of genes identified at 1% FDR: 3899 (precursor-level), 3257 (protein-level) (inference performed using proteotypic peptides only) [122:13] Quantification [122:13] Cross-run analysis [122:13] Reading quantification information: 9 files [122:14] Quantifying peptides [122:19] Quantifying proteins [122:19] Calculating q-values for protein and gene groups [122:20] Calculating global q-values for protein and gene groups [122:20] Writing report [122:37] Report saved to C:\DIA-NN\1.8.1\report.tsv. [122:37] Saving precursor levels matrix [122:38] Precursor levels matrix (1% precursor and protein group FDR) saved to C:\DIA-NN\1.8.1\report.pr_matrix.tsv. [122:38] Saving protein group levels matrix [122:38] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to C:\DIA-NN\1.8.1\report.pg_matrix.tsv. [122:38] Saving gene group levels matrix [122:38] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to C:\DIA-NN\1.8.1\report.gg_matrix.tsv. [122:38] Saving unique genes levels matrix [122:38] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to C:\DIA-NN\1.8.1\report.unique_genes_matrix.tsv. [122:38] Stats report saved to C:\DIA-NN\1.8.1\report.stats.tsv Finished