
DIA-NN 2.3.0 Academia  (Data-Independent Acquisition by Neural Networks)
Compiled on Sep 26 2025 08:30:52
Current date and time: Wed Jan  7 14:13:55 2026
CPU: GenuineIntel 13th Gen Intel(R) Core(TM) i9-13900F
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 
Logical CPU cores: 32
diann.exe --f D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw  --f D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw  --f D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw  --f D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw  --f D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw  --f D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw  --lib  --threads 24 --verbose 1 --out D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\diann_2.3.0_default.parquet --qvalue 0.01 --matrices --out-lib D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\efewwfw.parquet --gen-spec-lib --predictor --fasta D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta --fasta-search --met-excision --min-pep-len 6 --max-pep-len 30 --min-pr-mz 380 --max-pr-mz 980 --min-pr-charge 1 --max-pr-charge 5 --min-fr-mz 50 --max-fr-mz 2000 --cut K*,R* --missed-cleavages 1 --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --peptidoforms --reanalyse --rt-profiling 

Thread number set to 24
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
Deep learning will be used to generate a new in silico spectral library from peptides provided
DIA-NN will carry out FASTA digest for in silico lib generation
N-terminal methionine excision enabled
Min peptide length set to 6
Max peptide length set to 30
Min precursor m/z set to 380
Max precursor m/z set to 980
Min precursor charge set to 1
Max precursor charge set to 5
Min fragment m/z set to 50
Max fragment m/z set to 2000
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
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
DIA-NN will automatically optimise the mass accuracy for the first run of the experiment, use this mode for preliminary analyses only
WARNING: incorrect settings, the in silico-predicted library must be generated in a separate pipeline step and then used to process the raw data, now without activating FASTA digest
The following variable modifications will be localised: UniMod:35 UniMod:1 

6 files will be processed
[0:00] Loading FASTA D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[0:03] Processing FASTA
[0:05] Assembling elution groups
[0:10] 5275217 precursors generated
[0:10] Protein names missing for some isoforms
[0:10] Gene names missing for some isoforms
[0:10] Library contains 31685 proteins, and 0 genes
[0:15] [0:20] [9:26] [11:15] [11:20] [11:20] Saving the library to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\efewwfw.predicted.speclib
[11:30] Initialising library
[11:46] Loading spectral library D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\efewwfw.predicted.speclib
[11:52] Library annotated with sequence database(s): D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[11:53] Spectral library loaded: 31837 protein isoforms, 51765 protein groups and 5275217 precursors in 2716671 elution groups.
[11:53] Loading protein annotations from FASTA D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[11:54] Annotating library proteins with information from the FASTA database
[11:54] Protein names missing for some isoforms
[11:54] Gene names missing for some isoforms
[11:54] Library contains 31685 proteins, and 0 genes
[11:59] Initialising library

First pass: generating a spectral library from DIA data

[12:15] File #1/6
[12:15] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
[13:12] Pre-processing...
[13:15] 2931 MS1 and 293271 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 5270221 precursors in range
[13:16] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[13:43] RT window set to 1.24816
[13:43] Peak width: 2.828
[13:43] Scan window radius set to 6
[13:43] Recommended MS1 mass accuracy setting: 2.5 ppm
[14:19] Optimised mass accuracy: 7 ppm
[14:29] Searching decoys
[15:29] Main search
[17:29] Removing low confidence identifications
[17:49] Removing interfering precursors
[18:00] Training neural networks on 217602 target and 136117 decoy PSMs
[20:48] Training neural networks on 217602 target and 136861 decoy PSMs
[23:36] IDs at 0.01 FDR: 106619
[23:37] Precursors at 1% peptidoform FDR: 104464
[23:38] Number of IDs at 0.01 FDR: 113398
[23:38] Calculating protein q-values
[23:39] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[23:39] Quantification
[23:40] Precursors with scored PTMs at 1% FDR: 3551 out of 3969 considered
[23:40] Precursors with all scored PTM sites unoccupied at 1% FDR: 103762
[23:40] Precursors with PTMs localised (when required) with > 90% confidence: 3452 out of 3551
[23:42] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw.quant

