
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 09:28:58 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\PB8\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\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\PB8\reportPB6.parquet --qvalue 0.01 --matrices --out-lib H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\PB8.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 10 --mass-acc 10 --mass-acc-ms1 10 --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 10
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 1e-05 (MS2) and 1e-05 (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
[0:11] Library annotated with sequence database(s): H:\DELALANDE Frankois\ProteoBench\DIA Astral\Test 7\ProteoBenchFASTA_MixedSpecies_HYE.fasta
[0:12] Spectral library loaded: 31837 protein isoforms, 51765 protein groups and 5275217 precursors in 2716671 elution groups.
[0:12] Loading protein annotations from FASTA H:\DELALANDE Frankois\ProteoBench\DIA Astral\ProteoBenchFASTA_MixedSpecies_HYE.fasta
[0:13] Annotating library proteins with information from the FASTA database
[0:13] Protein names missing for some isoforms
[0:13] Gene names missing for some isoforms
[0:13] Library contains 31685 proteins, and 0 genes
[0:17] Initialising library

First pass: generating a spectral library from DIA data

[0:32] File #1/6
[0:32] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
[2:14] Pre-processing...
[2:16] 2931 MS1 and 293271 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 5270221 precursors in range
[2:17] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[2:30] RT window set to 1.24867
[2:30] Recommended MS1 mass accuracy setting: 2.3 ppm
[2:36] Searching decoys
[3:06] Main search
[4:07] Removing low confidence identifications
[4:23] Removing interfering precursors
[4:32] Training neural networks on 181748 target and 117411 decoy PSMs
[5:22] Training neural networks on 181748 target and 117547 decoy PSMs
[6:04] Number of IDs at 0.01 FDR: 103946
[6:05] Precursors at 1% peptidoform FDR: 101914
[6:06] Calculating protein q-values
[6:06] Number of proteins identified at 1% FDR: 10919 (precursor-level), 9956 (protein-level) (inference performed using proteotypic peptides only)
[6:06] Quantification
[6:08] Precursors with scored PTMs at 1% FDR: 3366 out of 3541 considered
[6:08] Precursors with all scored PTM sites unoccupied at 1% FDR: 98548
[6:08] Precursors with PTMs localised (when required) with > 90% confidence: 3276 out of 3366
[6:24] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw.quant

[6:24] File #2/6
[6:24] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
[8:00] Pre-processing...
[8:02] 2933 MS1 and 293433 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[8:02] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[8:16] RT window set to 1.32949
[8:17] Recommended MS1 mass accuracy setting: 2.2 ppm
[8:22] Searching decoys
[8:54] Main search
[9:58] Removing low confidence identifications
[10:14] Removing interfering precursors
[10:23] Training neural networks on 187437 target and 122762 decoy PSMs
[11:13] Training neural networks on 187437 target and 122821 decoy PSMs
[11:56] Number of IDs at 0.01 FDR: 105838
[11:57] Precursors at 1% peptidoform FDR: 103407
[11:58] Calculating protein q-values
[11:58] Number of proteins identified at 1% FDR: 10939 (precursor-level), 9855 (protein-level) (inference performed using proteotypic peptides only)
[11:58] Quantification
[12:00] Precursors with scored PTMs at 1% FDR: 3540 out of 3736 considered
[12:00] Precursors with all scored PTM sites unoccupied at 1% FDR: 99867
[12:00] Precursors with PTMs localised (when required) with > 90% confidence: 3453 out of 3540
[12:19] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw.quant

[12:19] File #3/6
[12:19] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
[13:56] Pre-processing...
[13:58] 2932 MS1 and 293358 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[13:59] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[14:12] RT window set to 1.26082
[14:12] Recommended MS1 mass accuracy setting: 2.5 ppm
[14:17] Searching decoys
[14:49] Main search
[15:52] Removing low confidence identifications
[16:07] Removing interfering precursors
[16:16] Training neural networks on 188016 target and 123556 decoy PSMs
[17:04] Training neural networks on 188016 target and 123372 decoy PSMs
[17:48] Number of IDs at 0.01 FDR: 106556
[17:49] Precursors at 1% peptidoform FDR: 103700
[17:50] Calculating protein q-values
[17:51] Number of proteins identified at 1% FDR: 11009 (precursor-level), 9988 (protein-level) (inference performed using proteotypic peptides only)
[17:51] Quantification
[17:52] Precursors with scored PTMs at 1% FDR: 3548 out of 3785 considered
[17:52] Precursors with all scored PTM sites unoccupied at 1% FDR: 100152
[17:52] Precursors with PTMs localised (when required) with > 90% confidence: 3444 out of 3548
[18:05] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw.quant

