
DIA-NN 2.2.0 Academia  (Data-Independent Acquisition by Neural Networks)
Compiled on May 29 2025 21:29:29
Current date and time: Mon Jul 21 09:17:08 2025
CPU: GenuineIntel Intel(R) Xeon(R) Gold 6430
SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 
Logical CPU cores: 128
diann.exe --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw  --lib H:\DELALANDE Frankois\ProteoBench\DIA Astral\Test 7\library7step1.predicted.speclib --threads 64 --verbose 1 --out H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\reportPB6.parquet --qvalue 0.01 --matrices --out-lib H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\PB6.parquet --gen-spec-lib --fasta H:\DELALANDE Frankois\ProteoBench\DIA Astral\ProteoBenchFASTA_MixedSpecies_HYE.fasta --met-excision --cut K*,R* --missed-cleavages 1 --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --window 6 --mass-acc 3 --mass-acc-ms1 7 --peptidoforms --reanalyse --rt-profiling --pg-level 1 

Thread number set to 64
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
A spectral library will be generated
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
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 6
Peptidoform scoring enabled
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
Implicit protein grouping: protein names; this determines which peptides are considered 'proteotypic' and thus affects protein FDR calculation
WARNING: for DIA-NN to switch to the new .raw reader library, please download and install .NET SDK 8.0.407 or later https://dotnet.microsoft.com/en-us/download/dotnet/8.0
Mass accuracy will be fixed to 3e-06 (MS2) and 7e-06 (MS1)
The following variable modifications will be localised: UniMod:35 UniMod:1 

6 files will be processed
[0:00] Loading spectral library H:\DELALANDE Frankois\ProteoBench\DIA Astral\Test 7\library7step1.predicted.speclib
[0:19] Library annotated with sequence database(s): H:\DELALANDE Frankois\ProteoBench\DIA Astral\Test 7\ProteoBenchFASTA_MixedSpecies_HYE.fasta
[0:19] Spectral library loaded: 31837 protein isoforms, 51765 protein groups and 5275217 precursors in 2716671 elution groups.
[0:19] Loading protein annotations from FASTA H:\DELALANDE Frankois\ProteoBench\DIA Astral\ProteoBenchFASTA_MixedSpecies_HYE.fasta
[0:20] Annotating library proteins with information from the FASTA database
[0:20] Protein names missing for some isoforms
[0:20] Gene names missing for some isoforms
[0:20] Library contains 31685 proteins, and 0 genes
[0:24] Initialising library

First pass: generating a spectral library from DIA data

[0:39] File #1/6
[0:39] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
[2:25] Pre-processing...
[2:27] 2931 MS1 and 293271 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 5270221 precursors in range
[2:28] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[2:40] RT window set to 1.15599
[2:40] Recommended MS1 mass accuracy setting: 2.5 ppm
[2:44] Searching decoys
[3:01] Main search
[3:37] Removing low confidence identifications
[3:48] Removing interfering precursors
[3:55] Training neural networks on 212592 target and 129831 decoy PSMs
[4:46] Training neural networks on 212592 target and 131977 decoy PSMs
[5:32] Number of IDs at 0.01 FDR: 95905
[5:33] Precursors at 1% peptidoform FDR: 93684
[5:34] Calculating protein q-values
[5:34] Number of proteins identified at 1% FDR: 10489 (precursor-level), 9590 (protein-level) (inference performed using proteotypic peptides only)
[5:34] Quantification
[5:35] Precursors with scored PTMs at 1% FDR: 2914 out of 3086 considered
[5:35] Precursors with all scored PTM sites unoccupied at 1% FDR: 90770
[5:35] Precursors with PTMs localised (when required) with > 90% confidence: 2826 out of 2914
[5:49] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw.quant

