DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks) Compiled on Apr 14 2022 15:31:19 Current date and time: Mon Jun 30 09:02:03 2025 CPU: GenuineIntel Intel(R) Xeon(R) W-2235 CPU @ 3.80GHz SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 Logical CPU cores: 12 diann.exe --f D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_1.raw --f D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_2.raw --f D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_3.raw --f D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_4.raw --f D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_5.raw --f D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_6.raw --f D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_7.raw --f D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_8.raw --f D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_9.raw --f D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_10.raw --lib --threads 6 --verbose 1 --out D:\data\DIA-NN\250627_FH_YS2\250627_FH_YS2.tsv --qvalue 0.01 --matrices --predictor --fasta D:\data\FASTA\original\uniprotkb_taxonomy_id_31033_2025_02_04_canonical_isoform.fasta --fasta-search --min-fr-mz 145 --max-fr-mz 1450 --met-excision --cut K*,R*,!*P --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 460 --max-pr-mz 860 --min-pr-charge 2 --max-pr-charge 4 --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --monitor-mod UniMod:1 --window 8 --individual-mass-acc --individual-windows --no-isotopes --reanalyse --relaxed-prot-inf --smart-profiling --pg-level 1 --peak-center --no-ifs-removal Thread number set to 6 Output will be filtered at 0.01 FDR Precursor/protein x samples expression level matrices will be saved along with the main report 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 145 Max fragment m/z set to 1450 N-terminal methionine excision enabled In silico digest will involve cuts at K*,R* But excluding cuts at *P Maximum number of missed cleavages set to 1 Min peptide length set to 7 Max peptide length set to 30 Min precursor m/z set to 460 Max precursor m/z set to 860 Min precursor charge set to 2 Max precursor charge set to 4 Cysteine carbamidomethylation enabled as a fixed modification Maximum number of variable modifications set to 1 Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable Modification UniMod:1 with mass delta 42.0106 at *n will be considered as variable Scan window radius set to 8 Mass accuracy will be determined separately for different runs Scan windows will be inferred separately for different runs Isotopologue chromatograms will not be used 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 Implicit protein grouping: protein names; this determines which peptides are considered 'proteotypic' and thus affects protein FDR calculation 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 separately for each 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 The following variable modifications will be scored: UniMod:1 10 files will be processed [0:00] Loading FASTA D:\data\FASTA\original\uniprotkb_taxonomy_id_31033_2025_02_04_canonical_isoform.fasta [0:09] Processing FASTA [0:18] Assembling elution groups [0:26] 2575737 precursors generated [0:26] Gene names missing for some isoforms [0:26] Library contains 52309 proteins, and 14284 genes [0:26] [0:31] [16:20] [20:31] [20:40] [20:41] Saving the library to lib.predicted.speclib [20:47] Initialising library [20:49] First pass: generating a spectral library from DIA data [20:49] File #1/10 [20:49] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_1.raw [22:10] 2575737 library precursors are potentially detectable [22:11] Processing... [23:37] RT window set to 4.46719 [23:38] Recommended MS1 mass accuracy setting: 5.47743 ppm [25:16] Optimised mass accuracy: 13.975 ppm [30:14] Removing low confidence identifications [30:14] Searching PTM decoys [30:20] Removing interfering precursors [30:24] Training neural networks: 102487 targets, 60015 decoys [30:32] Number of IDs at 0.01 FDR: 41558 [30:33] Calculating protein q-values [30:33] Number of proteins identified at 1% FDR: 3082 (precursor-level), 2749 (protein-level) (inference performed using proteotypic peptides only) [30:33] Quantification [30:34] Precursors with monitored PTMs at 1% FDR: 211 out of 215 [30:34] Unmodified precursors with monitored PTM sites at 1% FDR: 109 out of 111 [30:35] Quantification information saved to D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_1.raw.quant. [30:36] File #2/10 [30:36] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_2.raw [31:36] 