DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks) Compiled on Apr 14 2022 15:31:19 Current date and time: Tue Dec 5 12:34:56 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_new\231128machii\Hch1_1_S1.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hch1_1_S2.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hch1_1_S3.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hch1_2_S1.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hch1_2_S2.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hch1_2_S3.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hch1_3_S1.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hch1_3_S2.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hch1_3_S3.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hch2_1_S1.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hch2_1_S2.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hch2_1_S3.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hch2_2_S1.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hch2_2_S2.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hch2_2_S3.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hch2_3_S1.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hch2_3_S2.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hch2_3_S3.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hsa_1_S1.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hsa_1_S2.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hsa_1_S3.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hsa_2_S1.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hsa_2_S2.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hsa_2_S3.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hsa_3_S1.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hsa_3_S2.wiff --f D:\Data\niwa_DIANN_new\231128machii\Hsa_3_S3.wiff --lib --threads 16 --verbose 1 --out D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_report.tsv --qvalue 0.01 --matrices --out-lib D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_library.tsv --gen-spec-lib --predictor --fasta D:\Data\niwa_DIANN_new\fasta\cichlid_protein_ref_210709\Mzeb_uniprot.fasta --fasta-search --min-fr-mz 200 --max-fr-mz 1600 --met-excision --cut K*,R* --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 350 --max-pr-mz 1100 --min-pr-charge 2 --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 1600 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 350 Max precursor m/z set to 1100 Min precursor charge set to 2 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 27 files will be processed [0:00] Loading FASTA D:\Data\niwa_DIANN_new\fasta\cichlid_protein_ref_210709\Mzeb_uniprot.fasta [0:13] Processing FASTA [0:22] Assembling elution groups [0:31] 3348893 precursors generated [0:31] Gene names missing for some isoforms [0:31] Library contains 37263 proteins, and 2060 genes [0:40] [0:46] [38:07] [43:45] [43:51] [43:54] Saving the library to D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_library.predicted.speclib [44:19] Initialising library [44:22] First pass: generating a spectral library from DIA data [44:22] File #1/27 [44:22] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_1_S1.wiff [56:10] 3348893 library precursors are potentially detectable [56:11] Processing... [71:23] RT window set to 3.08949 [71:23] Peak width: 8.792 [71:23] Scan window radius set to 19 [71:23] Recommended MS1 mass accuracy setting: 19.3114 ppm [97:00] Optimised mass accuracy: 26.1855 ppm [112:09] Removing low confidence identifications [112:09] Removing interfering precursors [112:11] Training neural networks: 25060 targets, 16385 decoys [112:14] Number of IDs at 0.01 FDR: 9304 [112:14] Calculating protein q-values [112:14] Number of genes identified at 1% FDR: 197 (precursor-level), 155 (protein-level) (inference performed using proteotypic peptides only) [112:15] Quantification [112:16] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch1_1_S1.wiff.quant. [112:17] File #2/27 [112:17] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_1_S2.wiff [120:16] 3348893 library precursors are potentially detectable [120:17] Processing... [146:03] RT window set to 3.68951 [146:04] Recommended MS1 mass accuracy setting: 21.9762 ppm [165:27] Removing low confidence identifications [165:27] Removing interfering precursors [165:29] Training neural networks: 24359 targets, 16233 decoys [165:32] Number of IDs at 0.01 FDR: 9818 [165:32] Calculating protein q-values [165:33] Number of genes identified at 1% FDR: 212 (precursor-level), 173 (protein-level) (inference performed using proteotypic peptides only) [165:33] Quantification [165:35] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch1_1_S2.wiff.quant. [165:36] File #3/27 [165:36] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_1_S3.wiff [173:41] 3348893 library precursors are potentially detectable [173:41] Processing... [195:31] RT window set to 3.48316 [195:32] Recommended MS1 mass accuracy setting: 22.0431 ppm [213:05] Removing low confidence identifications [213:06] Removing interfering precursors [213:08] Training neural networks: 25067 targets, 16752 decoys [213:10] Number of IDs at 0.01 FDR: 9653 [213:11] Calculating protein q-values [213:11] Number of genes identified at 1% FDR: 201 (precursor-level), 171 (protein-level) (inference performed using proteotypic peptides only) [213:11] Quantification [213:13] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch1_1_S3.wiff.quant. [213:14] File #4/27 [213:14] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_2_S1.wiff [219:22] 3348893 library precursors are potentially detectable [219:22] Processing... [238:16] RT window set to 3.28578 [238:17] Recommended MS1 mass accuracy setting: 18.6637 ppm [253:43] Removing low confidence identifications [253:43] Removing interfering precursors [253:45] Training neural networks: 20879 targets, 14890 decoys [253:47] Number of IDs at 0.01 FDR: 8689 [253:47] Calculating protein q-values [253:48] Number of genes identified at 1% FDR: 190 (precursor-level), 150 (protein-level) (inference performed using proteotypic peptides only) [253:48] Quantification [253:49] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch1_2_S1.wiff.quant. [253:50] File #5/27 [253:50] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_2_S2.wiff [259:42] 3348893 library precursors are potentially detectable [259:42] Processing... [278:52] RT window set to 3.50616 [278:52] Recommended MS1 mass accuracy setting: 26.1456 ppm [295:21] Removing low confidence identifications [295:21] Removing interfering precursors [295:23] Training neural networks: 21494 targets, 15057 decoys [295:25] Number of IDs at 0.01 FDR: 8418 [295:26] Calculating protein q-values [295:26] Number of genes identified at 1% FDR: 179 (precursor-level), 145 (protein-level) (inference performed using proteotypic peptides only) [295:26] Quantification [295:27] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch1_2_S2.wiff.quant. [295:28] File #6/27 [295:28] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_2_S3.wiff [301:57] 3348893 library precursors are potentially detectable [301:57] Processing... [320:27] RT window set to 3.23067 [320:27] Recommended MS1 mass accuracy setting: 27.3152 ppm [334:17] Removing low confidence identifications [334:17] Removing interfering precursors [334:19] Training neural networks: 20755 targets, 14035 decoys [334:21] Number of IDs at 0.01 FDR: 8756 [334:21] Calculating protein q-values [334:22] Number of genes identified at 1% FDR: 192 (precursor-level), 133 (protein-level) (inference performed using proteotypic peptides only) [334:22] Quantification [334:23] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch1_2_S3.wiff.quant. [334:24] File #7/27 [334:24] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_3_S1.wiff [342:30] 3348893 library precursors are potentially detectable [342:31] Processing... [375:47] RT window set to 3.62787 [375:47] Recommended MS1 mass accuracy setting: 28.6833 ppm [394:41] Removing low confidence identifications [394:41] Removing interfering precursors [394:43] Training neural networks: 26073 targets, 17644 decoys [394:46] Number of IDs at 0.01 FDR: 11078 [394:46] Calculating protein q-values [394:47] Number of genes identified at 1% FDR: 219 (precursor-level), 184 (protein-level) (inference performed using proteotypic peptides only) [394:47] Quantification [394:49] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch1_3_S1.wiff.quant. [394:50] File #8/27 [394:50] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_3_S2.wiff [403:12] 3348893 library precursors are potentially detectable [403:12] Processing... [427:11] RT window set to 3.43657 [427:11] Recommended MS1 mass accuracy setting: 26.7712 ppm [444:11] Removing low confidence identifications [444:12] Removing interfering precursors [444:14] Training neural networks: 25955 targets, 17703 decoys [444:17] Number of IDs at 0.01 FDR: 10658 [444:17] Calculating protein q-values [444:17] Number of genes identified at 1% FDR: 220 (precursor-level), 159 (protein-level) (inference performed using proteotypic peptides only) [444:17] Quantification [444:19] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch1_3_S2.wiff.quant. [444:20] File #9/27 [444:20] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_3_S3.wiff [452:37] 3348893 library precursors are potentially detectable [452:37] Processing... [469:27] RT window set to 3.52685 [469:28] Recommended MS1 mass accuracy setting: 25.0317 ppm [486:21] Removing low confidence identifications [486:21] Removing interfering precursors [486:23] Training neural networks: 27179 targets, 18397 decoys [486:26] Number of IDs at 0.01 FDR: 10875 [486:27] Calculating protein q-values [486:27] Number of genes identified at 1% FDR: 221 (precursor-level), 189 (protein-level) (inference performed using proteotypic peptides only) [486:27] Quantification [486:29] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch1_3_S3.wiff.quant. [486:30] File #10/27 [486:30] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_1_S1.wiff [495:20] 3348893 library precursors are potentially detectable [495:20] Processing... [516:32] RT window set to 3.69431 [516:33] Recommended MS1 mass accuracy setting: 23.5754 ppm [534:14] Removing low confidence identifications [534:14] Removing interfering precursors [534:16] Training neural networks: 29276 targets, 20537 decoys [534:19] Number of IDs at 0.01 FDR: 11321 [534:20] Calculating protein q-values [534:20] Number of genes identified at 1% FDR: 240 (precursor-level), 206 (protein-level) (inference performed using proteotypic peptides only) [534:20] Quantification [534:22] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch2_1_S1.wiff.quant. [534:23] File #11/27 [534:23] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_1_S2.wiff [554:41] 3348893 library precursors are potentially detectable [554:42] Processing... [572:35] RT window set to 3.47266 [572:35] Recommended MS1 mass accuracy setting: 23.5841 ppm [589:34] Removing low confidence identifications [589:35] Removing interfering precursors [589:37] Training neural networks: 28085 targets, 19434 decoys [589:40] Number of IDs at 0.01 FDR: 11602 [589:40] Calculating protein q-values [589:41] Number of genes identified at 1% FDR: 246 (precursor-level), 213 (protein-level) (inference performed using proteotypic peptides only) [589:41] Quantification [589:43] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch2_1_S2.wiff.quant. [589:44] File #12/27 [589:44] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_1_S3.wiff [599:58] 3348893 library precursors are potentially detectable [599:58] Processing... [614:35] RT window set to 3.48675 [614:36] Recommended MS1 mass accuracy setting: 26.8101 ppm [630:58] Removing low confidence identifications [630:58] Removing interfering precursors [631:00] Training neural networks: 27834 targets, 19560 decoys [631:03] Number of IDs at 0.01 FDR: 11455 [631:03] Calculating protein q-values [631:04] Number of genes identified at 1% FDR: 246 (precursor-level), 192 (protein-level) (inference performed using proteotypic peptides only) [631:04] Quantification [631:06] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch2_1_S3.wiff.quant. [631:07] File #13/27 [631:07] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_2_S1.wiff [641:15] 3348893 library precursors are potentially detectable [641:15] Processing... [657:49] RT window set to 3.41342 [657:50] Recommended MS1 mass accuracy setting: 22.9944 ppm [673:58] Removing low confidence identifications [673:58] Removing interfering precursors [674:01] Training neural networks: 33626 targets, 22375 decoys [674:04] Number of IDs at 0.01 FDR: 12685 [674:04] Calculating protein q-values [674:05] Number of genes identified at 1% FDR: 258 (precursor-level), 217 (protein-level) (inference performed using proteotypic peptides only) [674:05] Quantification [674:07] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch2_2_S1.wiff.quant. [674:09] File #14/27 [674:09] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_2_S2.wiff [683:57] 3348893 library precursors are potentially detectable [683:57] Processing... [699:34] RT window set to 3.65993 [699:35] Recommended MS1 mass accuracy setting: 21.9068 ppm [716:42] Removing low confidence identifications [716:42] Removing interfering precursors [716:45] Training neural networks: 29712 targets, 20752 decoys [716:48] Number of IDs at 0.01 FDR: 12665 [716:48] Calculating protein q-values [716:49] Number of genes identified at 1% FDR: 269 (precursor-level), 209 (protein-level) (inference performed using proteotypic peptides only) [716:49] Quantification [716:51] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch2_2_S2.wiff.quant. [716:52] File #15/27 [716:52] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_2_S3.wiff [726:57] 3348893 library precursors are potentially detectable [726:57] Processing... [746:10] RT window set to 3.66385 [746:10] Recommended MS1 mass accuracy setting: 24.6772 ppm [764:24] Removing low confidence identifications [764:24] Removing interfering precursors [764:27] Training neural networks: 29197 targets, 19739 decoys [764:30] Number of IDs at 0.01 FDR: 12067 [764:30] Calculating protein q-values [764:31] Number of genes identified at 1% FDR: 248 (precursor-level), 214 (protein-level) (inference performed using proteotypic peptides only) [764:31] Quantification [764:33] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch2_2_S3.wiff.quant. [764:35] File #16/27 [764:35] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_3_S1.wiff [773:11] 3348893 library precursors are potentially detectable [773:11] Processing... [793:55] RT window set to 3.47247 [793:55] Recommended MS1 mass accuracy setting: 21.5614 ppm [810:10] Removing low confidence identifications [810:11] Removing interfering precursors [810:13] Training neural networks: 24968 targets, 17336 decoys [810:15] Number of IDs at 0.01 FDR: 10352 [810:15] Calculating protein q-values [810:16] Number of genes identified at 1% FDR: 224 (precursor-level), 167 (protein-level) (inference performed using proteotypic peptides only) [810:16] Quantification [810:18] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch2_3_S1.wiff.quant. [810:19] File #17/27 [810:19] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_3_S2.wiff [818:35] 3348893 library precursors are potentially detectable [818:35] Processing... [835:22] RT window set to 3.71162 [835:22] Recommended MS1 mass accuracy setting: 23.8181 ppm [852:25] Removing low confidence identifications [852:25] Removing interfering precursors [852:27] Training neural networks: 24802 targets, 17183 decoys [852:30] Number of IDs at 0.01 FDR: 10167 [852:30] Calculating protein q-values [852:31] Number of genes identified at 1% FDR: 215 (precursor-level), 159 (protein-level) (inference performed using proteotypic peptides only) [852:31] Quantification [852:32] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch2_3_S2.wiff.quant. [852:34] File #18/27 [852:34] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_3_S3.wiff [860:49] 3348893 library precursors are potentially detectable [860:50] Processing... [877:57] RT window set to 3.47381 [877:57] Recommended MS1 mass accuracy setting: 26.0163 ppm [894:59] Removing low confidence identifications [894:59] Removing interfering precursors [895:01] Training neural networks: 24985 targets, 17119 decoys [895:04] Number of IDs at 0.01 FDR: 10213 [895:05] Calculating protein q-values [895:05] Number of genes identified at 1% FDR: 216 (precursor-level), 179 (protein-level) (inference performed using proteotypic peptides only) [895:05] Quantification [895:07] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hch2_3_S3.wiff.quant. [895:08] File #19/27 [895:08] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_1_S1.wiff [903:32] 3348893 library precursors are potentially detectable [903:32] Processing... [915:33] RT window set to 3.52283 [915:34] Recommended MS1 mass accuracy setting: 20.7359 ppm [931:35] Removing low confidence identifications [931:35] Removing interfering precursors [931:38] Training neural networks: 31252 targets, 23120 decoys [931:41] Number of IDs at 0.01 FDR: 13540 [931:42] Calculating protein q-values [931:42] Number of genes identified at 1% FDR: 277 (precursor-level), 245 (protein-level) (inference performed using proteotypic peptides only) [931:42] Quantification [931:44] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hsa_1_S1.wiff.quant. [931:45] File #20/27 [931:45] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_1_S2.wiff [939:59] 3348893 library precursors are potentially detectable [939:59] Processing... [951:57] RT window set to 3.56798 [951:57] Recommended MS1 mass accuracy setting: 26.2406 ppm [968:10] Removing low confidence identifications [968:10] Removing interfering precursors [968:13] Training neural networks: 32383 targets, 23261 decoys [968:16] Number of IDs at 0.01 FDR: 13593 [968:17] Calculating protein q-values [968:17] Number of genes identified at 1% FDR: 293 (precursor-level), 242 (protein-level) (inference performed using proteotypic peptides only) [968:17] Quantification [968:19] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hsa_1_S2.wiff.quant. [968:21] File #21/27 [968:21] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_1_S3.wiff [977:07] 3348893 library precursors are potentially detectable [977:07] Processing... [991:25] RT window set to 3.55113 [991:25] Recommended MS1 mass accuracy setting: 31.1081 ppm [1008:00] Removing low confidence identifications [1008:00] Removing interfering precursors [1008:03] Training neural networks: 31902 targets, 22143 decoys [1008:06] Number of IDs at 0.01 FDR: 13074 [1008:06] Calculating