[23:42] File #2/6
[23:42] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
[24:44] Pre-processing...
[24:45] 2933 MS1 and 293433 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[24:47] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[25:14] RT window set to 1.33321
[25:14] Recommended MS1 mass accuracy setting: 2.5 ppm
[25:22] Searching decoys
[26:24] Main search
[28:05] Removing low confidence identifications
[28:19] Removing interfering precursors
[28:26] Training neural networks on 221886 target and 137810 decoy PSMs
[30:19] Training neural networks on 221886 target and 139475 decoy PSMs
[32:04] IDs at 0.01 FDR: 109504
[32:05] Precursors at 1% peptidoform FDR: 106168
[32:05] Number of IDs at 0.01 FDR: 116773
[32:05] Calculating protein q-values
[32:06] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[32:06] Quantification
[32:07] Precursors with scored PTMs at 1% FDR: 3580 out of 4255 considered
[32:07] Precursors with all scored PTM sites unoccupied at 1% FDR: 104655
[32:07] Precursors with PTMs localised (when required) with > 90% confidence: 3490 out of 3580
[32:07] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw.quant

[32:07] File #3/6
[32:07] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
[33:00] Pre-processing...
[33:02] 2932 MS1 and 293358 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[33:02] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[33:20] RT window set to 1.20998
[33:20] Recommended MS1 mass accuracy setting: 2.6 ppm
[33:25] Searching decoys
[34:05] Main search
[35:25] Removing low confidence identifications
[35:38] Removing interfering precursors
[35:45] Training neural networks on 223218 target and 137430 decoy PSMs
[37:29] Training neural networks on 223218 target and 139411 decoy PSMs
[39:13] IDs at 0.01 FDR: 109016
[39:14] Precursors at 1% peptidoform FDR: 105828
[39:14] Number of IDs at 0.01 FDR: 116647
[39:15] Calculating protein q-values
[39:15] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[39:15] Quantification
[39:16] Precursors with scored PTMs at 1% FDR: 3521 out of 4202 considered
[39:16] Precursors with all scored PTM sites unoccupied at 1% FDR: 104584
[39:16] Precursors with PTMs localised (when required) with > 90% confidence: 3426 out of 3521
[39:17] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw.quant

[39:17] File #4/6
[39:17] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
[40:14] Pre-processing...
[40:16] 2933 MS1 and 293382 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[40:16] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[40:35] RT window set to 1.14767
[40:35] Recommended MS1 mass accuracy setting: 2.6 ppm
[40:40] Searching decoys
[41:20] Main search
[42:39] Removing low confidence identifications
[42:52] Removing interfering precursors
[42:59] Training neural networks on 227126 target and 141959 decoy PSMs
[44:52] Training neural networks on 227126 target and 143713 decoy PSMs
[46:39] IDs at 0.01 FDR: 109085
[46:40] Precursors at 1% peptidoform FDR: 106495
[46:40] Number of IDs at 0.01 FDR: 116517
[46:40] Calculating protein q-values
[46:41] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[46:41] Quantification
[46:42] Precursors with scored PTMs at 1% FDR: 4315 out of 4832 considered
[46:42] Precursors with all scored PTM sites unoccupied at 1% FDR: 104794
[46:42] Precursors with PTMs localised (when required) with > 90% confidence: 4194 out of 4315
[46:43] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw.quant

[46:43] File #5/6
[46:43] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
[56:22] Pre-processing...
[56:23] 2933 MS1 and 293330 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[56:24] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[56:44] RT window set to 1.15676
[56:44] Recommended MS1 mass accuracy setting: 2.6 ppm
[56:49] Searching decoys
[57:31] Main search
[58:52] Removing low confidence identifications
[59:05] Removing interfering precursors
[59:12] Training neural networks on 223172 target and 138799 decoy PSMs
[61:01] Training neural networks on 223172 target and 140336 decoy PSMs
[62:47] IDs at 0.01 FDR: 108943
[62:47] Precursors at 1% peptidoform FDR: 106480
[62:48] Number of IDs at 0.01 FDR: 116349
[62:48] Calculating protein q-values
[62:48] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[62:48] Quantification
[62:49] Precursors with scored PTMs at 1% FDR: 4332 out of 4847 considered
[62:49] Precursors with all scored PTM sites unoccupied at 1% FDR: 104772
[62:49] Precursors with PTMs localised (when required) with > 90% confidence: 4216 out of 4332
[62:50] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw.quant

