
DIA-NN 2.1.0 Academia  (Data-Independent Acquisition by Neural Networks)
Compiled on Mar 25 2025 10:59:54
Current date and time: Thu May 22 18:38:44 2025
CPU: GenuineIntel Intel(R) Core(TM) i9-10980XE CPU @ 3.00GHz
SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 
Logical CPU cores: 36
diann.exe --f W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m002_s007_tOVISE_con1_2ME_2uL_DIA_T60.raw.dia  --f W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m004_s008_tOVISE_con2_2ME_2uL_DIA_T60.raw.dia  --f W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m006_s009_tOVISE_con3_2ME_2uL_DIA_T60.raw.dia  --f W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m008_s010_tOVISE_cis1_2ME_2uL_DIA_T60.raw.dia  --f W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m010_s011_tOVISE_cis2_2ME_2uL_DIA_T60.raw.dia  --f W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m012_s012_tOVISE_cis3_2ME_2uL_DIA_T60.raw.dia  --lib C:\DIA-NN\2.1.0\predlib\Human\250522_Human_UP000005640_E20644_mc2_vmod3_length7_45_z2_4_mz495_775_var2ME.predicted.speclib --threads 18 --verbose 1 --out W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\NN210_250520_Bsto240mtmt_OVISE_2ME\report.parquet --qvalue 0.01 --matrices --fasta W:\Database\2025\250318_Human_UP000005640_E20644.fasta --met-excision --cut K*,R* --missed-cleavages 1 --var-mods 2 --var-mod UniMod:35,15.994915,M --mass-acc 10 --mass-acc-ms1 10 --reanalyse --rt-profiling --var-mod UniMod:303,75.9982, C 

Thread number set to 18
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
Maximum number of variable modifications set to 2
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
MBR enabled; .quant files will only be saved to disk during the first pass
The spectral library (if generated) will retain the original spectra but will include empirically-aligned RTs
Modification UniMod:303 with mass delta 75.9982 at  C will be considered as variable
Mass accuracy will be fixed to 1e-05 (MS2) and 1e-05 (MS1)
WARNING: peptidoform scoring enabled because variable modifications have been declared; to disable, use --no-peptidoforms
The following variable modifications will be localised: UniMod:35 UniMod:303 

6 files will be processed
[0:00] Loading spectral library C:\DIA-NN\2.1.0\predlib\Human\250522_Human_UP000005640_E20644_mc2_vmod3_length7_45_z2_4_mz495_775_var2ME.predicted.speclib
[0:03] Library annotated with sequence database(s): W:\Database\2025\250318_Human_UP000005640_E20644.fasta
[0:04] Spectral library loaded: 20610 protein isoforms, 28643 protein groups and 4385150 precursors in 3659220 elution groups.
[0:04] Loading protein annotations from FASTA W:\Database\2025\250318_Human_UP000005640_E20644.fasta
[0:04] Annotating library proteins with information from the FASTA database
[0:04] Gene names missing for some isoforms
[0:04] Library contains 20610 proteins, and 20363 genes
[0:08] Initialising library

First pass: generating a spectral library from DIA data

[0:26] File #1/6
[0:26] Loading run W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m002_s007_tOVISE_con1_2ME_2uL_DIA_T60.raw.dia
[0:29] Pre-processing...
[0:30] 1031 MS1 and 30929 MS2 scans in 1031 (inferred) and 1031 (encoded) cycles, 4248108 precursors in range
[0:33] Calibrating with mass accuracies 25 (MS1), 21 (MS2)
[1:05] RT window set to 3.3542
[1:05] Peak width: 2.96
[1:05] Scan window radius set to 6
[1:05] Recommended MS1 mass accuracy setting: 36 ppm
[1:38] Searching decoys
[2:29] Main search
[4:16] Removing low confidence identifications
[4:36] Removing interfering precursors
[4:46] Training neural networks on 133005 target and 92864 decoy PSMs
[6:22] Training neural networks on 133005 target and 87999 decoy PSMs
[7:48] Number of IDs at 0.01 FDR: 69010
[7:49] Precursors at 1% peptidoform FDR: 61930
[7:50] Calculating protein q-values
[7:51] Number of genes identified at 1% FDR: 7813 (precursor-level), 7234 (protein-level) (inference performed using proteotypic peptides only)
[7:51] Quantification
[7:51] Precursors with scored PTMs at 1% FDR: 11586 out of 13926 considered
[7:51] Precursors with all scored PTM sites unoccupied at 1% FDR: 50344
[7:51] Precursors with PTMs localised (when required) with > 90% confidence: 11567 out of 11586
[7:58] Quantification information saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m002_s007_tOVISE_con1_2ME_2uL_DIA_T60.raw.dia.quant

