
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 09:48:01 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\PB12\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\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\PB12\reportPB12.parquet --qvalue 0.01 --matrices --out-lib H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\PB12.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 --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
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
[0:16] Library annotated with sequence database(s): H:\DELALANDE Frankois\ProteoBench\DIA Astral\Test 7\ProteoBenchFASTA_MixedSpecies_HYE.fasta
[0:17] Spectral library loaded: 31837 protein isoforms, 51765 protein groups and 5275217 precursors in 2716671 elution groups.
[0:17] Loading protein annotations from FASTA H:\DELALANDE Frankois\ProteoBench\DIA Astral\ProteoBenchFASTA_MixedSpecies_HYE.fasta
[0:18] Annotating library proteins with information from the FASTA database
[0:18] Protein names missing for some isoforms
[0:18] Gene names missing for some isoforms
[0:18] Library contains 31685 proteins, and 0 genes
[0:25] Initialising library

First pass: generating a spectral library from DIA data

[0:55] File #1/6
[0:55] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
[3:09] Pre-processing...
[3:13] 2931 MS1 and 293271 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 5270221 precursors in range
[3:14] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[3:38] RT window set to 1.15599
[3:38] Recommended MS1 mass accuracy setting: 2.5 ppm
[3:42] Searching decoys
[4:00] Main search
[4:39] Removing low confidence identifications
[4:51] Removing interfering precursors
[4:58] Training neural networks on 212592 target and 129831 decoy PSMs
[5:53] Training neural networks on 212592 target and 131977 decoy PSMs
[6:58] Number of IDs at 0.01 FDR: 95905
[6:59] Precursors at 1% peptidoform FDR: 93684
[6:59] Calculating protein q-values
[7:00] Number of proteins identified at 1% FDR: 10489 (precursor-level), 9590 (protein-level) (inference performed using proteotypic peptides only)
[7:01] Quantification
[7:02] Precursors with scored PTMs at 1% FDR: 2914 out of 3086 considered
[7:02] Precursors with all scored PTM sites unoccupied at 1% FDR: 90770
[7:02] Precursors with PTMs localised (when required) with > 90% confidence: 2826 out of 2914
[7:10] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw.quant

[7:10] File #2/6
[7:10] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
[8:39] Pre-processing...
[8:42] 2933 MS1 and 293433 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[8:43] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[9:02] RT window set to 1.42472
[9:02] Recommended MS1 mass accuracy setting: 2.6 ppm
[9:11] Searching decoys
[9:35] Main search
[10:23] Removing low confidence identifications
[10:36] Removing interfering precursors
[10:43] Training neural networks on 207819 target and 126767 decoy PSMs
[11:38] Training neural networks on 207819 target and 128080 decoy PSMs
[12:46] Number of IDs at 0.01 FDR: 97793
[12:47] Precursors at 1% peptidoform FDR: 94798
[12:48] Calculating protein q-values
[12:49] Number of proteins identified at 1% FDR: 10529 (precursor-level), 9604 (protein-level) (inference performed using proteotypic peptides only)
[12:50] Quantification
[12:52] Precursors with scored PTMs at 1% FDR: 2981 out of 3199 considered
[12:52] Precursors with all scored PTM sites unoccupied at 1% FDR: 91817
[12:52] Precursors with PTMs localised (when required) with > 90% confidence: 2910 out of 2981
[13:02] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw.quant

[13:02] File #3/6
[13:02] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
[14:37] Pre-processing...
[14:40] 2932 MS1 and 293358 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[14:41] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[15:00] RT window set to 1.26241
[15:00] Recommended MS1 mass accuracy setting: 2.7 ppm
[15:05] Searching decoys
[15:30] Main search
[16:21] Removing low confidence identifications
[16:40] Removing interfering precursors
[16:48] Training neural networks on 211591 target and 129408 decoy PSMs
[17:45] Training neural networks on 211591 target and 130609 decoy PSMs
[18:56] Number of IDs at 0.01 FDR: 98365
[18:58] Precursors at 1% peptidoform FDR: 95857
[18:59] Calculating protein q-values
[19:00] Number of proteins identified at 1% FDR: 10598 (precursor-level), 9625 (protein-level) (inference performed using proteotypic peptides only)
[19:00] Quantification
[19:02] Precursors with scored PTMs at 1% FDR: 3058 out of 3217 considered
[19:02] Precursors with all scored PTM sites unoccupied at 1% FDR: 92799
[19:02] Precursors with PTMs localised (when required) with > 90% confidence: 2971 out of 3058
[19:11] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw.quant