protein q-values [1008:07] Number of genes identified at 1% FDR: 283 (precursor-level), 238 (protein-level) (inference performed using proteotypic peptides only) [1008:07] Quantification [1008:08] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hsa_1_S3.wiff.quant. [1008:10] File #22/27 [1008:10] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_2_S1.wiff [1016:35] 3348893 library precursors are potentially detectable [1016:35] Processing... [1032:46] RT window set to 3.4947 [1032:46] Recommended MS1 mass accuracy setting: 19.9813 ppm [1048:16] Removing low confidence identifications [1048:16] Removing interfering precursors [1048:18] Training neural networks: 35351 targets, 24173 decoys [1048:22] Number of IDs at 0.01 FDR: 13765 [1048:23] Calculating protein q-values [1048:23] Number of genes identified at 1% FDR: 276 (precursor-level), 240 (protein-level) (inference performed using proteotypic peptides only) [1048:23] Quantification [1048:25] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hsa_2_S1.wiff.quant. [1048:26] File #23/27 [1048:26] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_2_S2.wiff [1056:23] 3348893 library precursors are potentially detectable [1056:23] Processing... [1068:09] RT window set to 3.57983 [1068:10] Recommended MS1 mass accuracy setting: 24.5505 ppm [1084:36] Removing low confidence identifications [1084:37] Removing interfering precursors [1084:39] Training neural networks: 33244 targets, 23305 decoys [1084:43] Number of IDs at 0.01 FDR: 13287 [1084:43] Calculating protein q-values [1084:43] Number of genes identified at 1% FDR: 274 (precursor-level), 229 (protein-level) (inference performed using proteotypic peptides only) [1084:43] Quantification [1084:45] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hsa_2_S2.wiff.quant. [1084:46] File #24/27 [1084:46] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_2_S3.wiff [1093:07] 3348893 library precursors are potentially detectable [1093:08] Processing... [1107:36] RT window set to 3.65379 [1107:36] Recommended MS1 mass accuracy setting: 30.9434 ppm [1124:50] Removing low confidence identifications [1124:50] Removing interfering precursors [1124:52] Training neural networks: 30328 targets, 22378 decoys [1124:56] Number of IDs at 0.01 FDR: 12801 [1124:56] Calculating protein q-values [1124:57] Number of genes identified at 1% FDR: 271 (precursor-level), 230 (protein-level) (inference performed using proteotypic peptides only) [1124:57] Quantification [1124:58] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hsa_2_S3.wiff.quant. [1125:00] File #25/27 [1125:00] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_3_S1.wiff [1133:56] 3348893 library precursors are potentially detectable [1133:57] Processing... [1146:45] RT window set to 3.68044 [1146:45] Recommended MS1 mass accuracy setting: 29.7951 ppm [1164:06] Removing low confidence identifications [1164:07] Removing interfering precursors [1164:09] Training neural networks: 36076 targets, 24622 decoys [1164:13] Number of IDs at 0.01 FDR: 14316 [1164:13] Calculating protein q-values [1164:14] Number of genes identified at 1% FDR: 283 (precursor-level), 247 (protein-level) (inference performed using proteotypic peptides only) [1164:14] Quantification [1164:16] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hsa_3_S1.wiff.quant. [1164:18] File #26/27 [1164:18] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_3_S2.wiff [1172:57] 3348893 library precursors are potentially detectable [1172:58] Processing... [1191:31] RT window set to 3.63732 [1191:31] Recommended MS1 mass accuracy setting: 33.9257 ppm [1209:45] Removing low confidence identifications [1209:46] Removing interfering precursors [1209:48] Training neural networks: 34223 targets, 24138 decoys [1209:52] Number of IDs at 0.01 FDR: 13807 [1209:52] Calculating protein q-values [1209:53] Number of genes identified at 1% FDR: 293 (precursor-level), 233 (protein-level) (inference performed using proteotypic peptides only) [1209:53] Quantification [1209:54] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hsa_3_S2.wiff.quant. [1209:56] File #27/27 [1209:56] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_3_S3.wiff [1218:41] 3348893 library precursors are potentially detectable [1218:41] Processing... [1231:38] RT window set to 3.60079 [1231:38] Recommended MS1 mass accuracy setting: 25.7429 ppm [1249:06] Removing low confidence identifications [1249:06] Removing interfering precursors [1249:09] Training neural networks: 34957 targets, 24210 decoys [1249:13] Number of IDs at 0.01 FDR: 13938 [1249:13] Calculating protein q-values [1249:13] Number of genes identified at 1% FDR: 293 (precursor-level), 261 (protein-level) (inference performed using proteotypic peptides only) [1249:13] Quantification [1249:15] Quantification information saved to D:\Data\niwa_DIANN_new\231128machii\Hsa_3_S3.wiff.quant. [1249:17] Cross-run analysis [1249:17] Reading quantification information: 27 files [1249:20] Quantifying peptides [1249:27] Assembling protein groups [1249:30] Quantifying proteins [1249:30] Calculating q-values for protein and gene groups [1249:31] Calculating global q-values for protein and gene groups [1249:31] Writing report [1249:52] Report saved to D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_report-first-pass.tsv. [1249:52] Saving precursor levels matrix [1249:53] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_report-first-pass.pr_matrix.tsv. [1249:53] Saving protein group levels matrix [1249:53] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_report-first-pass.pg_matrix.tsv. [1249:53] Saving gene group levels matrix [1249:53] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_report-first-pass.gg_matrix.tsv. [1249:53] Saving unique genes levels matrix [1249:53] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_report-first-pass.unique_genes_matrix.tsv. [1249:53] Stats report saved to D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_report-first-pass.stats.tsv [1249:53] Generating spectral library: [1249:53] 20070 precursors passing the FDR threshold are to be extracted [1249:53] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_1_S1.wiff [1257:51] 3348893 library precursors are potentially detectable [1257:52] 41 spectra added to the library [1257:52] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_1_S2.wiff [1265:29] 3348893 library precursors are potentially detectable [1265:30] 122 spectra added to the library [1265:30] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_1_S3.wiff [1273:08] 3348893 library precursors are potentially detectable [1273:09] 220 spectra added to the library [1273:09] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_2_S1.wiff [1279:04] 3348893 library precursors are potentially detectable [1279:05] 171 spectra added to the library [1279:05] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_2_S2.wiff [1284:32] 3348893 library precursors are potentially detectable [1284:33] 103 spectra added to the library [1284:33] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_2_S3.wiff [1290:57] 3348893 library precursors are potentially detectable [1290:57] 49 spectra added to the library [1290:58] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_3_S1.wiff [1298:41] 3348893 library precursors are potentially detectable [1298:41] 173 spectra added to the library [1298:42] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_3_S2.wiff [1306:30] 3348893 library precursors are potentially detectable [1306:30] 78 spectra added to the library [1306:31] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_3_S3.wiff [1314:31] 3348893 library precursors are potentially detectable [1314:31] 228 spectra added to the library [1314:32] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_1_S1.wiff [1322:54] 3348893 library precursors are potentially detectable [1322:55] 325 spectra added to the library [1322:55] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_1_S2.wiff [1331:23] 3348893 library precursors are potentially detectable [1331:24] 121 spectra added to the library [1331:24] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_1_S3.wiff [1339:45] 3348893 library precursors are potentially detectable [1339:46] 56 spectra added to the library [1339:46] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_2_S1.wiff [1349:36] 3348893 library precursors are potentially detectable [1349:37] 509 spectra added to the library [1349:37] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_2_S2.wiff [1359:10] 3348893 library precursors are potentially detectable [1359:10] 141 spectra added to the library [1359:11] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_2_S3.wiff [1368:43] 3348893 library precursors are potentially detectable [1368:43] 30 spectra added to the library [1368:44] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_3_S1.wiff [1376:35] 3348893 library precursors are potentially detectable [1376:36] 169 spectra added to the library [1376:36] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_3_S2.wiff [1384:26] 3348893 library precursors are potentially detectable [1384:27] 1455 spectra added to the library [1384:27] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_3_S3.wiff [1392:30] 3348893 library precursors are potentially detectable [1392:31] 706 spectra added to the library [1392:31] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_1_S1.wiff [1400:24] 3348893 library precursors are potentially detectable [1400:25] 1608 spectra added to the library [1400:25] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_1_S2.wiff [1408:00] 3348893 library precursors are potentially detectable [1408:01] 1013 spectra added to the library [1408:01] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_1_S3.wiff [1416:09] 3348893 library precursors are potentially detectable [1416:10] 72 spectra added to the library [1416:10] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_2_S1.wiff [1424:12] 3348893 library precursors are potentially detectable [1424:12] 1262 spectra added to the library [1424:13] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_2_S2.wiff [1431:51] 3348893 library precursors are potentially detectable [1431:51] 329 spectra added to the library [1431:51] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_2_S3.wiff [1439:36] 3348893 library precursors are potentially detectable [1439:36] 507 spectra added to the library [1439:37] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_3_S1.wiff [1447:54] 3348893 library precursors are potentially detectable [1447:54] 373 spectra added to the library [1447:55] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_3_S2.wiff [1456:17] 3348893 library precursors are potentially detectable [1456:17] 419 spectra added to the library [1456:18] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_3_S3.wiff [1464:34] 3348893 library precursors are potentially detectable [1464:34] 290 spectra added to the library [1464:35] Saving spectral library to D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_library.tsv [1464:39] 20070 precursors saved [1464:39] Loading the generated library and saving it in the .speclib format [1464:39] Loading spectral library D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_library.tsv [1464:40] Spectral library loaded: 7079 protein isoforms, 4831 protein groups and 20070 precursors in 16605 elution groups. [1464:40] Loading protein annotations from FASTA D:\Data\niwa_DIANN_new\fasta\cichlid_protein_ref_210709\Mzeb_uniprot.fasta [1464:42] Gene names missing for some isoforms [1464:42] Library contains 7079 proteins, and 378 genes [1464:42] Saving the library to D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_library.tsv.speclib [1464:45] Second pass: using the newly created spectral library to reanalyse the data [1464:45] File #1/27 [1464:45] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_1_S1.wiff [1472:30] 20070 library precursors are potentially detectable [1472:30] Processing... [1472:37] RT window set to 1.60727 [1472:37] Recommended MS1 mass accuracy setting: 22.6536 ppm [1472:41] Removing low confidence identifications [1472:41] Removing interfering precursors [1472:42] Training neural networks: 19509 targets, 18764 decoys [1472:44] Number of IDs at 0.01 FDR: 16012 [1472:44] Calculating protein q-values [1472:44] Number of genes identified at 1% FDR: 314 (precursor-level), 257 (protein-level) (inference performed using proteotypic peptides only) [1472:44] Quantification [1472:45] File #2/27 [1472:45] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_1_S2.wiff [1480:27] 20070 library precursors are potentially detectable [1480:27] Processing... [1480:34] RT window set to 1.62888 [1480:34] Recommended MS1 mass accuracy setting: 27.448 ppm [1480:38] Removing low confidence identifications [1480:38] Removing interfering precursors [1480:38] Training neural networks: 19585 targets, 18828 decoys [1480:40] Number of IDs at 0.01 FDR: 16286 [1480:40] Calculating protein q-values [1480:41] Number of genes identified at 1% FDR: 308 (precursor-level), 255 (protein-level) (inference performed using proteotypic peptides only) [1480:41] Quantification [1480:42] File #3/27 [1480:42] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_1_S3.wiff [1488:22] 20070 library precursors are potentially detectable [1488:22] Processing... [1488:29] RT window set to 1.62813 [1488:29] Recommended MS1 mass accuracy setting: 25.9428 ppm [1488:33] Removing low confidence identifications [1488:33] Removing interfering precursors [1488:33] Training neural networks: 19553 targets, 18886 decoys [1488:35] Number of IDs at 0.01 FDR: 16264 [1488:35] Calculating protein q-values [1488:35] Number of genes identified at 1% FDR: 320 (precursor-level), 239 (protein-level) (inference performed using proteotypic peptides only) [1488:35] Quantification [1488:37] File #4/27 [1488:37] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_2_S1.wiff [1494:47] 20070 library precursors are potentially detectable [1494:47] Processing... [1494:53] RT window set to 1.59566 [1494:53] Recommended MS1 mass accuracy setting: 22.8507 ppm [1494:57] Removing low confidence identifications [1494:57] Removing interfering precursors [1494:57] Training neural networks: 19333 targets, 17981 decoys [1494:59] Number of IDs at 0.01 FDR: 15041 [1494:59] Calculating protein q-values [1494:59] Number of genes identified at 1% FDR: 290 (precursor-level), 223 (protein-level) (inference performed using proteotypic peptides only) [1494:59] Quantification [1495:00] File #5/27 [1495:00] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_2_S2.wiff [1500:29] 20070 library precursors are potentially detectable [1500:29] Processing... [1500:35] RT window set to 1.59549 [1500:35] Recommended MS1 mass accuracy setting: 29.4007 ppm [1500:39] Removing low confidence identifications [1500:39] Removing interfering precursors [1500:40] Training neural networks: 19420 targets, 17951 decoys [1500:41] Number of IDs at 0.01 FDR: 15478 [1500:41] Calculating protein q-values [1500:41] Number of genes identified at 1% FDR: 302 (precursor-level), 230 (protein-level) (inference performed using proteotypic peptides only) [1500:41] Quantification [1500:42] File #6/27 [1500:42] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_2_S3.wiff [1507:00] 20070 library precursors are potentially detectable [1507:00] Processing... [1507:06] RT window set to 1.5737 [1507:06] Recommended MS1 mass accuracy setting: 32.7153 ppm [1507:10] Removing low confidence identifications [1507:10] Removing interfering precursors [1507:11] Training neural networks: 19381 targets, 17830 decoys [1507:12] Number of IDs at 0.01 FDR: 15470 [1507:13] Calculating protein q-values [1507:13] Number of genes identified at 1% FDR: 297 (precursor-level), 238 (protein-level) (inference performed using proteotypic peptides only) [1507:13] Quantification [1507:14] File #7/27 [1507:14] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_3_S1.wiff [1514:57] 20070 library precursors are potentially detectable [1514:57] Processing... [1515:04] RT window set to 1.66558 [1515:04] Recommended MS1 mass accuracy setting: 32.8498 ppm [1515:08] Removing low confidence identifications [1515:08] Removing interfering precursors [1515:09] Training neural networks: 19713 targets, 19080 decoys [1515:11] Number of IDs at 0.01 FDR: 17228 [1515:11] Calculating protein q-values [1515:11] Number of genes identified at 1% FDR: 313 (precursor-level), 290 (protein-level) (inference performed using proteotypic peptides only) [1515:11] Quantification [1515:13] File #8/27 [1515:13] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_3_S2.wiff [1522:57] 20070 library precursors are potentially detectable [1522:57] Processing... [1523:05] RT window set to 1.64199 [1523:05] Recommended MS1 mass accuracy setting: 31.9176 ppm [1523:09] Removing low confidence identifications [1523:09] Removing interfering precursors [1523:09] Training neural networks: 19668 targets, 19019 decoys [1523:11] Number of IDs at 0.01 FDR: 17313 [1523:11] Calculating protein q-values [1523:11] Number of genes identified at 1% FDR: 319 (precursor-level), 250 (protein-level) (inference performed using proteotypic peptides only) [1523:11] Quantification [1523:13] File #9/27 [1523:13] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch1_3_S3.wiff [1531:01] 20070 library precursors are potentially detectable [1531:01] Processing... [1531:06] RT window set to 1.63656 [1531:06] Recommended MS1 mass accuracy setting: 27.5376 ppm [1531:09] Removing low confidence identifications [1531:09] Removing interfering precursors [1531:10] Training neural networks: 19696 targets, 19058 decoys [1531:12] Number of IDs at 0.01 FDR: 17369 [1531:12] Calculating protein q-values [1531:12] Number of genes identified at 1% FDR: 309 (precursor-level), 264 (protein-level) (inference performed using proteotypic peptides only) [1531:12] Quantification [1531:14] File #10/27 [1531:14] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_1_S1.wiff [1539:33] 20070 library precursors are potentially detectable [1539:33] Processing... [1539:38] RT window set to 1.60401 [1539:38] Recommended MS1 mass accuracy setting: 27.6624 ppm [1539:41] Removing low confidence identifications [1539:41] Removing interfering precursors [1539:42] Training neural networks: 19590 targets, 18963 decoys [1539:44] Number of IDs at 0.01 FDR: 17709 [1539:44] Calculating protein q-values [1539:44] Number of genes identified at 1% FDR: 322 (precursor-level), 308 (protein-level) (inference performed using proteotypic peptides only) [1539:44] Quantification [1539:46] File #11/27 [1539:46] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_1_S2.wiff [1548:06] 20070 library