[7:58] File #2/6
[7:58] Loading run W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m004_s008_tOVISE_con2_2ME_2uL_DIA_T60.raw.dia
[8:01] Pre-processing...
[8:02] 1021 MS1 and 30620 MS2 scans in 1021 (inferred) and 1021 (encoded) cycles, 4248108 precursors in range
[8:05] Calibrating with mass accuracies 25 (MS1), 21 (MS2)
[8:43] RT window set to 3.40399
[8:43] Recommended MS1 mass accuracy setting: 37 ppm
[9:12] Searching decoys
[10:05] Main search
[11:52] Removing low confidence identifications
[12:11] Removing interfering precursors
[12:21] Training neural networks on 129705 target and 89883 decoy PSMs
[13:54] Training neural networks on 129705 target and 84730 decoy PSMs
[15:18] Number of IDs at 0.01 FDR: 67726
[15:19] Precursors at 1% peptidoform FDR: 60818
[15:20] Calculating protein q-values
[15:21] Number of genes identified at 1% FDR: 7680 (precursor-level), 6976 (protein-level) (inference performed using proteotypic peptides only)
[15:21] Quantification
[15:21] Precursors with scored PTMs at 1% FDR: 11411 out of 13612 considered
[15:21] Precursors with all scored PTM sites unoccupied at 1% FDR: 49407
[15:21] Precursors with PTMs localised (when required) with > 90% confidence: 11392 out of 11411
[15:27] Quantification information saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m004_s008_tOVISE_con2_2ME_2uL_DIA_T60.raw.dia.quant

[15:27] File #3/6
[15:27] Loading run W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m006_s009_tOVISE_con3_2ME_2uL_DIA_T60.raw.dia
[15:29] Pre-processing...
[15:30] 954 MS1 and 28595 MS2 scans in 954 (inferred) and 954 (encoded) cycles, 4248108 precursors in range
[15:33] Calibrating with mass accuracies 25 (MS1), 21 (MS2)
[16:07] RT window set to 3.29064
[16:07] Recommended MS1 mass accuracy setting: 37 ppm
[16:37] Searching decoys
[17:16] Main search
[18:38] Removing low confidence identifications
[18:55] Removing interfering precursors
[19:05] Training neural networks on 107947 target and 73051 decoy PSMs
[20:23] Training neural networks on 107947 target and 69036 decoy PSMs
[21:31] Number of IDs at 0.01 FDR: 61279
[21:32] Precursors at 1% peptidoform FDR: 55051
[21:33] Calculating protein q-values
[21:34] Number of genes identified at 1% FDR: 7434 (precursor-level), 6780 (protein-level) (inference performed using proteotypic peptides only)
[21:34] Quantification
[21:34] Precursors with scored PTMs at 1% FDR: 10460 out of 12481 considered
[21:34] Precursors with all scored PTM sites unoccupied at 1% FDR: 44591
[21:34] Precursors with PTMs localised (when required) with > 90% confidence: 10429 out of 10460
[21:40] Quantification information saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m006_s009_tOVISE_con3_2ME_2uL_DIA_T60.raw.dia.quant