[19:11] File #4/6
[19:11] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
[20:41] Pre-processing...
[20:43] 2933 MS1 and 293382 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[20:44] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[20:57] RT window set to 1.32292
[20:57] Recommended MS1 mass accuracy setting: 2.7 ppm
[21:02] Searching decoys
[21:24] Main search
[22:02] Removing low confidence identifications
[22:18] Removing interfering precursors
[22:29] Training neural networks on 213424 target and 131576 decoy PSMs
[23:33] Training neural networks on 213424 target and 132891 decoy PSMs
[25:03] Number of IDs at 0.01 FDR: 98159
[25:04] Precursors at 1% peptidoform FDR: 95314
[25:04] Calculating protein q-values
[25:05] Number of proteins identified at 1% FDR: 10336 (precursor-level), 9287 (protein-level) (inference performed using proteotypic peptides only)
[25:05] Quantification
[25:07] Precursors with scored PTMs at 1% FDR: 3511 out of 3811 considered
[25:07] Precursors with all scored PTM sites unoccupied at 1% FDR: 91803
[25:07] Precursors with PTMs localised (when required) with > 90% confidence: 3398 out of 3511
[25:24] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw.quant

[25:24] File #5/6
[25:24] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
[26:58] Pre-processing...
[27:02] 2933 MS1 and 293330 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[27:03] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[27:18] RT window set to 1.2753
[27:18] Recommended MS1 mass accuracy setting: 2.7 ppm
[27:24] Searching decoys
[27:44] Main search
[28:26] Removing low confidence identifications
[28:41] Removing interfering precursors
[28:52] Training neural networks on 211510 target and 129901 decoy PSMs
[29:50] Training neural networks on 211510 target and 131601 decoy PSMs
[31:05] Number of IDs at 0.01 FDR: 97517
[31:07] Precursors at 1% peptidoform FDR: 94719
[31:08] Calculating protein q-values
[31:09] Number of proteins identified at 1% FDR: 10288 (precursor-level), 9294 (protein-level) (inference performed using proteotypic peptides only)
[31:09] Quantification
[31:11] Precursors with scored PTMs at 1% FDR: 3518 out of 3798 considered
[31:11] Precursors with all scored PTM sites unoccupied at 1% FDR: 91201
[31:11] Precursors with PTMs localised (when required) with > 90% confidence: 3420 out of 3518
[31:23] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw.quant

[31:23] File #6/6
[31:23] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
[32:56] Pre-processing...
[32:58] 2934 MS1 and 293446 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[32:59] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[33:10] RT window set to 1.28987
[33:10] Recommended MS1 mass accuracy setting: 2.8 ppm
[33:15] Searching decoys
[33:35] Main search
[34:11] Removing low confidence identifications
[34:23] Removing interfering precursors
[34:31] Training neural networks on 213168 target and 132099 decoy PSMs
[35:23] Training neural networks on 213168 target and 132812 decoy PSMs
[36:16] Number of IDs at 0.01 FDR: 97973
[36:17] Precursors at 1% peptidoform FDR: 95465
[36:18] 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)
[36:19] Quantification
[36:20] Precursors with scored PTMs at 1% FDR: 3575 out of 3837 considered
[36:20] Precursors with all scored PTM sites unoccupied at 1% FDR: 91890
[36:20] Precursors with PTMs localised (when required) with > 90% confidence: 3457 out of 3575
[36:34] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw.quant

[36:34] Cross-run analysis
[36:34] Reading quantification information: 6 files
[37:02] Quantifying peptides
[39:36] Assembling protein groups
[39:40] Quantifying proteins
[39:40] Calculating q-values for protein and gene groups
[39:44] Calculating global q-values for protein and gene groups
[39:45] Protein groups with global q-value <= 0.01: 11035
[39:52] Compressed report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\reportPB12-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[39:52] Site report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\reportPB12-first-pass.site_report.parquet
[39:52] Saving precursor levels matrix
[39:56] Precursor levels matrix (1% precursor and protein group FDR) saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\reportPB12-first-pass.pr_matrix.tsv.
[39:56] Manifest saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\reportPB12-first-pass.manifest.txt
[39:56] Stats report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\reportPB12-first-pass.stats.tsv
[39:57] Generating spectral library:
[39:59] 119157 target and 954 decoy precursors saved
WARNING: 10344 precursors without any fragments annotated were skipped
[39:59] Spectral library saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\PB12.parquet