[18:05] File #4/6
[18:05] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
[19:22] Pre-processing...
[19:24] 2933 MS1 and 293382 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[19:25] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[19:40] RT window set to 1.30757
[19:41] Recommended MS1 mass accuracy setting: 2.6 ppm
[19:47] Searching decoys
[20:20] Main search
[21:31] Removing low confidence identifications
[21:50] Removing interfering precursors
[22:02] Training neural networks on 189626 target and 126406 decoy PSMs
[22:57] Training neural networks on 189626 target and 126286 decoy PSMs
[23:45] Number of IDs at 0.01 FDR: 106417
[23:46] Precursors at 1% peptidoform FDR: 103701
[23:46] Calculating protein q-values
[23:47] Number of proteins identified at 1% FDR: 10797 (precursor-level), 9702 (protein-level) (inference performed using proteotypic peptides only)
[23:47] Quantification
[23:49] Precursors with scored PTMs at 1% FDR: 4098 out of 4368 considered
[23:49] Precursors with all scored PTM sites unoccupied at 1% FDR: 99603
[23:49] Precursors with PTMs localised (when required) with > 90% confidence: 3969 out of 4098
[24:06] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw.quant

[24:06] File #5/6
[24:06] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
[25:20] Pre-processing...
[25:24] 2933 MS1 and 293330 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[25:25] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[25:48] RT window set to 1.27516
[25:48] Recommended MS1 mass accuracy setting: 2.4 ppm
[25:57] Searching decoys
[26:28] Main search
[27:32] Removing low confidence identifications
[27:51] Removing interfering precursors
[28:02] Training neural networks on 188268 target and 124074 decoy PSMs
[28:56] Training neural networks on 188268 target and 123659 decoy PSMs
[29:43] Number of IDs at 0.01 FDR: 106147
[29:44] Precursors at 1% peptidoform FDR: 103581
[29:45] Calculating protein q-values
[29:45] Number of proteins identified at 1% FDR: 10836 (precursor-level), 9737 (protein-level) (inference performed using proteotypic peptides only)
[29:45] Quantification
[29:47] Precursors with scored PTMs at 1% FDR: 4121 out of 4369 considered
[29:47] Precursors with all scored PTM sites unoccupied at 1% FDR: 99460
[29:47] Precursors with PTMs localised (when required) with > 90% confidence: 4014 out of 4121
[30:06] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw.quant

[30:06] File #6/6
[30:06] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
[31:19] Pre-processing...
[31:22] 2934 MS1 and 293446 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[31:24] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[31:38] RT window set to 1.39049
[31:38] Recommended MS1 mass accuracy setting: 2.7 ppm
[31:45] Searching decoys
[32:21] Main search
[33:34] Removing low confidence identifications
[33:54] Removing interfering precursors
[34:05] Training neural networks on 186380 target and 123343 decoy PSMs
[35:11] Training neural networks on 186380 target and 122959 decoy PSMs
[36:02] Number of IDs at 0.01 FDR: 105972
[36:04] Precursors at 1% peptidoform FDR: 103827
[36:04] Calculating protein q-values
[36:05] Number of proteins identified at 1% FDR: 10807 (precursor-level), 9674 (protein-level) (inference performed using proteotypic peptides only)
[36:06] Quantification
[36:08] Precursors with scored PTMs at 1% FDR: 4150 out of 4362 considered
[36:08] Precursors with all scored PTM sites unoccupied at 1% FDR: 99677
[36:08] Precursors with PTMs localised (when required) with > 90% confidence: 4034 out of 4150
[36:26] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw.quant

[36:26] Cross-run analysis
[36:26] Reading quantification information: 6 files
[37:05] Quantifying peptides
[40:30] Assembling protein groups
[40:34] Quantifying proteins
[40:34] Calculating q-values for protein and gene groups
[40:38] Calculating global q-values for protein and gene groups
[40:38] Protein groups with global q-value <= 0.01: 11444
[40:45] Compressed report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\reportPB6-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[40:45] Site report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\reportPB6-first-pass.site_report.parquet
[40:45] Saving precursor levels matrix
[40:52] Precursor levels matrix (1% precursor and protein group FDR) saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\reportPB6-first-pass.pr_matrix.tsv.
[40:52] Manifest saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\reportPB6-first-pass.manifest.txt
[40:52] Stats report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\reportPB6-first-pass.stats.tsv
[40:53] Generating spectral library:
[40:56] 137138 target and 1393 decoy precursors saved
[40:57] Spectral library saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\PB8.parquet

