
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 11:13:01 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\PB14\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\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\PB14\reportPB14.parquet --qvalue 0.01 --matrices --out-lib H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\PB14.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 --id-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 RTs and spectra
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
[0:29] Library annotated with sequence database(s): H:\DELALANDE Frankois\ProteoBench\DIA Astral\Test 7\ProteoBenchFASTA_MixedSpecies_HYE.fasta
[0:30] Spectral library loaded: 31837 protein isoforms, 51765 protein groups and 5275217 precursors in 2716671 elution groups.
[0:30] Loading protein annotations from FASTA H:\DELALANDE Frankois\ProteoBench\DIA Astral\ProteoBenchFASTA_MixedSpecies_HYE.fasta
[0:31] Annotating library proteins with information from the FASTA database
[0:31] Protein names missing for some isoforms
[0:31] Gene names missing for some isoforms
[0:31] Library contains 31685 proteins, and 0 genes
[0:37] Initialising library

First pass: generating a spectral library from DIA data

[0:54] File #1/6
[0:54] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
[2:48] Pre-processing...
[2:51] 2931 MS1 and 293271 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 5270221 precursors in range
[2:53] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[3:17] RT window set to 1.15599
[3:17] Recommended MS1 mass accuracy setting: 2.5 ppm
[3:23] Searching decoys
[3:44] Main search
[4:21] Removing low confidence identifications
[4:34] Removing interfering precursors
[4:42] Training neural networks on 212592 target and 129831 decoy PSMs
[5:47] Training neural networks on 212592 target and 131977 decoy PSMs
[6:57] Number of IDs at 0.01 FDR: 95905
[6:58] 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
[7:03] Precursors with scored PTMs at 1% FDR: 2914 out of 3086 considered
[7:03] Precursors with all scored PTM sites unoccupied at 1% FDR: 90770
[7:03] Precursors with PTMs localised (when required) with > 90% confidence: 2826 out of 2914
[7:30] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw.quant

[7:30] File #2/6
[7:30] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
[9:01] Pre-processing...
[9:04] 2933 MS1 and 293433 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[9:05] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[9:27] RT window set to 1.42472
[9:27] Recommended MS1 mass accuracy setting: 2.6 ppm
[9:35] Searching decoys
[10:05] Main search
[11:25] Removing low confidence identifications
[11:49] Removing interfering precursors
[11:58] Training neural networks on 207819 target and 126767 decoy PSMs
[12:59] Training neural networks on 207819 target and 128080 decoy PSMs
[13:48] Number of IDs at 0.01 FDR: 97793
[13:49] Precursors at 1% peptidoform FDR: 94798
[13:50] Calculating protein q-values
[13:50] Number of proteins identified at 1% FDR: 10529 (precursor-level), 9604 (protein-level) (inference performed using proteotypic peptides only)
[13:51] Quantification
[13:52] Precursors with scored PTMs at 1% FDR: 2981 out of 3199 considered
[13:52] Precursors with all scored PTM sites unoccupied at 1% FDR: 91817
[13:52] Precursors with PTMs localised (when required) with > 90% confidence: 2910 out of 2981
[14:07] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw.quant

[14:07] File #3/6
[14:07] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
[15:38] Pre-processing...
[15:41] 2932 MS1 and 293358 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[15:42] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[16:05] RT window set to 1.26241
[16:05] Recommended MS1 mass accuracy setting: 2.7 ppm
[16:10] Searching decoys
[16:35] Main search
[17:27] Removing low confidence identifications
[17:52] Removing interfering precursors
[18:05] Training neural networks on 211591 target and 129408 decoy PSMs
[19:19] Training neural networks on 211591 target and 130609 decoy PSMs
[20:13] Number of IDs at 0.01 FDR: 98365
[20:14] Precursors at 1% peptidoform FDR: 95857
[20:14] Calculating protein q-values
[20:15] Number of proteins identified at 1% FDR: 10598 (precursor-level), 9625 (protein-level) (inference performed using proteotypic peptides only)
[20:15] Quantification
[20:16] Precursors with scored PTMs at 1% FDR: 3058 out of 3217 considered
[20:16] Precursors with all scored PTM sites unoccupied at 1% FDR: 92799
[20:16] Precursors with PTMs localised (when required) with > 90% confidence: 2971 out of 3058
[20:36] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw.quant

