
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 09:43:47 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\PB10\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\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\PB10\reportPB10.parquet --qvalue 0.01 --matrices --out-lib H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\PB10.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 --smart-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
When generating an empirical library, empirical spectra will be added to it only if they are high quality
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
[0:20] Spectral library loaded: 31837 protein isoforms, 51765 protein groups and 5275217 precursors in 2716671 elution groups.
[0:20] Loading protein annotations from FASTA H:\DELALANDE Frankois\ProteoBench\DIA Astral\ProteoBenchFASTA_MixedSpecies_HYE.fasta
[0:21] Annotating library proteins with information from the FASTA database
[0:21] Protein names missing for some isoforms
[0:21] Gene names missing for some isoforms
[0:21] Library contains 31685 proteins, and 0 genes
[0:25] Initialising library

First pass: generating a spectral library from DIA data

[0:53] File #1/6
[0:53] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
[2:43] Pre-processing...
[2:45] 2931 MS1 and 293271 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 5270221 precursors in range
[2:45] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[2:59] RT window set to 1.15599
[2:59] Recommended MS1 mass accuracy setting: 2.5 ppm
[3:02] Searching decoys
[3:19] Main search
[4:00] Removing low confidence identifications
[4:20] Removing interfering precursors
[4:33] Training neural networks on 212592 target and 129831 decoy PSMs
[6:05] Training neural networks on 212592 target and 131977 decoy PSMs
[7:11] Number of IDs at 0.01 FDR: 95905
[7:12] Precursors at 1% peptidoform FDR: 93684
[7:13] Calculating protein q-values
[7:14] Number of proteins identified at 1% FDR: 10489 (precursor-level), 9590 (protein-level) (inference performed using proteotypic peptides only)
[7:14] Quantification
[7:17] Precursors with scored PTMs at 1% FDR: 2914 out of 3086 considered
[7:17] Precursors with all scored PTM sites unoccupied at 1% FDR: 90770
[7:17] Precursors with PTMs localised (when required) with > 90% confidence: 2826 out of 2914
[7:24] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw.quant

[7:24] File #2/6
[7:24] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
[9:31] Pre-processing...
[9:34] 2933 MS1 and 293433 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[9:35] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[9:51] RT window set to 1.42472
[9:51] Recommended MS1 mass accuracy setting: 2.6 ppm
[9:58] Searching decoys
[10:20] Main search
[11:12] Removing low confidence identifications
[11:25] Removing interfering precursors
[11:34] Training neural networks on 207819 target and 126767 decoy PSMs
[12:31] Training neural networks on 207819 target and 128080 decoy PSMs
[13:24] Number of IDs at 0.01 FDR: 97793
[13:25] Precursors at 1% peptidoform FDR: 94798
[13:27] Calculating protein q-values
[13:28] Number of proteins identified at 1% FDR: 10529 (precursor-level), 9604 (protein-level) (inference performed using proteotypic peptides only)
[13:29] Quantification
[13:32] Precursors with scored PTMs at 1% FDR: 2981 out of 3199 considered
[13:32] Precursors with all scored PTM sites unoccupied at 1% FDR: 91817
[13:32] Precursors with PTMs localised (when required) with > 90% confidence: 2910 out of 2981
[13:39] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw.quant

[13:39] File #3/6
[13:39] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
[15:08] Pre-processing...
[15:12] 2932 MS1 and 293358 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[15:13] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[15:31] RT window set to 1.26241
[15:31] Recommended MS1 mass accuracy setting: 2.7 ppm
[15:35] Searching decoys
[15:54] Main search
[16:47] Removing low confidence identifications
[17:06] Removing interfering precursors
[17:23] Training neural networks on 211591 target and 129408 decoy PSMs
[18:25] Training neural networks on 211591 target and 130609 decoy PSMs
[19:18] Number of IDs at 0.01 FDR: 98365
[19:20] Precursors at 1% peptidoform FDR: 95857
[19:21] Calculating protein q-values
[19:23] Number of proteins identified at 1% FDR: 10598 (precursor-level), 9625 (protein-level) (inference performed using proteotypic peptides only)
[19:23] Quantification
[19:26] Precursors with scored PTMs at 1% FDR: 3058 out of 3217 considered
[19:26] Precursors with all scored PTM sites unoccupied at 1% FDR: 92799
[19:26] Precursors with PTMs localised (when required) with > 90% confidence: 2971 out of 3058
[19:34] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw.quant