[5:49] File #2/6
[5:49] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
[8:31] Pre-processing...
[8:33] 2933 MS1 and 293433 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[8:33] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[8:46] RT window set to 1.42472
[8:46] Recommended MS1 mass accuracy setting: 2.6 ppm
[8:51] Searching decoys
[9:11] Main search
[9:52] Removing low confidence identifications
[10:04] Removing interfering precursors
[10:11] Training neural networks on 207819 target and 126767 decoy PSMs
[11:01] Training neural networks on 207819 target and 128080 decoy PSMs
[11:46] Number of IDs at 0.01 FDR: 97793
[11:47] Precursors at 1% peptidoform FDR: 94798
[11:48] Calculating protein q-values
[11:48] Number of proteins identified at 1% FDR: 10529 (precursor-level), 9604 (protein-level) (inference performed using proteotypic peptides only)
[11:49] Quantification
[11:50] Precursors with scored PTMs at 1% FDR: 2981 out of 3199 considered
[11:50] Precursors with all scored PTM sites unoccupied at 1% FDR: 91817
[11:50] Precursors with PTMs localised (when required) with > 90% confidence: 2910 out of 2981
[12:09] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw.quant

[12:10] File #3/6
[12:10] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
[13:51] Pre-processing...
[13:53] 2932 MS1 and 293358 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[13:54] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[14:07] RT window set to 1.26241
[14:07] Recommended MS1 mass accuracy setting: 2.7 ppm
[14:11] Searching decoys
[14:29] Main search
[15:10] Removing low confidence identifications
[15:23] Removing interfering precursors
[15:31] Training neural networks on 211591 target and 129408 decoy PSMs
[16:26] Training neural networks on 211591 target and 130609 decoy PSMs
[17:17] Number of IDs at 0.01 FDR: 98365
[17:18] Precursors at 1% peptidoform FDR: 95857
[17:19] Calculating protein q-values
[17:19] Number of proteins identified at 1% FDR: 10598 (precursor-level), 9625 (protein-level) (inference performed using proteotypic peptides only)
[17:20] Quantification
[17:21] Precursors with scored PTMs at 1% FDR: 3058 out of 3217 considered
[17:21] Precursors with all scored PTM sites unoccupied at 1% FDR: 92799
[17:21] Precursors with PTMs localised (when required) with > 90% confidence: 2971 out of 3058
[17:33] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw.quant

[17:34] File #4/6
[17:34] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
[19:17] Pre-processing...
[19:19] 2933 MS1 and 293382 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[19:20] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[19:29] RT window set to 1.32292
[19:29] Recommended MS1 mass accuracy setting: 2.7 ppm
[19:33] Searching decoys
[19:51] Main search
[20:32] Removing low confidence identifications
[20:45] Removing interfering precursors
[20:54] Training neural networks on 213424 target and 131576 decoy PSMs
[21:50] Training neural networks on 213424 target and 132891 decoy PSMs
[22:41] Number of IDs at 0.01 FDR: 98159
[22:42] Precursors at 1% peptidoform FDR: 95314
[22:43] Calculating protein q-values
[22:43] Number of proteins identified at 1% FDR: 10336 (precursor-level), 9287 (protein-level) (inference performed using proteotypic peptides only)
[22:44] Quantification
[22:45] Precursors with scored PTMs at 1% FDR: 3511 out of 3811 considered
[22:45] Precursors with all scored PTM sites unoccupied at 1% FDR: 91803
[22:45] Precursors with PTMs localised (when required) with > 90% confidence: 3398 out of 3511
[22:58] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw.quant