precursors are potentially detectable [1548:06] Processing... [1548:11] RT window set to 1.5443 [1548:11] Recommended MS1 mass accuracy setting: 28.8096 ppm [1548:15] Removing low confidence identifications [1548:15] Removing interfering precursors [1548:15] Training neural networks: 19585 targets, 18855 decoys [1548:17] Number of IDs at 0.01 FDR: 17623 [1548:17] Calculating protein q-values [1548:17] Number of genes identified at 1% FDR: 330 (precursor-level), 278 (protein-level) (inference performed using proteotypic peptides only) [1548:17] Quantification [1548:19] File #12/27 [1548:19] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_1_S3.wiff [1556:51] 20070 library precursors are potentially detectable [1556:51] Processing... [1556:54] RT window set to 1.58275 [1556:54] Recommended MS1 mass accuracy setting: 29.1837 ppm [1556:57] Removing low confidence identifications [1556:57] Removing interfering precursors [1556:58] Training neural networks: 19600 targets, 18976 decoys [1557:00] Number of IDs at 0.01 FDR: 17662 [1557:00] Calculating protein q-values [1557:00] Number of genes identified at 1% FDR: 324 (precursor-level), 280 (protein-level) (inference performed using proteotypic peptides only) [1557:00] Quantification [1557:02] File #13/27 [1557:02] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_2_S1.wiff [1566:50] 20070 library precursors are potentially detectable [1566:50] Processing... [1566:55] RT window set to 1.60864 [1566:55] Recommended MS1 mass accuracy setting: 26.6601 ppm [1566:59] Removing low confidence identifications [1566:59] Removing interfering precursors [1566:59] Training neural networks: 19711 targets, 19266 decoys [1567:01] Number of IDs at 0.01 FDR: 18144 [1567:01] Calculating protein q-values [1567:01] Number of genes identified at 1% FDR: 327 (precursor-level), 244 (protein-level) (inference performed using proteotypic peptides only) [1567:01] Quantification [1567:03] File #14/27 [1567:03] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_2_S2.wiff [1576:32] 20070 library precursors are potentially detectable [1576:32] Processing... [1576:38] RT window set to 1.6017 [1576:38] Recommended MS1 mass accuracy setting: 25.9648 ppm [1576:41] Removing low confidence identifications [1576:41] Removing interfering precursors [1576:42] Training neural networks: 19659 targets, 19250 decoys [1576:44] Number of IDs at 0.01 FDR: 17923 [1576:44] Calculating protein q-values [1576:44] Number of genes identified at 1% FDR: 330 (precursor-level), 256 (protein-level) (inference performed using proteotypic peptides only) [1576:44] Quantification [1576:46] File #15/27 [1576:46] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_2_S3.wiff [1586:57] 20070 library precursors are potentially detectable [1586:57] Processing... [1587:03] RT window set to 1.58289 [1587:03] Recommended MS1 mass accuracy setting: 28.3735 ppm [1587:06] Removing low confidence identifications [1587:06] Removing interfering precursors [1587:07] Training neural networks: 19653 targets, 19234 decoys [1587:09] Number of IDs at 0.01 FDR: 17855 [1587:10] Calculating protein q-values [1587:10] Number of genes identified at 1% FDR: 327 (precursor-level), 256 (protein-level) (inference performed using proteotypic peptides only) [1587:10] Quantification [1587:12] File #16/27 [1587:12] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_3_S1.wiff [1595:22] 20070 library precursors are potentially detectable [1595:22] Processing... [1595:30] RT window set to 1.64412 [1595:30] Recommended MS1 mass accuracy setting: 25.8007 ppm [1595:34] Removing low confidence identifications [1595:34] Removing interfering precursors [1595:35] Training neural networks: 19648 targets, 18947 decoys [1595:37] Number of IDs at 0.01 FDR: 17036 [1595:37] Calculating protein q-values [1595:37] Number of genes identified at 1% FDR: 311 (precursor-level), 245 (protein-level) (inference performed using proteotypic peptides only) [1595:37] Quantification [1595:39] File #17/27 [1595:39] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_3_S2.wiff [1603:39] 20070 library precursors are potentially detectable [1603:39] Processing... [1603:46] RT window set to 1.63156 [1603:46] Recommended MS1 mass accuracy setting: 27.544 ppm [1603:50] Removing low confidence identifications [1603:50] Removing interfering precursors [1603:51] Training neural networks: 19650 targets, 18903 decoys [1603:53] Number of IDs at 0.01 FDR: 17131 [1603:53] Calculating protein q-values [1603:53] Number of genes identified at 1% FDR: 322 (precursor-level), 241 (protein-level) (inference performed using proteotypic peptides only) [1603:53] Quantification [1603:55] File #18/27 [1603:55] Loading run D:\Data\niwa_DIANN_new\231128machii\Hch2_3_S3.wiff [1612:20] 20070 library precursors are potentially detectable [1612:20] Processing... [1612:27] RT window set to 1.61599 [1612:27] Recommended MS1 mass accuracy setting: 28.7079 ppm [1612:31] Removing low confidence identifications [1612:31] Removing interfering precursors [1612:32] Training neural networks: 19646 targets, 18966 decoys [1612:34] Number of IDs at 0.01 FDR: 17008 [1612:34] Calculating protein q-values [1612:34] Number of genes identified at 1% FDR: 312 (precursor-level), 247 (protein-level) (inference performed using proteotypic peptides only) [1612:34] Quantification [1612:36] File #19/27 [1612:36] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_1_S1.wiff [1620:53] 20070 library precursors are potentially detectable [1620:53] Processing... [1620:55] RT window set to 1.59745 [1620:55] Recommended MS1 mass accuracy setting: 22.2906 ppm [1620:59] Removing low confidence identifications [1620:59] Removing interfering precursors [1621:00] Training neural networks: 19601 targets, 18865 decoys [1621:02] Number of IDs at 0.01 FDR: 17973 [1621:02] Calculating protein q-values [1621:02] Number of genes identified at 1% FDR: 331 (precursor-level), 279 (protein-level) (inference performed using proteotypic peptides only) [1621:02] Quantification [1621:03] File #20/27 [1621:03] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_1_S2.wiff [1628:51] 20070 library precursors are potentially detectable [1628:51] Processing... [1628:53] RT window set to 1.5819 [1628:53] Recommended