[40:01] Loading spectral library H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\PB12.parquet
[40:02] Spectral library loaded: 12252 protein isoforms, 12107 protein groups and 120111 precursors in 112216 elution groups.
[40:02] Loading protein annotations from FASTA H:\DELALANDE Frankois\ProteoBench\DIA Astral\ProteoBenchFASTA_MixedSpecies_HYE.fasta
[40:03] Annotating library proteins with information from the FASTA database
[40:03] Gene names missing for some isoforms
[40:03] Library contains 12241 proteins, and 0 genes
[40:03] Initialising library
[40:05] Saving the library to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\PB12.parquet.skyline.speclib


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

[40:10] File #1/6
[40:10] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
[42:20] Pre-processing...
[42:22] 2931 MS1 and 293271 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 119157 precursors in range
[42:22] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[42:22] RT window set to 0.433456
[42:22] Recommended MS1 mass accuracy setting: 3.3 ppm
[42:23] Searching decoys
[42:23] Main search
[42:24] Removing low confidence identifications
[42:29] Removing interfering precursors
[42:30] Training neural networks on 99798 target and 33892 decoy PSMs
[42:52] Training neural networks on 99764 target and 39345 decoy PSMs
[43:11] Number of IDs at 0.01 FDR: 97210
[43:11] Precursors at 1% peptidoform FDR: 96296
[43:11] Calculating protein q-values
[43:11] Number of proteins identified at 1% FDR: 10073 (precursor-level), 8990 (protein-level) (inference performed using proteotypic peptides only)
[43:11] Quantification
[43:12] Precursors with scored PTMs at 1% FDR: 3255 out of 3286 considered
[43:12] Precursors with all scored PTM sites unoccupied at 1% FDR: 93041
[43:12] Precursors with PTMs localised (when required) with > 90% confidence: 3178 out of 3255

[43:13] File #2/6
[43:13] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
[45:05] Pre-processing...
[45:07] 2933 MS1 and 293433 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 119157 precursors in range
[45:07] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[45:07] RT window set to 0.42944
[45:07] Recommended MS1 mass accuracy setting: 3.2 ppm
[45:08] Searching decoys
[45:08] Main search
[45:09] Removing low confidence identifications
[45:13] Removing interfering precursors
[45:15] Training neural networks on 100049 target and 35217 decoy PSMs
[45:37] Training neural networks on 100022 target and 40185 decoy PSMs
[45:54] Number of IDs at 0.01 FDR: 97890
[45:55] Precursors at 1% peptidoform FDR: 97135
[45:55] Calculating protein q-values
[45:55] Number of proteins identified at 1% FDR: 10026 (precursor-level), 8991 (protein-level) (inference performed using proteotypic peptides only)
[45:55] Quantification
[45:56] Precursors with scored PTMs at 1% FDR: 3273 out of 3299 considered
[45:56] Precursors with all scored PTM sites unoccupied at 1% FDR: 93862
[45:56] Precursors with PTMs localised (when required) with > 90% confidence: 3207 out of 3273

[45:57] File #3/6
[45:57] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
[47:45] Pre-processing...
[47:47] 2932 MS1 and 293358 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 119157 precursors in range
[47:48] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[47:48] RT window set to 0.44048
[47:48] Recommended MS1 mass accuracy setting: 2.9 ppm
[47:48] Searching decoys
[47:49] Main search
[47:51] Removing low confidence identifications
[47:56] Removing interfering precursors
[47:58] Training neural networks on 99971 target and 35579 decoy PSMs
[48:18] Training neural networks on 99946 target and 40476 decoy PSMs
[48:37] Number of IDs at 0.01 FDR: 97774
[48:37] Precursors at 1% peptidoform FDR: 97275
[48:37] Calculating protein q-values
[48:37] Number of proteins identified at 1% FDR: 10011 (precursor-level), 8989 (protein-level) (inference performed using proteotypic peptides only)
[48:37] Quantification
[48:38] Precursors with scored PTMs at 1% FDR: 3311 out of 3339 considered
[48:38] Precursors with all scored PTM sites unoccupied at 1% FDR: 93964
[48:38] Precursors with PTMs localised (when required) with > 90% confidence: 3229 out of 3311