[21:40] File #4/6
[21:40] Loading run W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m008_s010_tOVISE_cis1_2ME_2uL_DIA_T60.raw.dia
[21:43] Pre-processing...
[21:44] 1040 MS1 and 31182 MS2 scans in 1040 (inferred) and 1040 (encoded) cycles, 4248108 precursors in range
[21:47] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[22:26] RT window set to 3.18935
[22:26] Recommended MS1 mass accuracy setting: 37 ppm
[22:59] Searching decoys
[23:50] Main search
[25:37] Removing low confidence identifications
[25:57] Removing interfering precursors
[26:06] Training neural networks on 124868 target and 84958 decoy PSMs
[27:36] Training neural networks on 124868 target and 79940 decoy PSMs
[28:56] Number of IDs at 0.01 FDR: 62528
[28:56] Precursors at 1% peptidoform FDR: 55634
[28:58] Calculating protein q-values
[28:58] Number of genes identified at 1% FDR: 7197 (precursor-level), 6560 (protein-level) (inference performed using proteotypic peptides only)
[28:59] Quantification
[28:59] Precursors with scored PTMs at 1% FDR: 9881 out of 12027 considered
[28:59] Precursors with all scored PTM sites unoccupied at 1% FDR: 45753
[28:59] Precursors with PTMs localised (when required) with > 90% confidence: 9865 out of 9881
[29:04] Quantification information saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m008_s010_tOVISE_cis1_2ME_2uL_DIA_T60.raw.dia.quant

[29:04] File #5/6
[29:04] Loading run W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m010_s011_tOVISE_cis2_2ME_2uL_DIA_T60.raw.dia
[29:08] Pre-processing...
[29:09] 1035 MS1 and 31032 MS2 scans in 1035 (inferred) and 1035 (encoded) cycles, 4248108 precursors in range
[29:12] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[29:50] RT window set to 3.5129
[29:50] Recommended MS1 mass accuracy setting: 34 ppm
[30:28] Searching decoys
[31:23] Main search
[33:19] Removing low confidence identifications
[33:38] Removing interfering precursors
[33:47] Training neural networks on 122101 target and 82204 decoy PSMs
[35:14] Training neural networks on 122101 target and 76579 decoy PSMs
[36:32] Number of IDs at 0.01 FDR: 63013
[36:33] Precursors at 1% peptidoform FDR: 55683
[36:34] Calculating protein q-values
[36:35] Number of genes identified at 1% FDR: 7180 (precursor-level), 6592 (protein-level) (inference performed using proteotypic peptides only)
[36:35] Quantification
[36:35] Precursors with scored PTMs at 1% FDR: 9969 out of 12202 considered
[36:35] Precursors with all scored PTM sites unoccupied at 1% FDR: 45714
[36:35] Precursors with PTMs localised (when required) with > 90% confidence: 9950 out of 9969
[36:41] Quantification information saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m010_s011_tOVISE_cis2_2ME_2uL_DIA_T60.raw.dia.quant

[36:41] File #6/6
[36:41] Loading run W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m012_s012_tOVISE_cis3_2ME_2uL_DIA_T60.raw.dia
[36:44] Pre-processing...
[36:45] 1044 MS1 and 31296 MS2 scans in 1044 (inferred) and 1044 (encoded) cycles, 4248108 precursors in range
[36:48] Calibrating with mass accuracies 25 (MS1), 21 (MS2)
[37:26] RT window set to 3.15306
[37:26] Recommended MS1 mass accuracy setting: 35 ppm
[38:00] Searching decoys
[38:52] Main search
[40:40] Removing low confidence identifications
[40:59] Removing interfering precursors
[41:09] Training neural networks on 125912 target and 86689 decoy PSMs
[42:40] Training neural networks on 125912 target and 81759 decoy PSMs
[44:01] Number of IDs at 0.01 FDR: 63017
[44:02] Precursors at 1% peptidoform FDR: 56081
[44:03] Calculating protein q-values
[44:04] Number of genes identified at 1% FDR: 7167 (precursor-level), 6539 (protein-level) (inference performed using proteotypic peptides only)
[44:04] Quantification
[44:04] Precursors with scored PTMs at 1% FDR: 9928 out of 12049 considered
[44:04] Precursors with all scored PTM sites unoccupied at 1% FDR: 46153
[44:04] Precursors with PTMs localised (when required) with > 90% confidence: 9907 out of 9928
[44:10] Quantification information saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m012_s012_tOVISE_cis3_2ME_2uL_DIA_T60.raw.dia.quant