[22:58] File #5/6
[22:58] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
[24:41] Pre-processing...
[24:43] 2933 MS1 and 293330 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[24:44] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[24:53] RT window set to 1.2753
[24:53] Recommended MS1 mass accuracy setting: 2.7 ppm
[24:57] Searching decoys
[25:14] Main search
[25:48] Removing low confidence identifications
[26:00] Removing interfering precursors
[26:07] Training neural networks on 211510 target and 129901 decoy PSMs
[27:05] Training neural networks on 211510 target and 131601 decoy PSMs
[27:57] Number of IDs at 0.01 FDR: 97517
[27:58] Precursors at 1% peptidoform FDR: 94719
[27:59] Calculating protein q-values
[27:59] Number of proteins identified at 1% FDR: 10288 (precursor-level), 9294 (protein-level) (inference performed using proteotypic peptides only)
[28:00] Quantification
[28:01] Precursors with scored PTMs at 1% FDR: 3518 out of 3798 considered
[28:01] Precursors with all scored PTM sites unoccupied at 1% FDR: 91201
[28:01] Precursors with PTMs localised (when required) with > 90% confidence: 3420 out of 3518
[28:16] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw.quant

[28:17] File #6/6
[28:17] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
[29:52] Pre-processing...
[29:54] 2934 MS1 and 293446 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[29:56] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[30:11] RT window set to 1.28987
[30:11] Recommended MS1 mass accuracy setting: 2.8 ppm
[30:18] Searching decoys
[30:39] Main search
[31:19] Removing low confidence identifications
[31:40] Removing interfering precursors
[31:55] Training neural networks on 213168 target and 132099 decoy PSMs
[33:28] Training neural networks on 213168 target and 132812 decoy PSMs
[34:32] Number of IDs at 0.01 FDR: 97973
[34:33] Precursors at 1% peptidoform FDR: 95465
[34:34] Calculating protein q-values
[34:34] Number of proteins identified at 1% FDR: 10395 (precursor-level), 9360 (protein-level) (inference performed using proteotypic peptides only)
[34:35] Quantification
[34:37] Precursors with scored PTMs at 1% FDR: 3575 out of 3837 considered
[34:37] Precursors with all scored PTM sites unoccupied at 1% FDR: 91890
[34:37] Precursors with PTMs localised (when required) with > 90% confidence: 3457 out of 3575
[34:49] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw.quant

[34:49] Cross-run analysis
[34:49] Reading quantification information: 6 files
[35:31] Quantifying peptides
[40:05] Assembling protein groups
[40:13] Quantifying proteins
[40:13] Calculating q-values for protein and gene groups
[40:18] Calculating global q-values for protein and gene groups
[40:18] Protein groups with global q-value <= 0.01: 11035
[40:34] Compressed report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\reportPB6-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[40:34] Site report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\reportPB6-first-pass.site_report.parquet
[40:34] Saving precursor levels matrix
[40:37] Precursor levels matrix (1% precursor and protein group FDR) saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\reportPB6-first-pass.pr_matrix.tsv.
[40:37] Manifest saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\reportPB6-first-pass.manifest.txt
[40:37] Stats report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\reportPB6-first-pass.stats.tsv
[40:39] Generating spectral library:
[40:44] 129146 target and 1309 decoy precursors saved
[40:44] Spectral library saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\PB6.parquet

[40:46] Loading spectral library H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\PB6.parquet
[40:51] Spectral library loaded: 12926 protein isoforms, 12760 protein groups and 130455 precursors in 121948 elution groups.
[40:51] Loading protein annotations from FASTA H:\DELALANDE Frankois\ProteoBench\DIA Astral\ProteoBenchFASTA_MixedSpecies_HYE.fasta
[40:52] Annotating library proteins with information from the FASTA database
[40:52] Gene names missing for some isoforms
[40:52] Library contains 12911 proteins, and 0 genes
[40:52] Initialising library
[41:00] Saving the library to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\PB6.parquet.skyline.speclib