[62:50] File #6/6
[62:50] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
[67:38] Pre-processing...
[67:39] 2934 MS1 and 293446 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5270221 precursors in range
[67:39] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[67:57] RT window set to 1.17156
[67:57] Recommended MS1 mass accuracy setting: 2.8 ppm
[68:02] Searching decoys
[68:42] Main search
[70:00] Removing low confidence identifications
[70:13] Removing interfering precursors
[70:20] Training neural networks on 222706 target and 137311 decoy PSMs
[72:06] Training neural networks on 222706 target and 139673 decoy PSMs
[73:50] IDs at 0.01 FDR: 109825
[73:50] Precursors at 1% peptidoform FDR: 106838
[73:51] Number of IDs at 0.01 FDR: 116197
[73:51] Calculating protein q-values
[73:51] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[73:51] Quantification
[73:52] Precursors with scored PTMs at 1% FDR: 4210 out of 4929 considered
[73:52] Precursors with all scored PTM sites unoccupied at 1% FDR: 104783
[73:52] Precursors with PTMs localised (when required) with > 90% confidence: 4085 out of 4210
[73:53] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw.quant

[73:53] Cross-run analysis
[73:53] Reading quantification information: 6 files
[77:50] Quantifying peptides
[78:17] Assembling protein groups
[78:18] Quantifying proteins
[78:19] Calculating q-values for protein and gene groups
[78:20] Calculating global q-values for protein and gene groups
[78:20] Protein groups with global q-value <= 0.01: 11581
[78:22] Compressed report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\diann_2.3.0_default-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[78:22] Site report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\diann_2.3.0_default-first-pass.site_report.parquet
[78:22] Saving precursor levels matrix
[78:23] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\diann_2.3.0_default-first-pass.pr_matrix.tsv.
[78:23] Manifest saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\diann_2.3.0_default-first-pass.manifest.txt
[78:23] Stats report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\diann_2.3.0_default-first-pass.stats.tsv
[78:23] Generating spectral library:
[78:25] 142137 target and 1455 decoy precursors saved
[78:25] Spectral library saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\efewwfw.parquet

[78:26] Loading spectral library D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\efewwfw.parquet
[78:27] Spectral library loaded: 12991 protein isoforms, 12869 protein groups and 143592 precursors in 133852 elution groups.
[78:27] Loading protein annotations from FASTA D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[78:37] Annotating library proteins with information from the FASTA database
[78:37] Gene names missing for some isoforms
[78:37] Library contains 12979 proteins, and 0 genes
[78:37] Initialising library
[78:38] Saving the library to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\efewwfw.parquet.skyline.speclib


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

[78:38] File #1/6
[78:38] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
[87:19] Pre-processing...
[87:20] 2931 MS1 and 293271 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 142137 precursors in range
[87:20] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[87:21] RT window set to 0.439971
[87:21] Recommended MS1 mass accuracy setting: 3.4 ppm
[87:21] Searching decoys
[87:22] Main search
[87:24] Removing low confidence identifications
[87:28] Removing interfering precursors
[87:30] Training neural networks on 124580 target and 59507 decoy PSMs
[88:17] Training neural networks on 124520 target and 69487 decoy PSMs
[89:09] IDs at 0.01 FDR: 120636
[89:09] Precursors at 1% peptidoform FDR: 118475
[89:09] Number of IDs at 0.01 FDR: 123443
[89:09] Calculating protein q-values
[89:09] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[89:09] Quantification
[89:10] Precursors with scored PTMs at 1% FDR: 4209 out of 4361 considered
[89:10] Precursors with all scored PTM sites unoccupied at 1% FDR: 115792
[89:10] Precursors with PTMs localised (when required) with > 90% confidence: 4103 out of 4209