[44:10] Cross-run analysis
[44:10] Reading quantification information: 6 files
[44:27] Quantifying peptides
[45:05] Assembling protein groups
[45:07] Quantifying proteins
[45:07] Calculating q-values for protein and gene groups
[45:10] Calculating global q-values for protein and gene groups
[45:10] Protein groups with global q-value <= 0.01: 7596
[45:16] Compressed report saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\NN210_250520_Bsto240mtmt_OVISE_2ME\report-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[45:16] Saving precursor levels matrix
[45:19] Precursor levels matrix (1% precursor and protein group FDR) saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\NN210_250520_Bsto240mtmt_OVISE_2ME\report-first-pass.pr_matrix.tsv.
[45:19] Manifest saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\NN210_250520_Bsto240mtmt_OVISE_2ME\report-first-pass.manifest.txt
[45:19] Stats report saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\NN210_250520_Bsto240mtmt_OVISE_2ME\report-first-pass.stats.tsv
[45:20] Generating spectral library:
[45:22] 86564 target and 889 decoy precursors saved
[45:23] Spectral library saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\NN210_250520_Bsto240mtmt_OVISE_2ME\report-lib.parquet

[45:23] Loading spectral library W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\NN210_250520_Bsto240mtmt_OVISE_2ME\report-lib.parquet
[45:25] Spectral library loaded: 8782 protein isoforms, 8695 protein groups and 87453 precursors in 85482 elution groups.
[45:25] Loading protein annotations from FASTA W:\Database\2025\250318_Human_UP000005640_E20644.fasta
[45:25] Annotating library proteins with information from the FASTA database
[45:25] Gene names missing for some isoforms
[45:25] Library contains 8782 proteins, and 8779 genes
[45:25] Initialising library
[45:26] Saving the library to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\NN210_250520_Bsto240mtmt_OVISE_2ME\report-lib.parquet.skyline.speclib


Second pass: using the newly created spectral library to reanalyse the data

[45:29] File #1/6
[45:29] Loading run W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m002_s007_tOVISE_con1_2ME_2uL_DIA_T60.raw.dia
[45:32] Pre-processing...
[45:33] 1031 MS1 and 30929 MS2 scans in 1031 (inferred) and 1031 (encoded) cycles, 86564 precursors in range
[45:33] Calibrating with mass accuracies 25 (MS1), 21 (MS2)
[45:34] RT window set to 1.0703
[45:34] Recommended MS1 mass accuracy setting: 41 ppm
[45:34] Searching decoys
[45:35] Main search
[45:37] Removing low confidence identifications
[45:43] Removing interfering precursors
[45:44] Training neural networks on 78900 target and 40874 decoy PSMs
[46:28] Training neural networks on 78891 target and 42519 decoy PSMs
[47:12] Number of IDs at 0.01 FDR: 73427
[47:13] Precursors at 1% peptidoform FDR: 65634
[47:13] Calculating protein q-values
[47:13] Number of genes identified at 1% FDR: 7790 (precursor-level), 7249 (protein-level) (inference performed using proteotypic peptides only)
[47:13] Quantification
[47:13] Precursors with scored PTMs at 1% FDR: 12901 out of 14725 considered
[47:13] Precursors with all scored PTM sites unoccupied at 1% FDR: 52733
[47:13] Precursors with PTMs localised (when required) with > 90% confidence: 12877 out of 12901

[47:13] File #2/6
[47:13] Loading run W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m004_s008_tOVISE_con2_2ME_2uL_DIA_T60.raw.dia
[47:17] Pre-processing...
[47:17] 1021 MS1 and 30620 MS2 scans in 1021 (inferred) and 1021 (encoded) cycles, 86564 precursors in range
[47:17] Calibrating with mass accuracies 25 (MS1), 21 (MS2)
[47:18] RT window set to 1.07238
[47:18] Recommended MS1 mass accuracy setting: 40 ppm
[47:19] Searching decoys
[47:20] Main search
[47:22] Removing low confidence identifications
[47:27] Removing interfering precursors
[47:28] Training neural networks on 79623 target and 41213 decoy PSMs
[48:13] Training neural networks on 79613 target and 42797 decoy PSMs
[48:58] Number of IDs at 0.01 FDR: 73725
[48:58] Precursors at 1% peptidoform FDR: 65274
[48:58] Calculating protein q-values
[48:58] Number of genes identified at 1% FDR: 7759 (precursor-level), 7258 (protein-level) (inference performed using proteotypic peptides only)
[48:58] Quantification
[48:58] Precursors with scored PTMs at 1% FDR: 12786 out of 14774 considered
[48:58] Precursors with all scored PTM sites unoccupied at 1% FDR: 52488
[48:58] Precursors with PTMs localised (when required) with > 90% confidence: 12764 out of 12786