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

[41:05] File #1/6
[41:05] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
[42:39] Pre-processing...
[42:42] 2931 MS1 and 293271 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 129146 precursors in range
[42:42] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[42:43] RT window set to 0.441974
[42:43] Recommended MS1 mass accuracy setting: 3.2 ppm
[42:44] Searching decoys
[42:45] Main search
[42:48] Removing low confidence identifications
[42:59] Removing interfering precursors
[43:02] Training neural networks on 110482 target and 39965 decoy PSMs
[43:38] Training neural networks on 110433 target and 45221 decoy PSMs
[44:13] Number of IDs at 0.01 FDR: 106515
[44:14] Precursors at 1% peptidoform FDR: 104580
[44:15] Calculating protein q-values
[44:15] Number of proteins identified at 1% FDR: 10546 (precursor-level), 9569 (protein-level) (inference performed using proteotypic peptides only)
[44:15] Quantification
[44:17] Precursors with scored PTMs at 1% FDR: 3500 out of 3605 considered
[44:17] Precursors with all scored PTM sites unoccupied at 1% FDR: 101080
[44:17] Precursors with PTMs localised (when required) with > 90% confidence: 3409 out of 3500

[44:18] File #2/6
[44:18] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
[46:03] Pre-processing...
[46:06] 2933 MS1 and 293433 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[46:06] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[46:07] RT window set to 0.428373
[46:07] Recommended MS1 mass accuracy setting: 3.3 ppm
[46:09] Searching decoys
[46:10] Main search
[46:14] Removing low confidence identifications
[46:23] Removing interfering precursors
[46:27] Training neural networks on 110681 target and 39019 decoy PSMs
[47:00] Training neural networks on 110646 target and 44117 decoy PSMs
[47:29] Number of IDs at 0.01 FDR: 106617
[47:29] Precursors at 1% peptidoform FDR: 105296
[47:29] Calculating protein q-values
[47:29] Number of proteins identified at 1% FDR: 10484 (precursor-level), 9512 (protein-level) (inference performed using proteotypic peptides only)
[47:29] Quantification
[47:30] Precursors with scored PTMs at 1% FDR: 3562 out of 3623 considered
[47:30] Precursors with all scored PTM sites unoccupied at 1% FDR: 101734
[47:30] Precursors with PTMs localised (when required) with > 90% confidence: 3492 out of 3562

[47:31] File #3/6
[47:31] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
[48:35] Pre-processing...
[48:36] 2932 MS1 and 293358 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[48:36] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[48:37] RT window set to 0.438533
[48:37] Recommended MS1 mass accuracy setting: 3 ppm
[48:37] Searching decoys
[48:38] Main search
[48:40] Removing low confidence identifications
[48:50] Removing interfering precursors
[48:53] Training neural networks on 110749 target and 40023 decoy PSMs
[49:35] Training neural networks on 110709 target and 44812 decoy PSMs
[49:56] Number of IDs at 0.01 FDR: 107552
[49:57] Precursors at 1% peptidoform FDR: 105818
[49:57] Calculating protein q-values
[49:57] Number of proteins identified at 1% FDR: 10539 (precursor-level), 9529 (protein-level) (inference performed using proteotypic peptides only)
[49:57] Quantification
[49:59] Precursors with scored PTMs at 1% FDR: 3563 out of 3673 considered
[49:59] Precursors with all scored PTM sites unoccupied at 1% FDR: 102255
[49:59] Precursors with PTMs localised (when required) with > 90% confidence: 3483 out of 3563

[50:00] File #4/6
[50:00] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
[51:30] Pre-processing...
[51:31] 2933 MS1 and 293382 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[51:31] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[51:32] RT window set to 0.455627
[51:32] Recommended MS1 mass accuracy setting: 3.3 ppm
[51:32] Searching decoys
[51:33] Main search
[51:34] Removing low confidence identifications
[51:39] Removing interfering precursors
[51:40] Training neural networks on 111460 target and 40989 decoy PSMs
[52:04] Training neural networks on 111427 target and 45890 decoy PSMs
[52:28] Number of IDs at 0.01 FDR: 108088
[52:29] Precursors at 1% peptidoform FDR: 106117
[52:29] Calculating protein q-values
[52:29] Number of proteins identified at 1% FDR: 10447 (precursor-level), 9403 (protein-level) (inference performed using proteotypic peptides only)
[52:29] Quantification
[52:31] Precursors with scored PTMs at 1% FDR: 3797 out of 3902 considered
[52:31] Precursors with all scored PTM sites unoccupied at 1% FDR: 102320
[52:31] Precursors with PTMs localised (when required) with > 90% confidence: 3707 out of 3797