[20:36] File #4/6
[20:36] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
[21:58] Pre-processing...
[22:02] 2933 MS1 and 293382 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[22:04] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[22:25] RT window set to 1.32292
[22:25] Recommended MS1 mass accuracy setting: 2.7 ppm
[22:35] Searching decoys
[22:58] Main search
[23:50] Removing low confidence identifications
[24:12] Removing interfering precursors
[24:25] Training neural networks on 213424 target and 131576 decoy PSMs
[25:39] Training neural networks on 213424 target and 132891 decoy PSMs
[26:38] Number of IDs at 0.01 FDR: 98159
[26:39] Precursors at 1% peptidoform FDR: 95314
[26:39] Calculating protein q-values
[26:40] Number of proteins identified at 1% FDR: 10336 (precursor-level), 9287 (protein-level) (inference performed using proteotypic peptides only)
[26:40] Quantification
[26:41] Precursors with scored PTMs at 1% FDR: 3511 out of 3811 considered
[26:41] Precursors with all scored PTM sites unoccupied at 1% FDR: 91803
[26:41] Precursors with PTMs localised (when required) with > 90% confidence: 3398 out of 3511
[26:58] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw.quant

[26:58] File #5/6
[26:58] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
[28:51] Pre-processing...
[28:55] 2933 MS1 and 293330 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[28:56] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[29:24] RT window set to 1.2753
[29:24] Recommended MS1 mass accuracy setting: 2.7 ppm
[29:29] Searching decoys
[29:54] Main search
[30:39] Removing low confidence identifications
[30:56] Removing interfering precursors
[31:04] Training neural networks on 211510 target and 129901 decoy PSMs
[32:14] Training neural networks on 211510 target and 131601 decoy PSMs
[33:06] Number of IDs at 0.01 FDR: 97517
[33:07] Precursors at 1% peptidoform FDR: 94719
[33:08] Calculating protein q-values
[33:09] Number of proteins identified at 1% FDR: 10288 (precursor-level), 9294 (protein-level) (inference performed using proteotypic peptides only)
[33:09] Quantification
[33:10] Precursors with scored PTMs at 1% FDR: 3518 out of 3798 considered
[33:10] Precursors with all scored PTM sites unoccupied at 1% FDR: 91201
[33:10] Precursors with PTMs localised (when required) with > 90% confidence: 3420 out of 3518
[33:26] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw.quant

[33:26] File #6/6
[33:26] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
[34:35] Pre-processing...
[34:38] 2934 MS1 and 293446 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[34:39] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[34:51] RT window set to 1.28987
[34:51] Recommended MS1 mass accuracy setting: 2.8 ppm
[34:57] Searching decoys
[35:15] Main search
[36:02] Removing low confidence identifications
[36:16] Removing interfering precursors
[36:28] Training neural networks on 213168 target and 132099 decoy PSMs
[37:25] Training neural networks on 213168 target and 132812 decoy PSMs
[38:09] Number of IDs at 0.01 FDR: 97973
[38:10] Precursors at 1% peptidoform FDR: 95465
[38:11] Calculating protein q-values
[38:11] Number of proteins identified at 1% FDR: 10395 (precursor-level), 9360 (protein-level) (inference performed using proteotypic peptides only)
[38:11] Quantification
[38:13] Precursors with scored PTMs at 1% FDR: 3575 out of 3837 considered
[38:13] Precursors with all scored PTM sites unoccupied at 1% FDR: 91890
[38:13] Precursors with PTMs localised (when required) with > 90% confidence: 3457 out of 3575
[38:30] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw.quant

[38:30] Cross-run analysis
[38:30] Reading quantification information: 6 files
[39:00] Quantifying peptides
[42:36] Assembling protein groups
[42:39] Quantifying proteins
[42:39] Calculating q-values for protein and gene groups
[42:42] Calculating global q-values for protein and gene groups
[42:42] Protein groups with global q-value <= 0.01: 11035
[42:48] Compressed report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\reportPB14-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[42:48] Site report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\reportPB14-first-pass.site_report.parquet
[42:48] Saving precursor levels matrix
[42:51] Precursor levels matrix (1% precursor and protein group FDR) saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\reportPB14-first-pass.pr_matrix.tsv.
[42:51] Manifest saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\reportPB14-first-pass.manifest.txt
[42:51] Stats report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\reportPB14-first-pass.stats.tsv
[42:52] Generating spectral library:
[42:55] 129146 target and 1309 decoy precursors saved
[42:55] Spectral library saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\PB14.parquet