[48:59] File #3/6
[48:59] Loading run W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m006_s009_tOVISE_con3_2ME_2uL_DIA_T60.raw.dia
[49:01] Pre-processing...
[49:02] 954 MS1 and 28595 MS2 scans in 954 (inferred) and 954 (encoded) cycles, 86564 precursors in range
[49:02] Calibrating with mass accuracies 25 (MS1), 21 (MS2)
[49:02] RT window set to 1.03694
[49:02] Recommended MS1 mass accuracy setting: 39 ppm
[49:03] Searching decoys
[49:03] Main search
[49:05] Removing low confidence identifications
[49:10] Removing interfering precursors
[49:11] Training neural networks on 73437 target and 35922 decoy PSMs
[49:52] Training neural networks on 73427 target and 37189 decoy PSMs
[50:32] Number of IDs at 0.01 FDR: 66869
[50:32] Precursors at 1% peptidoform FDR: 59470
[50:32] Calculating protein q-values
[50:32] Number of genes identified at 1% FDR: 7534 (precursor-level), 7086 (protein-level) (inference performed using proteotypic peptides only)
[50:32] Quantification
[50:33] Precursors with scored PTMs at 1% FDR: 11826 out of 13551 considered
[50:33] Precursors with all scored PTM sites unoccupied at 1% FDR: 47644
[50:33] Precursors with PTMs localised (when required) with > 90% confidence: 11799 out of 11826

[50:33] File #4/6
[50:33] Loading run W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m008_s010_tOVISE_cis1_2ME_2uL_DIA_T60.raw.dia
[50:36] Pre-processing...
[50:37] 1040 MS1 and 31182 MS2 scans in 1040 (inferred) and 1040 (encoded) cycles, 86564 precursors in range
[50:37] Calibrating with mass accuracies 25 (MS1), 21 (MS2)
[50:38] RT window set to 1.07661
[50:38] Recommended MS1 mass accuracy setting: 38 ppm
[50:39] Searching decoys
[50:39] Main search
[50:42] Removing low confidence identifications
[50:47] Removing interfering precursors
[50:48] Training neural networks on 78202 target and 40863 decoy PSMs
[51:33] Training neural networks on 78183 target and 42564 decoy PSMs
[52:17] Number of IDs at 0.01 FDR: 69031
[52:17] Precursors at 1% peptidoform FDR: 59898
[52:17] Calculating protein q-values
[52:17] Number of genes identified at 1% FDR: 7415 (precursor-level), 6844 (protein-level) (inference performed using proteotypic peptides only)
[52:17] Quantification
[52:18] Precursors with scored PTMs at 1% FDR: 11456 out of 13602 considered
[52:18] Precursors with all scored PTM sites unoccupied at 1% FDR: 48442
[52:18] Precursors with PTMs localised (when required) with > 90% confidence: 11427 out of 11456