[52:32] File #5/6
[52:32] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
[53:53] Pre-processing...
[53:56] 2933 MS1 and 293330 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[53:56] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[53:58] RT window set to 0.458947
[53:58] Recommended MS1 mass accuracy setting: 3.2 ppm
[53:59] Searching decoys
[53:59] Main search
[54:03] Removing low confidence identifications
[54:09] Removing interfering precursors
[54:11] Training neural networks on 111577 target and 40952 decoy PSMs
[54:36] Training neural networks on 111544 target and 45832 decoy PSMs
[55:29] Number of IDs at 0.01 FDR: 108234
[55:30] Precursors at 1% peptidoform FDR: 106360
[55:30] Calculating protein q-values
[55:30] Number of proteins identified at 1% FDR: 10530 (precursor-level), 9485 (protein-level) (inference performed using proteotypic peptides only)
[55:30] Quantification
[55:32] Precursors with scored PTMs at 1% FDR: 3854 out of 3936 considered
[55:32] Precursors with all scored PTM sites unoccupied at 1% FDR: 102506
[55:32] Precursors with PTMs localised (when required) with > 90% confidence: 3760 out of 3854

[55:34] File #6/6
[55:34] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
[57:20] Pre-processing...
[57:22] 2934 MS1 and 293446 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[57:22] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[57:22] RT window set to 0.456243
[57:22] Recommended MS1 mass accuracy setting: 3.1 ppm
[57:23] Searching decoys
[57:23] Main search
[57:24] Removing low confidence identifications
[57:28] Removing interfering precursors
[57:29] Training neural networks on 111490 target and 40760 decoy PSMs
[57:49] Training neural networks on 111452 target and 45956 decoy PSMs
[58:14] Number of IDs at 0.01 FDR: 108063
[58:15] Precursors at 1% peptidoform FDR: 106286
[58:15] Calculating protein q-values
[58:15] Number of proteins identified at 1% FDR: 10458 (precursor-level), 9482 (protein-level) (inference performed using proteotypic peptides only)
[58:15] Quantification
[58:16] Precursors with scored PTMs at 1% FDR: 3879 out of 3979 considered
[58:16] Precursors with all scored PTM sites unoccupied at 1% FDR: 102407
[58:16] Precursors with PTMs localised (when required) with > 90% confidence: 3783 out of 3879

[58:18] Cross-run analysis
[58:18] Reading quantification information: 6 files
[58:23] Quantifying peptides
[63:04] Quantification parameters: 0.374341, 0.00137144, 0.00161153, 0.0119278, 0.0123968, 0.0121261, 0.167592, 0.242585, 0.199603, 0.0131006, 0.0373903, 0.0139944, 0.230408, 0.0521126, 0.0699023, 0.0114328
[64:33] Quantifying proteins
[64:33] Calculating q-values for protein and gene groups
[64:33] Calculating global q-values for protein and gene groups
[64:33] Protein groups with global q-value <= 0.01: 10582
[64:43] Compressed report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\reportPB6.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[64:44] Site report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\reportPB6.site_report.parquet
[64:44] Saving precursor levels matrix
[64:47] Precursor levels matrix (1% precursor and protein group FDR) saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\reportPB6.pr_matrix.tsv.
[64:47] Saving protein group levels matrix
[64:48] Protein groups matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\reportPB6.pg_matrix.tsv.
[64:48] Saving gene group levels matrix
[64:48] Gene groups matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\reportPB6.gg_matrix.tsv.
[64:48] Saving unique genes levels matrix
[64:48] Unique genes matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\reportPB6.unique_genes_matrix.tsv.
[64:49] Manifest saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\reportPB6.manifest.txt
[64:49] Stats report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB6\reportPB6.stats.tsv