2575737 library precursors are potentially detectable [31:37] Processing... [33:23] RT window set to 4.06283 [33:24] Recommended MS1 mass accuracy setting: 5.62931 ppm [35:21] Optimised mass accuracy: 20.9068 ppm [39:57] Removing low confidence identifications [39:57] Searching PTM decoys [40:02] Removing interfering precursors [40:06] Training neural networks: 87029 targets, 52719 decoys [40:14] Number of IDs at 0.01 FDR: 34958 [40:14] Calculating protein q-values [40:14] Number of proteins identified at 1% FDR: 2624 (precursor-level), 2355 (protein-level) (inference performed using proteotypic peptides only) [40:14] Quantification [40:15] Precursors with monitored PTMs at 1% FDR: 171 out of 184 [40:15] Unmodified precursors with monitored PTM sites at 1% FDR: 83 out of 90 [40:16] Quantification information saved to D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_2.raw.quant. [40:17] File #3/10 [40:17] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_3.raw [41:10] 2575737 library precursors are potentially detectable [41:11] Processing... [42:39] RT window set to 4.0473 [42:40] Recommended MS1 mass accuracy setting: 6.23276 ppm [44:15] Optimised mass accuracy: 13.7359 ppm [47:56] Removing low confidence identifications [47:56] Searching PTM decoys [48:00] Removing interfering precursors [48:04] Training neural networks: 92800 targets, 55259 decoys [48:12] Number of IDs at 0.01 FDR: 37601 [48:12] Calculating protein q-values [48:13] Number of proteins identified at 1% FDR: 2826 (precursor-level), 2538 (protein-level) (inference performed using proteotypic peptides only) [48:13] Quantification [48:13] Precursors with monitored PTMs at 1% FDR: 187 out of 200 [48:13] Unmodified precursors with monitored PTM sites at 1% FDR: 91 out of 101 [48:14] Quantification information saved to D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_3.raw.quant. [48:15] File #4/10 [48:15] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_4.raw [49:12] 2575737 library precursors are potentially detectable [49:12] Processing... [50:58] RT window set to 4.13706 [50:58] Recommended MS1 mass accuracy setting: 5.55008 ppm [52:55] Optimised mass accuracy: 13.0341 ppm [56:38] Removing low confidence identifications [56:38] Searching PTM decoys [56:42] Removing interfering precursors [56:45] Training neural networks: 78762 targets, 46840 decoys [56:52] Number of IDs at 0.01 FDR: 31211 [56:52] Calculating protein q-values [56:53] Number of proteins identified at 1% FDR: 2460 (precursor-level), 2178 (protein-level) (inference performed using proteotypic peptides only) [56:53] Quantification [56:54] Precursors with monitored PTMs at 1% FDR: 116 out of 151 [56:54] Unmodified precursors with monitored PTM sites at 1% FDR: 50 out of 72 [56:54] Quantification information saved to D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_4.raw.quant. [56:55] File #5/10 [56:55] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_5.raw [57:47] 2575737 library precursors are potentially detectable [57:47] Processing... [59:13] RT window set to 4.02076 [59:14] Recommended MS1 mass accuracy setting: 6.6231 ppm [60:50] Optimised mass accuracy: 16.8497 ppm [64:47] Removing low confidence identifications [64:47] Searching PTM decoys [64:51] Removing interfering precursors [64:55] Training neural networks: 95285 targets, 57706 decoys [65:04] Number of IDs at 0.01 FDR: 39145 [65:04] Calculating protein q-values [65:04] Number of proteins identified at 1% FDR: 2934 (precursor-level), 2658 (protein-level) (inference performed using proteotypic peptides only) [65:05] Quantification [65:05] Precursors with monitored PTMs at 1% FDR: 189 out of 198 [65:05] Unmodified precursors with monitored PTM sites at 1% FDR: 89 out of 104 [65:06] Quantification information saved to D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_5.raw.quant. [65:07] File #6/10 [65:07] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_6.raw [65:43] 2575737 library precursors are potentially detectable [65:43] Processing... [67:06] RT window set to 3.78872 [67:07] Recommended MS1 mass accuracy setting: 5.92004 ppm [68:32] Optimised mass accuracy: 16.2496 ppm [71:51] Removing low confidence identifications [71:51] Searching PTM decoys [71:54] Removing interfering precursors [71:58] Training neural networks: 82199 targets, 50440 decoys [72:06] Number of IDs at 0.01 FDR: 36804 [72:06] Calculating protein q-values [72:06] Number of proteins identified at 1% FDR: 2725 (precursor-level), 2490 (protein-level) (inference performed using proteotypic peptides