[42:56] Loading spectral library H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\PB14.parquet
[42:58] Spectral library loaded: 12926 protein isoforms, 12760 protein groups and 130455 precursors in 121948 elution groups.
[42:59] Loading protein annotations from FASTA H:\DELALANDE Frankois\ProteoBench\DIA Astral\ProteoBenchFASTA_MixedSpecies_HYE.fasta
[42:59] Annotating library proteins with information from the FASTA database
[42:59] Gene names missing for some isoforms
[42:59] Library contains 12911 proteins, and 0 genes
[42:59] Initialising library
[43:02] Saving the library to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\PB14.parquet.skyline.speclib


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

[43:07] File #1/6
[43:07] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
[44:47] Pre-processing...
[44:49] 2931 MS1 and 293271 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 129146 precursors in range
[44:49] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[44:49] RT window set to 1.04916
[44:49] Recommended MS1 mass accuracy setting: 3.2 ppm
[44:49] Searching decoys
[44:50] Main search
[44:52] Removing low confidence identifications
[44:56] Removing interfering precursors
[44:57] Training neural networks on 110123 target and 55115 decoy PSMs
[45:19] Training neural networks on 110100 target and 58401 decoy PSMs
[45:41] Number of IDs at 0.01 FDR: 99842
[45:42] Precursors at 1% peptidoform FDR: 97701
[45:42] Calculating protein q-values
[45:42] Number of proteins identified at 1% FDR: 10148 (precursor-level), 9341 (protein-level) (inference performed using proteotypic peptides only)
[45:42] Quantification
[45:43] Precursors with scored PTMs at 1% FDR: 3236 out of 3352 considered
[45:43] Precursors with all scored PTM sites unoccupied at 1% FDR: 94465
[45:43] Precursors with PTMs localised (when required) with > 90% confidence: 3152 out of 3236

[45:44] File #2/6
[45:44] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
[47:27] Pre-processing...
[47:28] 2933 MS1 and 293433 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[47:28] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[47:28] RT window set to 1.10914
[47:28] Recommended MS1 mass accuracy setting: 3.3 ppm
[47:29] Searching decoys
[47:29] Main search
[47:31] Removing low confidence identifications
[47:35] Removing interfering precursors
[47:37] Training neural networks on 110680 target and 55637 decoy PSMs
[48:03] Training neural networks on 110663 target and 58685 decoy PSMs
[48:28] Number of IDs at 0.01 FDR: 100583
[48:29] Precursors at 1% peptidoform FDR: 98430
[48:29] Calculating protein q-values
[48:29] Number of proteins identified at 1% FDR: 10151 (precursor-level), 9412 (protein-level) (inference performed using proteotypic peptides only)
[48:29] Quantification
[48:31] Precursors with scored PTMs at 1% FDR: 3274 out of 3425 considered
[48:31] Precursors with all scored PTM sites unoccupied at 1% FDR: 95156
[48:31] Precursors with PTMs localised (when required) with > 90% confidence: 3203 out of 3274

[48:32] File #3/6
[48:32] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
[50:16] Pre-processing...
[50:17] 2932 MS1 and 293358 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[50:17] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[50:17] RT window set to 1.08407
[50:17] Recommended MS1 mass accuracy setting: 3 ppm
[50:18] Searching decoys
[50:18] Main search
[50:20] Removing low confidence identifications
[50:25] Removing interfering precursors
[50:27] Training neural networks on 110364 target and 55400 decoy PSMs
[51:10] Training neural networks on 110350 target and 58596 decoy PSMs
[51:54] Number of IDs at 0.01 FDR: 100175
[51:55] Precursors at 1% peptidoform FDR: 97982
[51:55] Calculating protein q-values
[51:55] Number of proteins identified at 1% FDR: 10102 (precursor-level), 9344 (protein-level) (inference performed using proteotypic peptides only)
[51:55] Quantification
[51:56] Precursors with scored PTMs at 1% FDR: 3229 out of 3346 considered
[51:56] Precursors with all scored PTM sites unoccupied at 1% FDR: 94753
[51:56] Precursors with PTMs localised (when required) with > 90% confidence: 3159 out of 3229