[19:34] File #4/6
[19:34] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
[21:11] Pre-processing...
[21:14] 2933 MS1 and 293382 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[21:15] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[21:28] RT window set to 1.32292
[21:29] Recommended MS1 mass accuracy setting: 2.7 ppm
[21:34] Searching decoys
[21:54] Main search
[22:47] Removing low confidence identifications
[23:06] Removing interfering precursors
[23:17] Training neural networks on 213424 target and 131576 decoy PSMs
[24:06] Training neural networks on 213424 target and 132891 decoy PSMs
[24:50] Number of IDs at 0.01 FDR: 98159
[24:51] Precursors at 1% peptidoform FDR: 95314
[24:52] Calculating protein q-values
[24:52] Number of proteins identified at 1% FDR: 10336 (precursor-level), 9287 (protein-level) (inference performed using proteotypic peptides only)
[24:52] Quantification
[24:54] Precursors with scored PTMs at 1% FDR: 3511 out of 3811 considered
[24:54] Precursors with all scored PTM sites unoccupied at 1% FDR: 91803
[24:54] Precursors with PTMs localised (when required) with > 90% confidence: 3398 out of 3511
[25:03] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw.quant

[25:03] File #5/6
[25:03] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
[26:11] Pre-processing...
[26:13] 2933 MS1 and 293330 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[26:14] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[26:25] RT window set to 1.2753
[26:25] Recommended MS1 mass accuracy setting: 2.7 ppm
[26:29] Searching decoys
[26:46] Main search
[27:33] Removing low confidence identifications
[27:52] Removing interfering precursors
[28:05] Training neural networks on 211510 target and 129901 decoy PSMs
[29:31] Training neural networks on 211510 target and 131601 decoy PSMs
[30:14] Number of IDs at 0.01 FDR: 97517
[30:15] Precursors at 1% peptidoform FDR: 94719
[30:15] Calculating protein q-values
[30:16] Number of proteins identified at 1% FDR: 10288 (precursor-level), 9294 (protein-level) (inference performed using proteotypic peptides only)
[30:16] Quantification
[30:20] Precursors with scored PTMs at 1% FDR: 3518 out of 3798 considered
[30:20] Precursors with all scored PTM sites unoccupied at 1% FDR: 91201
[30:20] Precursors with PTMs localised (when required) with > 90% confidence: 3420 out of 3518
[30:51] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw.quant

[30:51] File #6/6
[30:51] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
[32:24] Pre-processing...
[32:27] 2934 MS1 and 293446 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[32:28] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[32:40] RT window set to 1.28987
[32:40] Recommended MS1 mass accuracy setting: 2.8 ppm
[32:46] Searching decoys
[33:02] Main search
[33:47] Removing low confidence identifications
[34:03] Removing interfering precursors
[34:17] Training neural networks on 213168 target and 132099 decoy PSMs
[35:33] Training neural networks on 213168 target and 132812 decoy PSMs
[36:15] Number of IDs at 0.01 FDR: 97973
[36:16] Precursors at 1% peptidoform FDR: 95465
[36:17] Calculating protein q-values
[36:18] Number of proteins identified at 1% FDR: 10395 (precursor-level), 9360 (protein-level) (inference performed using proteotypic peptides only)
[36:18] Quantification
[36:19] Precursors with scored PTMs at 1% FDR: 3575 out of 3837 considered
[36:19] Precursors with all scored PTM sites unoccupied at 1% FDR: 91890
[36:19] Precursors with PTMs localised (when required) with > 90% confidence: 3457 out of 3575
[36:41] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw.quant

[36:41] Cross-run analysis
[36:41] Reading quantification information: 6 files
[37:07] Quantifying peptides
[40:49] Assembling protein groups
[40:52] Quantifying proteins
[40:52] Calculating q-values for protein and gene groups
[40:55] Calculating global q-values for protein and gene groups
[40:55] Protein groups with global q-value <= 0.01: 11035
[41:01] Compressed report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\reportPB10-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[41:02] Site report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\reportPB10-first-pass.site_report.parquet
[41:02] Saving precursor levels matrix
[41:05] Precursor levels matrix (1% precursor and protein group FDR) saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\reportPB10-first-pass.pr_matrix.tsv.
[41:05] Manifest saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\reportPB10-first-pass.manifest.txt
[41:05] Stats report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\reportPB10-first-pass.stats.tsv
[41:06] Generating spectral library:
[41:08] 129146 target and 1309 decoy precursors saved
[41:09] Spectral library saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\PB10.parquet