only) [72:06] Quantification [72:07] Precursors with monitored PTMs at 1% FDR: 211 out of 218 [72:07] Unmodified precursors with monitored PTM sites at 1% FDR: 82 out of 85 [72:08] Quantification information saved to D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_6.raw.quant. [72:08] File #7/10 [72:08] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_7.raw [72:52] 2575737 library precursors are potentially detectable [72:52] Processing... [74:19] RT window set to 3.85509 [74:19] Recommended MS1 mass accuracy setting: 5.82631 ppm [75:48] Optimised mass accuracy: 19.3895 ppm [79:35] Removing low confidence identifications [79:35] Searching PTM decoys [79:39] Removing interfering precursors [79:42] Training neural networks: 83664 targets, 52301 decoys [79:50] Number of IDs at 0.01 FDR: 37825 [79:50] Calculating protein q-values [79:51] Number of proteins identified at 1% FDR: 2831 (precursor-level), 2595 (protein-level) (inference performed using proteotypic peptides only) [79:51] Quantification [79:52] Precursors with monitored PTMs at 1% FDR: 184 out of 195 [79:52] Unmodified precursors with monitored PTM sites at 1% FDR: 87 out of 92 [79:52] Quantification information saved to D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_7.raw.quant. [79:53] File #8/10 [79:53] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_8.raw [80:36] 2575737 library precursors are potentially detectable [80:36] Processing... [82:35] RT window set to 3.80075 [82:36] Recommended MS1 mass accuracy setting: 6.82478 ppm [84:39] Optimised mass accuracy: 16.587 ppm [88:09] Removing low confidence identifications [88:09] Searching PTM decoys [88:13] Removing interfering precursors [88:16] Training neural networks: 82769 targets, 49898 decoys [88:24] Number of IDs at 0.01 FDR: 34395 [88:24] Calculating protein q-values [88:25] Number of proteins identified at 1% FDR: 2615 (precursor-level), 2390 (protein-level) (inference performed using proteotypic peptides only) [88:25] Quantification [88:26] Precursors with monitored PTMs at 1% FDR: 173 out of 182 [88:26] Unmodified precursors with monitored PTM sites at 1% FDR: 79 out of 82 [88:26] Quantification information saved to D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_8.raw.quant. [88:27] File #9/10 [88:27] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_9.raw [89:07] 2575737 library precursors are potentially detectable [89:07] Processing... [90:17] RT window set to 4.05708 [90:17] Recommended MS1 mass accuracy setting: 6.67109 ppm [91:23] Optimised mass accuracy: 9.91131 ppm [94:27] Removing low confidence identifications [94:27] Searching PTM decoys [94:31] Removing interfering precursors [94:35] Training neural networks: 97103 targets, 58282 decoys [94:44] Number of IDs at 0.01 FDR: 41746 [94:44] Calculating protein q-values [94:45] Number of proteins identified at 1% FDR: 3098 (precursor-level), 2773 (protein-level) (inference performed using proteotypic peptides only) [94:45] Quantification [94:45] Precursors with monitored PTMs at 1% FDR: 213 out of 213 [94:45] Unmodified precursors with monitored PTM sites at 1% FDR: 99 out of 99 [94:46] Quantification information saved to D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_9.raw.quant. [94:47] File #10/10 [94:47] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_10.raw [95:32] 2575737 library precursors are potentially detectable [95:32] Processing... [97:12] RT window set to 3.94357 [97:12] Recommended MS1 mass accuracy setting: 5.99133 ppm [98:59] Optimised mass accuracy: 18.6313 ppm [102:46] Removing low confidence identifications [102:46] Searching PTM decoys [102:50] Removing interfering precursors [102:54] Training neural networks: 84069 targets, 51039 decoys [103:01] Number of IDs at 0.01 FDR: 35316 [103:02] Calculating protein q-values [103:02] Number of proteins identified at 1% FDR: 2653 (precursor-level), 2348 (protein-level) (inference performed using proteotypic peptides only) [103:02] Quantification [103:03] Precursors with monitored PTMs at 1% FDR: 166 out of 168 [103:03] Unmodified precursors with monitored PTM sites at 1% FDR: 85 out of 87 [103:03] Quantification information saved to D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_10.raw.quant. [103:04] Cross-run analysis [103:04] Reading quantification information: 10 files [103:07] Averaged recommended settings for this experiment: Mass accuracy = 14ppm, MS1 accuracy = 5ppm, Scan window = 8 [103:07] Quantifying peptides [103:12] Assembling protein groups [103:15] Quantifying proteins [103:16] Calculating