[48:39] File #4/6
[48:39] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
[50:21] Pre-processing...
[50:22] 2933 MS1 and 293382 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 119157 precursors in range
[50:22] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[50:22] RT window set to 0.452264
[50:22] Recommended MS1 mass accuracy setting: 3.2 ppm
[50:23] Searching decoys
[50:23] Main search
[50:24] Removing low confidence identifications
[50:30] Removing interfering precursors
[50:32] Training neural networks on 100441 target and 35856 decoy PSMs
[50:53] Training neural networks on 100412 target and 40770 decoy PSMs
[51:14] Number of IDs at 0.01 FDR: 98265
[51:15] Precursors at 1% peptidoform FDR: 97519
[51:15] Calculating protein q-values
[51:15] Number of proteins identified at 1% FDR: 9931 (precursor-level), 8819 (protein-level) (inference performed using proteotypic peptides only)
[51:15] Quantification
[51:16] Precursors with scored PTMs at 1% FDR: 3546 out of 3578 considered
[51:16] Precursors with all scored PTM sites unoccupied at 1% FDR: 93973
[51:16] Precursors with PTMs localised (when required) with > 90% confidence: 3462 out of 3546

[51:17] File #5/6
[51:17] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
[53:03] Pre-processing...
[53:04] 2933 MS1 and 293330 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 119157 precursors in range
[53:04] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[53:04] RT window set to 0.448805
[53:04] Recommended MS1 mass accuracy setting: 2.9 ppm
[53:05] Searching decoys
[53:05] Main search
[53:06] Removing low confidence identifications
[53:09] Removing interfering precursors
[53:11] Training neural networks on 100549 target and 35676 decoy PSMs
[53:32] Training neural networks on 100525 target and 40697 decoy PSMs
[53:54] Number of IDs at 0.01 FDR: 98866
[53:55] Precursors at 1% peptidoform FDR: 98181
[53:55] Calculating protein q-values
[53:55] Number of proteins identified at 1% FDR: 10001 (precursor-level), 8905 (protein-level) (inference performed using proteotypic peptides only)
[53:55] Quantification
[53:56] Precursors with scored PTMs at 1% FDR: 3625 out of 3639 considered
[53:56] Precursors with all scored PTM sites unoccupied at 1% FDR: 94556
[53:56] Precursors with PTMs localised (when required) with > 90% confidence: 3544 out of 3625

[53:58] File #6/6
[53:58] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
[55:36] Pre-processing...
[55:37] 2934 MS1 and 293446 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 119157 precursors in range
[55:37] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[55:37] RT window set to 0.445132
[55:37] Recommended MS1 mass accuracy setting: 3.1 ppm
[55:38] Searching decoys
[55:38] Main search
[55:39] Removing low confidence identifications
[55:42] Removing interfering precursors
[55:44] Training neural networks on 100476 target and 33198 decoy PSMs
[56:00] Training neural networks on 100451 target and 38775 decoy PSMs
[56:19] Number of IDs at 0.01 FDR: 98651
[56:19] Precursors at 1% peptidoform FDR: 97878
[56:19] Calculating protein q-values
[56:19] Number of proteins identified at 1% FDR: 9996 (precursor-level), 8956 (protein-level) (inference performed using proteotypic peptides only)
[56:19] Quantification
[56:21] Precursors with scored PTMs at 1% FDR: 3633 out of 3681 considered
[56:21] Precursors with all scored PTM sites unoccupied at 1% FDR: 94245
[56:21] Precursors with PTMs localised (when required) with > 90% confidence: 3545 out of 3633

[56:22] Cross-run analysis
[56:22] Reading quantification information: 6 files
[56:25] Quantifying peptides
[59:12] Quantification parameters: 0.327925, 0.00141594, 0.00137949, 0.0119027, 0.0121215, 0.0120077, 0.128729, 0.234487, 0.190309, 0.0129665, 0.0367774, 0.0152707, 0.206941, 0.0520695, 0.0693261, 0.0113354
[60:30] Quantifying proteins
[60:30] Calculating q-values for protein and gene groups
[60:30] Calculating global q-values for protein and gene groups
[60:30] Protein groups with global q-value <= 0.01: 10301
[60:37] Compressed report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\reportPB12.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[60:37] Site report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\reportPB12.site_report.parquet
[60:37] Saving precursor levels matrix
[60:48] Precursor levels matrix (1% precursor and protein group FDR) saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\reportPB12.pr_matrix.tsv.
[60:48] Saving protein group levels matrix
[60:48] Protein groups matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\reportPB12.pg_matrix.tsv.
[60:48] Saving gene group levels matrix
[60:48] Gene groups matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\reportPB12.gg_matrix.tsv.
[60:48] Saving unique genes levels matrix
[60:48] Unique genes matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\reportPB12.unique_genes_matrix.tsv.
[60:51] Manifest saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\reportPB12.manifest.txt
[60:51] Stats report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB12\reportPB12.stats.tsv