[52:18] File #5/6
[52:18] Loading run W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m010_s011_tOVISE_cis2_2ME_2uL_DIA_T60.raw.dia
[52:21] Pre-processing...
[52:22] 1035 MS1 and 31032 MS2 scans in 1035 (inferred) and 1035 (encoded) cycles, 86564 precursors in range
[52:22] Calibrating with mass accuracies 25 (MS1), 21 (MS2)
[52:23] RT window set to 1.0664
[52:23] Recommended MS1 mass accuracy setting: 38 ppm
[52:24] Searching decoys
[52:24] Main search
[52:27] Removing low confidence identifications
[52:32] Removing interfering precursors
[52:33] Training neural networks on 78272 target and 40737 decoy PSMs
[53:17] Training neural networks on 78263 target and 42341 decoy PSMs
[54:01] Number of IDs at 0.01 FDR: 69527
[54:02] Precursors at 1% peptidoform FDR: 60667
[54:02] Calculating protein q-values
[54:02] Number of genes identified at 1% FDR: 7388 (precursor-level), 6846 (protein-level) (inference performed using proteotypic peptides only)
[54:02] Quantification
[54:02] Precursors with scored PTMs at 1% FDR: 11570 out of 13688 considered
[54:02] Precursors with all scored PTM sites unoccupied at 1% FDR: 49097
[54:02] Precursors with PTMs localised (when required) with > 90% confidence: 11540 out of 11570

[54:03] File #6/6
[54:03] Loading run W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\Bsto240mtmt_m012_s012_tOVISE_cis3_2ME_2uL_DIA_T60.raw.dia
[54:06] Pre-processing...
[54:07] 1044 MS1 and 31296 MS2 scans in 1044 (inferred) and 1044 (encoded) cycles, 86564 precursors in range
[54:07] Calibrating with mass accuracies 25 (MS1), 21 (MS2)
[54:07] RT window set to 1.06872
[54:08] Recommended MS1 mass accuracy setting: 40 ppm
[54:08] Searching decoys
[54:09] Main search
[54:11] Removing low confidence identifications
[54:16] Removing interfering precursors
[54:17] Training neural networks on 78601 target and 41677 decoy PSMs
[55:02] Training neural networks on 78585 target and 43061 decoy PSMs
[55:46] Number of IDs at 0.01 FDR: 69492
[55:47] Precursors at 1% peptidoform FDR: 59814
[55:47] Calculating protein q-values
[55:47] Number of genes identified at 1% FDR: 7410 (precursor-level), 6839 (protein-level) (inference performed using proteotypic peptides only)
[55:47] Quantification
[55:47] Precursors with scored PTMs at 1% FDR: 11405 out of 13665 considered
[55:47] Precursors with all scored PTM sites unoccupied at 1% FDR: 48409
[55:47] Precursors with PTMs localised (when required) with > 90% confidence: 11379 out of 11405

[55:48] Cross-run analysis
[55:48] Reading quantification information: 6 files
[55:49] Quantifying peptides
[58:27] Quantification parameters: 0.262609, 0.00214751, 0.000564109, 0.0112201, 0.012355, 0.0118046, 0.11281, 0.0153823, 0.0254492, 0.0264177, 0.0489404, 0.0451854, 0.2527, 0.0502947, 0.0558259, 0.0117221
[58:47] Quantifying proteins
[58:47] Calculating q-values for protein and gene groups
[58:47] Calculating global q-values for protein and gene groups
[58:48] Protein groups with global q-value <= 0.01: 7525
[58:54] Compressed report saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\NN210_250520_Bsto240mtmt_OVISE_2ME\report.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[58:54] Saving precursor levels matrix
[58:57] Precursor levels matrix (1% precursor and protein group FDR) saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\NN210_250520_Bsto240mtmt_OVISE_2ME\report.pr_matrix.tsv.
[58:57] Saving protein group levels matrix
[58:57] Protein groups matrix saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\NN210_250520_Bsto240mtmt_OVISE_2ME\report.pg_matrix.tsv.
[58:57] Saving gene group levels matrix
[58:58] Gene groups matrix saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\NN210_250520_Bsto240mtmt_OVISE_2ME\report.gg_matrix.tsv.
[58:58] Saving unique genes levels matrix
[58:58] Unique genes matrix saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\NN210_250520_Bsto240mtmt_OVISE_2ME\report.unique_genes_matrix.tsv.
[58:59] Manifest saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\NN210_250520_Bsto240mtmt_OVISE_2ME\report.manifest.txt
[58:59] Stats report saved to W:\Exploris240_Data\2025\m05\250520_Bsto240mtmt_OVISE_IAA_2ME\NN210_250520_Bsto240mtmt_OVISE_2ME\report.stats.tsv