q-values for protein and gene groups [103:16] Calculating global q-values for protein and gene groups [103:16] Writing report [103:36] Report saved to D:\data\DIA-NN\250627_FH_YS2\250627_FH_YS2-first-pass.tsv. [103:36] Saving precursor levels matrix [103:36] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\data\DIA-NN\250627_FH_YS2\250627_FH_YS2-first-pass.pr_matrix.tsv. [103:36] Saving protein group levels matrix [103:36] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\data\DIA-NN\250627_FH_YS2\250627_FH_YS2-first-pass.pg_matrix.tsv. [103:36] Saving gene group levels matrix [103:36] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to D:\data\DIA-NN\250627_FH_YS2\250627_FH_YS2-first-pass.gg_matrix.tsv. [103:36] Saving unique genes levels matrix [103:36] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to D:\data\DIA-NN\250627_FH_YS2\250627_FH_YS2-first-pass.unique_genes_matrix.tsv. [103:36] Stats report saved to D:\data\DIA-NN\250627_FH_YS2\250627_FH_YS2-first-pass.stats.tsv [103:36] Generating spectral library: [103:36] 55897 precursors passing the FDR threshold are to be extracted [103:36] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_1.raw [105:00] 2575737 library precursors are potentially detectable [105:01] 10278 spectra added to the library [105:02] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_2.raw [106:00] 2575737 library precursors are potentially detectable [106:00] 2391 spectra added to the library [106:01] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_3.raw [106:54] 2575737 library precursors are potentially detectable [106:55] 4969 spectra added to the library [106:55] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_4.raw [107:51] 2575737 library precursors are potentially detectable [107:51] 2513 spectra added to the library [107:52] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_5.raw [108:44] 2575737 library precursors are potentially detectable [108:45] 4975 spectra added to the library [108:45] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_6.raw [109:21] 2575737 library precursors are potentially detectable [109:22] 4077 spectra added to the library [109:22] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_7.raw [110:06] 2575737 library precursors are potentially detectable [110:06] 4115 spectra added to the library [110:07] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_8.raw [110:49] 2575737 library precursors are potentially detectable [110:49] 1680 spectra added to the library [110:50] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_9.raw [111:29] 2575737 library precursors are potentially detectable [111:30] 5712 spectra added to the library [111:30] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_10.raw [112:16] 2575737 library precursors are potentially detectable [112:16] 513 spectra added to the library [112:17] Saving spectral library to lib.tsv [112:24] 55897 precursors saved [112:24] Loading the generated library and saving it in the .speclib format [112:24] Loading spectral library lib.tsv [112:26] Spectral library loaded: 24793 protein isoforms, 13465 protein groups and 55897 precursors in 51028 elution groups. [112:26] Loading protein annotations from FASTA D:\data\FASTA\original\uniprotkb_taxonomy_id_31033_2025_02_04_canonical_isoform.fasta [112:28] Gene names missing for some isoforms [112:28] Library contains 24789 proteins, and 6069 genes [112:28] Saving the library to lib.tsv.speclib [112:30] Second pass: using the newly created spectral library to reanalyse the data [112:30] File #1/10 [112:30] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_1.raw [113:51] 55897 library precursors are potentially detectable [113:51] Processing... [113:53] RT window set to 2.02948 [113:53] Recommended MS1 mass accuracy setting: 5.25374 ppm [113:55] Optimised mass accuracy: 16.0778 ppm [113:59] Removing low confidence identifications [113:59] Searching PTM decoys [113:59] Removing interfering precursors [114:00] Training neural networks: 54430 targets, 45212 decoys [114:06] Number of IDs at 0.01 FDR: 46826 [114:06] Calculating protein q-values [114:06] Number of proteins identified at 1% FDR: 3305 (precursor-level), 2805 (protein-level) (inference performed using proteotypic peptides only) [114:06] Quantification [114:07] Precursors with monitored PTMs at 1% FDR: 240 out of 247 [114:07] Unmodified precursors with monitored PTM sites at 1% FDR: 122 out of 122 [114:08] File #2/10 [114:08] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_2.raw [115:06] 55897 library precursors are potentially