[40:57] Loading spectral library H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\PB8.parquet
[41:00] Spectral library loaded: 13385 protein isoforms, 13231 protein groups and 138531 precursors in 128896 elution groups.
[41:00] Loading protein annotations from FASTA H:\DELALANDE Frankois\ProteoBench\DIA Astral\ProteoBenchFASTA_MixedSpecies_HYE.fasta
[41:00] Annotating library proteins with information from the FASTA database
[41:00] Gene names missing for some isoforms
[41:00] Library contains 13373 proteins, and 0 genes
[41:00] Initialising library
[41:03] Saving the library to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\PB8.parquet.skyline.speclib


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

[41:09] File #1/6
[41:09] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
[42:29] Pre-processing...
[42:31] 2931 MS1 and 293271 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 137138 precursors in range
[42:31] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[42:31] RT window set to 0.436141
[42:32] Recommended MS1 mass accuracy setting: 2.7 ppm
[42:33] Searching decoys
[42:33] Main search
[42:36] Removing low confidence identifications
[42:44] Removing interfering precursors
[42:47] Training neural networks on 117929 target and 61410 decoy PSMs
[43:40] Training neural networks on 117873 target and 66029 decoy PSMs
[44:09] Number of IDs at 0.01 FDR: 115075
[44:10] Precursors at 1% peptidoform FDR: 113240
[44:10] Calculating protein q-values
[44:10] Number of proteins identified at 1% FDR: 11034 (precursor-level), 10098 (protein-level) (inference performed using proteotypic peptides only)
[44:10] Quantification
[44:11] Precursors with scored PTMs at 1% FDR: 3976 out of 4091 considered
[44:11] Precursors with all scored PTM sites unoccupied at 1% FDR: 109264
[44:11] Precursors with PTMs localised (when required) with > 90% confidence: 3879 out of 3976

[44:12] File #2/6
[44:12] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
[46:00] Pre-processing...
[46:02] 2933 MS1 and 293433 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 137138 precursors in range
[46:02] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[46:02] RT window set to 0.437084
[46:02] Recommended MS1 mass accuracy setting: 2.7 ppm
[46:03] Searching decoys
[46:04] Main search
[46:07] Removing low confidence identifications
[46:14] Removing interfering precursors
[46:17] Training neural networks on 118519 target and 61422 decoy PSMs
[46:44] Training neural networks on 118474 target and 66088 decoy PSMs
[47:12] Number of IDs at 0.01 FDR: 116843
[47:12] Precursors at 1% peptidoform FDR: 114736
[47:12] Calculating protein q-values
[47:12] Number of proteins identified at 1% FDR: 11093 (precursor-level), 10101 (protein-level) (inference performed using proteotypic peptides only)
[47:13] Quantification
[47:14] Precursors with scored PTMs at 1% FDR: 4040 out of 4191 considered
[47:14] Precursors with all scored PTM sites unoccupied at 1% FDR: 110696
[47:14] Precursors with PTMs localised (when required) with > 90% confidence: 3950 out of 4040

[47:15] File #3/6
[47:15] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
[48:32] Pre-processing...
[48:33] 2932 MS1 and 293358 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 137138 precursors in range
[48:33] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[48:34] RT window set to 0.429879
[48:34] Recommended MS1 mass accuracy setting: 2.7 ppm
[48:34] Searching decoys
[48:35] Main search
[48:37] Removing low confidence identifications
[48:43] Removing interfering precursors
[48:46] Training neural networks on 118465 target and 61150 decoy PSMs
[49:21] Training neural networks on 118416 target and 66256 decoy PSMs
[50:03] Number of IDs at 0.01 FDR: 116648
[50:04] Precursors at 1% peptidoform FDR: 115047
[50:04] Calculating protein q-values
[50:04] Number of proteins identified at 1% FDR: 11046 (precursor-level), 10086 (protein-level) (inference performed using proteotypic peptides only)
[50:04] Quantification
[50:05] Precursors with scored PTMs at 1% FDR: 4116 out of 4208 considered
[50:05] Precursors with all scored PTM sites unoccupied at 1% FDR: 110931
[50:05] Precursors with PTMs localised (when required) with > 90% confidence: 4021 out of 4116