[51:58] File #4/6
[51:58] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
[53:41] Pre-processing...
[53:42] 2933 MS1 and 293382 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[53:42] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[53:42] RT window set to 1.09352
[53:42] Recommended MS1 mass accuracy setting: 3.3 ppm
[53:43] Searching decoys
[53:43] Main search
[53:45] Removing low confidence identifications
[53:50] Removing interfering precursors
[53:52] Training neural networks on 111098 target and 55811 decoy PSMs
[54:18] Training neural networks on 111089 target and 59304 decoy PSMs
[54:43] Number of IDs at 0.01 FDR: 100955
[54:44] Precursors at 1% peptidoform FDR: 98997
[54:44] Calculating protein q-values
[54:44] Number of proteins identified at 1% FDR: 9994 (precursor-level), 9232 (protein-level) (inference performed using proteotypic peptides only)
[54:44] Quantification
[54:45] Precursors with scored PTMs at 1% FDR: 3582 out of 3683 considered
[54:45] Precursors with all scored PTM sites unoccupied at 1% FDR: 95415
[54:45] Precursors with PTMs localised (when required) with > 90% confidence: 3491 out of 3582

[54:46] File #5/6
[54:46] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
[56:34] Pre-processing...
[56:36] 2933 MS1 and 293330 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[56:36] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[56:36] RT window set to 1.08986
[56:36] Recommended MS1 mass accuracy setting: 3.2 ppm
[56:37] Searching decoys
[56:37] Main search
[56:39] Removing low confidence identifications
[56:44] Removing interfering precursors
[56:46] Training neural networks on 110719 target and 54164 decoy PSMs
[57:17] Training neural networks on 110708 target and 58108 decoy PSMs
[57:49] Number of IDs at 0.01 FDR: 100874
[57:50] Precursors at 1% peptidoform FDR: 98829
[57:50] Calculating protein q-values
[57:50] Number of proteins identified at 1% FDR: 10028 (precursor-level), 9145 (protein-level) (inference performed using proteotypic peptides only)
[57:50] Quantification
[57:51] Precursors with scored PTMs at 1% FDR: 3594 out of 3705 considered
[57:51] Precursors with all scored PTM sites unoccupied at 1% FDR: 95235
[57:51] Precursors with PTMs localised (when required) with > 90% confidence: 3511 out of 3594

[57:52] File #6/6
[57:52] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
[59:35] Pre-processing...
[59:36] 2934 MS1 and 293446 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[59:36] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[59:37] RT window set to 1.06989
[59:37] Recommended MS1 mass accuracy setting: 3.1 ppm
[59:38] Searching decoys
[59:38] Main search
[59:41] Removing low confidence identifications
[59:50] Removing interfering precursors
[59:54] Training neural networks on 111210 target and 55812 decoy PSMs
[60:42] Training neural networks on 111183 target and 59280 decoy PSMs
[61:12] Number of IDs at 0.01 FDR: 101452
[61:13] Precursors at 1% peptidoform FDR: 99302
[61:13] Calculating protein q-values
[61:13] Number of proteins identified at 1% FDR: 10080 (precursor-level), 9280 (protein-level) (inference performed using proteotypic peptides only)
[61:13] Quantification
[61:14] Precursors with scored PTMs at 1% FDR: 3641 out of 3752 considered
[61:14] Precursors with all scored PTM sites unoccupied at 1% FDR: 95661
[61:14] Precursors with PTMs localised (when required) with > 90% confidence: 3548 out of 3641

[61:15] Cross-run analysis
[61:15] Reading quantification information: 6 files
[61:18] Quantifying peptides
[64:20] Quantification parameters: 0.368591, 0.00141226, 0.00158916, 0.0119058, 0.0121219, 0.0120109, 0.173434, 0.23032, 0.194815, 0.0133262, 0.0375506, 0.0146678, 0.236702, 0.0519567, 0.0690644, 0.0111547
[65:28] Quantifying proteins
[65:28] Calculating q-values for protein and gene groups
[65:29] Calculating global q-values for protein and gene groups
[65:29] Protein groups with global q-value <= 0.01: 10596
[65:35] Compressed report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\reportPB14.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[65:35] Site report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\reportPB14.site_report.parquet
[65:35] Saving precursor levels matrix
[65:38] Precursor levels matrix (1% precursor and protein group FDR) saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\reportPB14.pr_matrix.tsv.
[65:38] Saving protein group levels matrix
[65:38] Protein groups matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\reportPB14.pg_matrix.tsv.
[65:38] Saving gene group levels matrix
[65:38] Gene groups matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\reportPB14.gg_matrix.tsv.
[65:38] Saving unique genes levels matrix
[65:39] Unique genes matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\reportPB14.unique_genes_matrix.tsv.
[65:39] Manifest saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\reportPB14.manifest.txt
[65:39] Stats report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB14\reportPB14.stats.tsv