detectable [115:06] Processing... [115:08] RT window set to 1.84117 [115:08] Recommended MS1 mass accuracy setting: 5.27012 ppm [115:09] Optimised mass accuracy: 12.3944 ppm [115:12] Removing low confidence identifications [115:12] Searching PTM decoys [115:12] Removing interfering precursors [115:14] Training neural networks: 52797 targets, 35842 decoys [115:18] Number of IDs at 0.01 FDR: 45031 [115:19] Calculating protein q-values [115:19] Number of proteins identified at 1% FDR: 3242 (precursor-level), 2738 (protein-level) (inference performed using proteotypic peptides only) [115:19] Quantification [115:19] Precursors with monitored PTMs at 1% FDR: 226 out of 242 [115:19] Unmodified precursors with monitored PTM sites at 1% FDR: 108 out of 111 [115:20] File #3/10 [115:20] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_3.raw [116:13] 55897 library precursors are potentially detectable [116:13] Processing... [116:15] RT window set to 1.82854 [116:15] Recommended MS1 mass accuracy setting: 6.53297 ppm [116:16] Optimised mass accuracy: 14.1776 ppm [116:19] Removing low confidence identifications [116:19] Searching PTM decoys [116:19] Removing interfering precursors [116:21] Training neural networks: 52930 targets, 36816 decoys [116:25] Number of IDs at 0.01 FDR: 46154 [116:26] Calculating protein q-values [116:26] Number of proteins identified at 1% FDR: 3351 (precursor-level), 2807 (protein-level) (inference performed using proteotypic peptides only) [116:26] Quantification [116:26] Precursors with monitored PTMs at 1% FDR: 231 out of 247 [116:26] Unmodified precursors with monitored PTM sites at 1% FDR: 100 out of 107 [116:27] File #4/10 [116:27] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_4.raw [117:22] 55897 library precursors are potentially detectable [117:22] Processing... [117:24] RT window set to 1.83771 [117:24] Recommended MS1 mass accuracy setting: 5.74141 ppm [117:25] Optimised mass accuracy: 11.7573 ppm [117:28] Removing low confidence identifications [117:28] Searching PTM decoys [117:28] Removing interfering precursors [117:29] Training neural networks: 51062 targets, 32165 decoys [117:34] Number of IDs at 0.01 FDR: 41423 [117:34] Calculating protein q-values [117:34] Number of proteins identified at 1% FDR: 3065 (precursor-level), 2597 (protein-level) (inference performed using proteotypic peptides only) [117:34] Quantification [117:35] Precursors with monitored PTMs at 1% FDR: 191 out of 223 [117:35] Unmodified precursors with monitored PTM sites at 1% FDR: 83 out of 103 [117:35] File #5/10 [117:35] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_5.raw [118:27] 55897 library precursors are potentially detectable [118:27] Processing... [118:29] RT window set to 1.85952 [118:29] Recommended MS1 mass accuracy setting: 5.96484 ppm [118:30] Optimised mass accuracy: 14.1435 ppm [118:33] Removing low confidence identifications [118:33] Searching PTM decoys [118:33] Removing interfering precursors [118:35] Training neural networks: 53458 targets, 37089 decoys [118:40] Number of IDs at 0.01 FDR: 47907 [118:40] Calculating protein q-values [118:40] Number of proteins identified at 1% FDR: 3428 (precursor-level), 2762 (protein-level) (inference performed using proteotypic peptides only) [118:40] Quantification [118:41] Precursors with monitored PTMs at 1% FDR: 244 out of 251 [118:41] Unmodified precursors with monitored PTM sites at 1% FDR: 108 out of 112 [118:42] File #6/10 [118:42] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_6.raw [119:17] 55897 library precursors are potentially detectable [119:17] Processing... [119:19] RT window set to 1.83291 [119:19] Recommended MS1 mass accuracy setting: 5.5888 ppm [119:20] Optimised mass accuracy: 15.928 ppm [119:23] Removing low confidence identifications [119:23] Searching PTM decoys [119:23] Removing interfering precursors [119:25] Training neural networks: 52384 targets, 35955 decoys [119:30] Number of IDs at 0.01 FDR: 46596 [119:31] Calculating protein q-values [119:31] Number of proteins identified at 1% FDR: 3340 (precursor-level), 2949 (protein-level) (inference performed using proteotypic peptides only) [119:31] Quantification [119:31] Precursors with monitored PTMs at 1% FDR: 265 out of 271 [119:31] Unmodified precursors with monitored PTM sites at 1% FDR: 101 out of 105 [119:32] File #7/10 [119:32] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_7.raw [120:15] 55897 library precursors are potentially detectable [120:15] Processing... [120:17] RT window set to 1.84383 [120:17] Recommended MS1 mass accuracy