[50:06] File #4/6
[50:06] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
[51:31] Pre-processing...
[51:33] 2933 MS1 and 293382 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 137138 precursors in range
[51:33] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[51:33] RT window set to 0.441873
[51:33] Recommended MS1 mass accuracy setting: 2.6 ppm
[51:34] Searching decoys
[51:34] Main search
[51:36] Removing low confidence identifications
[51:42] Removing interfering precursors
[51:44] Training neural networks on 118930 target and 62203 decoy PSMs
[52:09] Training neural networks on 118887 target and 66906 decoy PSMs
[52:36] Number of IDs at 0.01 FDR: 116826
[52:37] Precursors at 1% peptidoform FDR: 114905
[52:37] Calculating protein q-values
[52:37] Number of proteins identified at 1% FDR: 10984 (precursor-level), 10075 (protein-level) (inference performed using proteotypic peptides only)
[52:37] Quantification
[52:38] Precursors with scored PTMs at 1% FDR: 4379 out of 4498 considered
[52:38] Precursors with all scored PTM sites unoccupied at 1% FDR: 110526
[52:38] Precursors with PTMs localised (when required) with > 90% confidence: 4286 out of 4379

[52:39] File #5/6
[52:39] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
[54:18] Pre-processing...
[54:19] 2933 MS1 and 293330 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 137138 precursors in range
[54:19] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[54:19] RT window set to 0.451017
[54:19] Recommended MS1 mass accuracy setting: 2.7 ppm
[54:19] Searching decoys
[54:20] Main search
[54:22] Removing low confidence identifications
[54:27] Removing interfering precursors
[54:29] Training neural networks on 118982 target and 62156 decoy PSMs
[54:58] Training neural networks on 118920 target and 66860 decoy PSMs
[55:24] Number of IDs at 0.01 FDR: 117087
[55:25] Precursors at 1% peptidoform FDR: 115618
[55:25] Calculating protein q-values
[55:25] Number of proteins identified at 1% FDR: 11064 (precursor-level), 10111 (protein-level) (inference performed using proteotypic peptides only)
[55:25] Quantification
[55:26] Precursors with scored PTMs at 1% FDR: 4453 out of 4541 considered
[55:26] Precursors with all scored PTM sites unoccupied at 1% FDR: 111165
[55:26] Precursors with PTMs localised (when required) with > 90% confidence: 4358 out of 4453

[55:27] File #6/6
[55:27] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
[57:08] Pre-processing...
[57:08] 2934 MS1 and 293446 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 137138 precursors in range
[57:09] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[57:09] RT window set to 0.449392
[57:09] Recommended MS1 mass accuracy setting: 2.9 ppm
[57:09] Searching decoys
[57:10] Main search
[57:12] Removing low confidence identifications
[57:18] Removing interfering precursors
[57:20] Training neural networks on 118898 target and 62024 decoy PSMs
[57:45] Training neural networks on 118846 target and 66825 decoy PSMs
[58:10] Number of IDs at 0.01 FDR: 117184
[58:11] Precursors at 1% peptidoform FDR: 115321
[58:11] Calculating protein q-values
[58:11] Number of proteins identified at 1% FDR: 11057 (precursor-level), 10116 (protein-level) (inference performed using proteotypic peptides only)
[58:11] Quantification
[58:12] Precursors with scored PTMs at 1% FDR: 4406 out of 4490 considered
[58:12] Precursors with all scored PTM sites unoccupied at 1% FDR: 110915
[58:12] Precursors with PTMs localised (when required) with > 90% confidence: 4303 out of 4406

[58:13] Cross-run analysis
[58:13] Reading quantification information: 6 files
[58:16] Quantifying peptides
[61:24] Quantification parameters: 0.367875, 0.00131634, 0.00156307, 0.0120831, 0.0118799, 0.0120779, 0.19274, 0.239461, 0.196432, 0.0134732, 0.0392282, 0.0151694, 0.256402, 0.0525787, 0.0725225, 0.0114817
[62:49] Quantifying proteins
[62:50] Calculating q-values for protein and gene groups
[62:50] Calculating global q-values for protein and gene groups
[62:50] Protein groups with global q-value <= 0.01: 11074
[62:57] Compressed report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\reportPB6.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[62:57] Site report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\reportPB6.site_report.parquet
[62:57] Saving precursor levels matrix
[63:04] Precursor levels matrix (1% precursor and protein group FDR) saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\reportPB6.pr_matrix.tsv.
[63:04] Saving protein group levels matrix
[63:04] Protein groups matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\reportPB6.pg_matrix.tsv.
[63:04] Saving gene group levels matrix
[63:04] Gene groups matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\reportPB6.gg_matrix.tsv.
[63:04] Saving unique genes levels matrix
[63:04] Unique genes matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\reportPB6.unique_genes_matrix.tsv.
[63:07] Manifest saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\reportPB6.manifest.txt
[63:07] Stats report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB8\reportPB6.stats.tsv