MS1 mass accuracy setting: 28.3111 ppm [1628:57] Removing low confidence identifications [1628:57] Removing interfering precursors [1628:57] Training neural networks: 19601 targets, 18812 decoys [1628:59] Number of IDs at 0.01 FDR: 18007 [1629:00] Calculating protein q-values [1629:00] Number of genes identified at 1% FDR: 333 (precursor-level), 295 (protein-level) (inference performed using proteotypic peptides only) [1629:00] Quantification [1629:01] File #21/27 [1629:01] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_1_S3.wiff [1637:25] 20070 library precursors are potentially detectable [1637:25] Processing... [1637:27] RT window set to 1.51175 [1637:27] Recommended MS1 mass accuracy setting: 34.3804 ppm [1637:30] Removing low confidence identifications [1637:30] Removing interfering precursors [1637:31] Training neural networks: 19529 targets, 18721 decoys [1637:33] Number of IDs at 0.01 FDR: 17790 [1637:33] Calculating protein q-values [1637:33] Number of genes identified at 1% FDR: 332 (precursor-level), 260 (protein-level) (inference performed using proteotypic peptides only) [1637:33] Quantification [1637:35] File #22/27 [1637:35] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_2_S1.wiff [1645:32] 20070 library precursors are potentially detectable [1645:32] Processing... [1645:37] RT window set to 1.64576 [1645:37] Recommended MS1 mass accuracy setting: 26.5081 ppm [1645:41] Removing low confidence identifications [1645:41] Removing interfering precursors [1645:41] Training neural networks: 19680 targets, 19104 decoys [1645:43] Number of IDs at 0.01 FDR: 18030 [1645:44] Calculating protein q-values [1645:44] Number of genes identified at 1% FDR: 337 (precursor-level), 300 (protein-level) (inference performed using proteotypic peptides only) [1645:44] Quantification [1645:45] File #23/27 [1645:45] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_2_S2.wiff [1653:22] 20070 library precursors are potentially detectable [1653:22] Processing... [1653:24] RT window set to 1.63964 [1653:24] Recommended MS1 mass accuracy setting: 27.302 ppm [1653:28] Removing low confidence identifications [1653:28] Removing interfering precursors [1653:28] Training neural networks: 19675 targets, 19056 decoys [1653:30] Number of IDs at 0.01 FDR: 17956 [1653:31] Calculating protein q-values [1653:31] Number of genes identified at 1% FDR: 339 (precursor-level), 291 (protein-level) (inference performed using proteotypic peptides only) [1653:31] Quantification [1653:32] File #24/27 [1653:32] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_2_S3.wiff [1661:21] 20070 library precursors are potentially detectable [1661:21] Processing... [1661:23] RT window set to 1.58125 [1661:23] Recommended MS1 mass accuracy setting: 31.4595 ppm [1661:27] Removing low confidence identifications [1661:27] Removing interfering precursors [1661:28] Training neural networks: 19634 targets, 19058 decoys [1661:30] Number of IDs at 0.01 FDR: 17930 [1661:30] Calculating protein q-values [1661:30] Number of genes identified at 1% FDR: 332 (precursor-level), 306 (protein-level) (inference performed using proteotypic peptides only) [1661:30] Quantification [1661:31] File #25/27 [1661:31] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_3_S1.wiff [1669:56] 20070 library precursors are potentially detectable [1669:56] Processing... [1669:59] RT window set to 1.64294 [1669:59] Recommended MS1 mass accuracy setting: 30.7444 ppm [1670:02] Removing low confidence identifications [1670:02] Removing interfering precursors [1670:03] Training neural networks: 19706 targets, 19224 decoys [1670:05] Number of IDs at 0.01 FDR: 18088 [1670:05] Calculating protein q-values [1670:05] Number of genes identified at 1% FDR: 330 (precursor-level), 249 (protein-level) (inference performed using proteotypic peptides only) [1670:05] Quantification [1670:07] File #26/27 [1670:07] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_3_S2.wiff [1678:33] 20070 library precursors are potentially detectable [1678:33] Processing... [1678:39] RT window set to 1.6313 [1678:39] Recommended MS1 mass accuracy setting: 38.5742 ppm [1678:42] Removing low confidence identifications [1678:42] Removing interfering precursors [1678:43] Training neural networks: 19656 targets, 19242 decoys [1678:45] Number of IDs at 0.01 FDR: 17964 [1678:45] Calculating protein q-values [1678:45] Number of genes identified at 1% FDR: 331 (precursor-level), 275 (protein-level) (inference performed using proteotypic peptides only) [1678:45] Quantification [1678:47] File #27/27 [1678:47] Loading run D:\Data\niwa_DIANN_new\231128machii\Hsa_3_S3.wiff [1687:06] 20070 library precursors are potentially detectable [1687:06] Processing... [1687:09] RT window set to 1.62651 [1687:09] Recommended MS1 mass accuracy setting: 27.1781 ppm [1687:12] Removing low confidence identifications [1687:12] Removing interfering precursors [1687:13] Training neural networks: 19669 targets, 19324 decoys [1687:15] Number of IDs at 0.01 FDR: 18056 [1687:15] Calculating protein q-values [1687:15] Number of genes identified at 1% FDR: 332 (precursor-level), 278 (protein-level) (inference performed using proteotypic peptides only) [1687:15] Quantification [1687:17] Cross-run analysis [1687:17] Reading quantification information: 27 files [1687:18] Quantifying peptides [1687:27] Quantifying proteins [1687:28] Calculating q-values for protein and gene groups [1687:28] Calculating global q-values for protein and gene groups [1687:28] Writing report [1687:58] Report saved to D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_report.tsv. [1687:58] Saving precursor levels matrix [1687:59] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_report.pr_matrix.tsv. [1687:59] Saving protein group levels matrix [1687:59] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_report.pg_matrix.tsv. [1687:59] Saving gene group levels matrix [1687:59] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_report.gg_matrix.tsv. [1687:59] Saving unique genes levels matrix [1687:59] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_report.unique_genes_matrix.tsv. [1687:59] Stats report saved to D:\Data\niwa_DIANN_new\231128machii\231128machii_DIAretry_PTS_report.stats.tsv Finished