setting: 5.71993 ppm [120:18] Optimised mass accuracy: 15.9185 ppm [120:21] Removing low confidence identifications [120:21] Searching PTM decoys [120:21] Removing interfering precursors [120:23] Training neural networks: 52929 targets, 37357 decoys [120:27] Number of IDs at 0.01 FDR: 47451 [120:28] Calculating protein q-values [120:28] Number of proteins identified at 1% FDR: 3406 (precursor-level), 2774 (protein-level) (inference performed using proteotypic peptides only) [120:28] Quantification [120:28] Precursors with monitored PTMs at 1% FDR: 246 out of 260 [120:28] Unmodified precursors with monitored PTM sites at 1% FDR: 108 out of 114 [120:29] File #8/10 [120:29] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_8.raw [121:11] 55897 library precursors are potentially detectable [121:11] Processing... [121:13] RT window set to 1.81679 [121:13] Recommended MS1 mass accuracy setting: 5.42034 ppm [121:14] Optimised mass accuracy: 14.4691 ppm [121:17] Removing low confidence identifications [121:17] Searching PTM decoys [121:17] Removing interfering precursors [121:19] Training neural networks: 51621 targets, 33795 decoys [121:23] Number of IDs at 0.01 FDR: 44839 [121:24] Calculating protein q-values [121:24] Number of proteins identified at 1% FDR: 3255 (precursor-level), 2668 (protein-level) (inference performed using proteotypic peptides only) [121:24] Quantification [121:24] Precursors with monitored PTMs at 1% FDR: 233 out of 253 [121:24] Unmodified precursors with monitored PTM sites at 1% FDR: 95 out of 100 [121:25] File #9/10 [121:25] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_9.raw [122:05] 55897 library precursors are potentially detectable [122:05] Processing... [122:07] RT window set to 1.89364 [122:07] Recommended MS1 mass accuracy setting: 5.41451 ppm [122:08] Optimised mass accuracy: 15.2969 ppm [122:11] Removing low confidence identifications [122:11] Searching PTM decoys [122:11] Removing interfering precursors [122:13] Training neural networks: 53103 targets, 36692 decoys [122:17] Number of IDs at 0.01 FDR: 48607 [122:18] Calculating protein q-values [122:18] Number of proteins identified at 1% FDR: 3460 (precursor-level), 2831 (protein-level) (inference performed using proteotypic peptides only) [122:18] Quantification [122:18] Precursors with monitored PTMs at 1% FDR: 260 out of 266 [122:18] Unmodified precursors with monitored PTM sites at 1% FDR: 115 out of 121 [122:19] File #10/10 [122:19] Loading run D:\data\Rawdata\250627_FH_YS2\OE_250627_FH_YS2_10.raw [123:04] 55897 library precursors are potentially detectable [123:04] Processing... [123:06] RT window set to 1.88979 [123:06] Recommended MS1 mass accuracy setting: 5.84675 ppm [123:07] Optimised mass accuracy: 12.3045 ppm [123:10] Removing low confidence identifications [123:10] Searching PTM decoys [123:10] Removing interfering precursors [123:11] Training neural networks: 51760 targets, 32900 decoys [123:16] Number of IDs at 0.01 FDR: 45101 [123:17] Calculating protein q-values [123:17] Number of proteins identified at 1% FDR: 3249 (precursor-level), 2592 (protein-level) (inference performed using proteotypic peptides only) [123:17] Quantification [123:17] Precursors with monitored PTMs at 1% FDR: 236 out of 250 [123:17] Unmodified precursors with monitored PTM sites at 1% FDR: 98 out of 104 [123:18] Cross-run analysis [123:18] Reading quantification information: 10 files [123:19] Averaged recommended settings for this experiment: Mass accuracy = 16ppm, MS1 accuracy = 5ppm, Scan window = 8 [123:19] Quantifying peptides [123:24] Quantifying proteins [123:25] Calculating q-values for protein and gene groups [123:25] Calculating global q-values for protein and gene groups [123:25] Writing report [123:47] Report saved to D:\data\DIA-NN\250627_FH_YS2\250627_FH_YS2.tsv. [123:47] Saving precursor levels matrix [123:47] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\data\DIA-NN\250627_FH_YS2\250627_FH_YS2.pr_matrix.tsv. [123:47] Saving protein group levels matrix [123:47] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\data\DIA-NN\250627_FH_YS2\250627_FH_YS2.pg_matrix.tsv. [123:47] Saving gene group levels matrix [123:47] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to D:\data\DIA-NN\250627_FH_YS2\250627_FH_YS2.gg_matrix.tsv. [123:47] Saving unique genes levels matrix [123:48] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to D:\data\DIA-NN\250627_FH_YS2\250627_FH_YS2.unique_genes_matrix.tsv. [123:48] Stats report saved to D:\data\DIA-NN\250627_FH_YS2\250627_FH_YS2.stats.tsv Finished