[41:10] Loading spectral library H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\PB10.parquet
[41:12] Spectral library loaded: 12926 protein isoforms, 12760 protein groups and 130455 precursors in 121948 elution groups.
[41:12] Loading protein annotations from FASTA H:\DELALANDE Frankois\ProteoBench\DIA Astral\ProteoBenchFASTA_MixedSpecies_HYE.fasta
[41:12] Annotating library proteins with information from the FASTA database
[41:12] Gene names missing for some isoforms
[41:12] Library contains 12911 proteins, and 0 genes
[41:12] Initialising library
[41:15] Saving the library to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\PB10.parquet.skyline.speclib


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

[41:21] File #1/6
[41:21] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
[43:15] Pre-processing...
[43:16] 2931 MS1 and 293271 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 129146 precursors in range
[43:16] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[43:16] RT window set to 0.446497
[43:16] Recommended MS1 mass accuracy setting: 3.2 ppm
[43:17] Searching decoys
[43:17] Main search
[43:18] Removing low confidence identifications
[43:22] Removing interfering precursors
[43:23] Training neural networks on 109792 target and 41553 decoy PSMs
[43:43] Training neural networks on 109770 target and 46635 decoy PSMs
[44:04] Number of IDs at 0.01 FDR: 103810
[44:05] Precursors at 1% peptidoform FDR: 101942
[44:05] Calculating protein q-values
[44:05] Number of proteins identified at 1% FDR: 10477 (precursor-level), 9456 (protein-level) (inference performed using proteotypic peptides only)
[44:05] Quantification
[44:06] Precursors with scored PTMs at 1% FDR: 3389 out of 3470 considered
[44:06] Precursors with all scored PTM sites unoccupied at 1% FDR: 98553
[44:06] Precursors with PTMs localised (when required) with > 90% confidence: 3306 out of 3389

[44:07] File #2/6
[44:07] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
[46:14] Pre-processing...
[46:15] 2933 MS1 and 293433 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[46:15] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[46:16] RT window set to 0.436376
[46:16] Recommended MS1 mass accuracy setting: 3.1 ppm
[46:16] Searching decoys
[46:16] Main search
[46:18] Removing low confidence identifications
[46:21] Removing interfering precursors
[46:22] Training neural networks on 109931 target and 40151 decoy PSMs
[46:42] Training neural networks on 109915 target and 45206 decoy PSMs
[47:05] Number of IDs at 0.01 FDR: 104019
[47:06] Precursors at 1% peptidoform FDR: 102396
[47:06] Calculating protein q-values
[47:06] Number of proteins identified at 1% FDR: 10428 (precursor-level), 9393 (protein-level) (inference performed using proteotypic peptides only)
[47:06] Quantification
[47:08] Precursors with scored PTMs at 1% FDR: 3396 out of 3465 considered
[47:08] Precursors with all scored PTM sites unoccupied at 1% FDR: 99000
[47:08] Precursors with PTMs localised (when required) with > 90% confidence: 3333 out of 3396

[47:09] File #3/6
[47:09] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
[49:00] Pre-processing...
[49:02] 2932 MS1 and 293358 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[49:02] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[49:02] RT window set to 0.442972
[49:02] Recommended MS1 mass accuracy setting: 3.2 ppm
[49:03] Searching decoys
[49:03] Main search
[49:04] Removing low confidence identifications
[49:07] Removing interfering precursors
[49:09] Training neural networks on 109966 target and 41230 decoy PSMs
[49:29] Training neural networks on 109949 target and 45952 decoy PSMs
[49:52] Number of IDs at 0.01 FDR: 104257
[49:53] Precursors at 1% peptidoform FDR: 102595
[49:53] Calculating protein q-values
[49:53] Number of proteins identified at 1% FDR: 10421 (precursor-level), 9392 (protein-level) (inference performed using proteotypic peptides only)
[49:53] Quantification
[49:55] Precursors with scored PTMs at 1% FDR: 3455 out of 3531 considered
[49:55] Precursors with all scored PTM sites unoccupied at 1% FDR: 99140
[49:55] Precursors with PTMs localised (when required) with > 90% confidence: 3369 out of 3455

[49:56] File #4/6
[49:56] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
[51:49] Pre-processing...
[51:50] 2933 MS1 and 293382 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[51:50] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[51:51] RT window set to 0.459865
[51:51] Recommended MS1 mass accuracy setting: 3.3 ppm
[51:51] Searching decoys
[51:51] Main search
[51:53] Removing low confidence identifications
[51:56] Removing interfering precursors
[51:57] Training neural networks on 110509 target and 42341 decoy PSMs
[52:20] Training neural networks on 110492 target and 46903 decoy PSMs
[52:43] Number of IDs at 0.01 FDR: 104881
[52:44] Precursors at 1% peptidoform FDR: 102943
[52:44] Calculating protein q-values
[52:44] Number of proteins identified at 1% FDR: 10323 (precursor-level), 9251 (protein-level) (inference performed using proteotypic peptides only)
[52:44] Quantification
[52:45] Precursors with scored PTMs at 1% FDR: 3742 out of 3835 considered
[52:45] Precursors with all scored PTM sites unoccupied at 1% FDR: 99201
[52:45] Precursors with PTMs localised (when required) with > 90% confidence: 3653 out of 3742

[52:47] File #5/6
[52:47] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
[54:28] Pre-processing...
[54:29] 2933 MS1 and 293330 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[54:29] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[54:30] RT window set to 0.456773
[54:30] Recommended MS1 mass accuracy setting: 3.1 ppm
[54:30] Searching decoys
[54:30] Main search
[54:32] Removing low confidence identifications
[54:35] Removing interfering precursors
[54:37] Training neural networks on 110435 target and 41073 decoy PSMs
[55:01] Training neural networks on 110424 target and 45992 decoy PSMs
[55:24] Number of IDs at 0.01 FDR: 105301
[55:25] Precursors at 1% peptidoform FDR: 103653
[55:25] Calculating protein q-values
[55:25] Number of proteins identified at 1% FDR: 10420 (precursor-level), 9356 (protein-level) (inference performed using proteotypic peptides only)
[55:25] Quantification
[55:27] Precursors with scored PTMs at 1% FDR: 3764 out of 3819 considered
[55:27] Precursors with all scored PTM sites unoccupied at 1% FDR: 99889
[55:27] Precursors with PTMs localised (when required) with > 90% confidence: 3673 out of 3764

[55:28] File #6/6
[55:28] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
[57:22] Pre-processing...
[57:23] 2934 MS1 and 293446 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[57:23] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[57:24] RT window set to 0.458218
[57:24] Recommended MS1 mass accuracy setting: 3.1 ppm
[57:24] Searching decoys
[57:25] Main search
[57:27] Removing low confidence identifications
[57:32] Removing interfering precursors
[57:34] Training neural networks on 110378 target and 40243 decoy PSMs
[57:57] Training neural networks on 110360 target and 45570 decoy PSMs
[58:18] Number of IDs at 0.01 FDR: 105647
[58:19] Precursors at 1% peptidoform FDR: 104024
[58:19] Calculating protein q-values
[58:19] Number of proteins identified at 1% FDR: 10421 (precursor-level), 9388 (protein-level) (inference performed using proteotypic peptides only)
[58:19] Quantification
[58:20] Precursors with scored PTMs at 1% FDR: 3800 out of 3878 considered
[58:20] Precursors with all scored PTM sites unoccupied at 1% FDR: 100224
[58:20] Precursors with PTMs localised (when required) with > 90% confidence: 3700 out of 3800

[58:21] Cross-run analysis
[58:21] Reading quantification information: 6 files
[58:24] Quantifying peptides
[61:27] Quantification parameters: 0.36197, 0.00137911, 0.00149523, 0.0116367, 0.0121525, 0.0120709, 0.15409, 0.232723, 0.194053, 0.0130045, 0.0383481, 0.0144233, 0.218886, 0.0517061, 0.0674721, 0.0113128
[62:38] Quantifying proteins
[62:38] Calculating q-values for protein and gene groups
[62:38] Calculating global q-values for protein and gene groups
[62:38] Protein groups with global q-value <= 0.01: 10585
[62:45] Compressed report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\reportPB10.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[62:45] Site report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\reportPB10.site_report.parquet
[62:45] Saving precursor levels matrix
[62:52] Precursor levels matrix (1% precursor and protein group FDR) saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\reportPB10.pr_matrix.tsv.
[62:52] Saving protein group levels matrix
[62:53] Protein groups matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\reportPB10.pg_matrix.tsv.
[62:53] Saving gene group levels matrix
[62:53] Gene groups matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\reportPB10.gg_matrix.tsv.
[62:53] Saving unique genes levels matrix
[62:53] Unique genes matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\reportPB10.unique_genes_matrix.tsv.
[62:56] Manifest saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\reportPB10.manifest.txt
[62:56] Stats report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB10\reportPB10.stats.tsv