[89:11] File #2/6
[89:11] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
[101:30] Pre-processing...
[101:30] 2933 MS1 and 293433 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 142137 precursors in range
[101:30] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[101:31] RT window set to 0.43695
[101:31] Recommended MS1 mass accuracy setting: 3.1 ppm
[101:31] Searching decoys
[101:32] Main search
[101:34] Removing low confidence identifications
[101:38] Removing interfering precursors
[101:39] Training neural networks on 124815 target and 59532 decoy PSMs
[102:27] Training neural networks on 124747 target and 69428 decoy PSMs
[103:19] IDs at 0.01 FDR: 120612
[103:19] Precursors at 1% peptidoform FDR: 118816
[103:19] Number of IDs at 0.01 FDR: 123821
[103:19] Calculating protein q-values
[103:19] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[103:19] Quantification
[103:20] Precursors with scored PTMs at 1% FDR: 4279 out of 4428 considered
[103:20] Precursors with all scored PTM sites unoccupied at 1% FDR: 116295
[103:20] Precursors with PTMs localised (when required) with > 90% confidence: 4178 out of 4279

[103:21] File #3/6
[103:21] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
[110:05] Pre-processing...
[110:06] 2932 MS1 and 293358 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 142137 precursors in range
[110:06] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[110:06] RT window set to 0.441446
[110:06] Recommended MS1 mass accuracy setting: 3.4 ppm
[110:07] Searching decoys
[110:07] Main search
[110:09] Removing low confidence identifications
[110:13] Removing interfering precursors
[110:15] Training neural networks on 124836 target and 59983 decoy PSMs
[111:00] Training neural networks on 124767 target and 69816 decoy PSMs
[111:50] IDs at 0.01 FDR: 121326
[111:50] Precursors at 1% peptidoform FDR: 119084
[111:50] Number of IDs at 0.01 FDR: 124329
[111:50] Calculating protein q-values
[111:50] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[111:50] Quantification
[111:51] Precursors with scored PTMs at 1% FDR: 4290 out of 4458 considered
[111:51] Precursors with all scored PTM sites unoccupied at 1% FDR: 116479
[111:51] Precursors with PTMs localised (when required) with > 90% confidence: 4187 out of 4290

[111:52] File #4/6
[111:52] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
[122:00] Pre-processing...
[122:01] 2933 MS1 and 293382 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 142137 precursors in range
[122:01] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[122:02] RT window set to 0.452786
[122:02] Recommended MS1 mass accuracy setting: 3.3 ppm
[122:02] Searching decoys
[122:03] Main search
[122:05] Removing low confidence identifications
[122:09] Removing interfering precursors
[122:11] Training neural networks on 125379 target and 60881 decoy PSMs
[122:57] Training neural networks on 125326 target and 70346 decoy PSMs
[123:47] IDs at 0.01 FDR: 121600
[123:47] Precursors at 1% peptidoform FDR: 119516
[123:47] Number of IDs at 0.01 FDR: 124722
[123:47] Calculating protein q-values
[123:47] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[123:47] Quantification
[123:48] Precursors with scored PTMs at 1% FDR: 4608 out of 4711 considered
[123:48] Precursors with all scored PTM sites unoccupied at 1% FDR: 116670
[123:48] Precursors with PTMs localised (when required) with > 90% confidence: 4504 out of 4608

[123:49] File #5/6
[123:49] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
[134:01] Pre-processing...
[134:03] 2933 MS1 and 293330 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 142137 precursors in range
[134:03] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[134:03] RT window set to 0.448898
[134:03] Recommended MS1 mass accuracy setting: 3.3 ppm
[134:04] Searching decoys
[134:05] Main search
[134:09] Removing low confidence identifications
[134:15] Removing interfering precursors
[134:18] Training neural networks on 125496 target and 60333 decoy PSMs
[135:29] Training neural networks on 125433 target and 70565 decoy PSMs
[136:45] IDs at 0.01 FDR: 122431
[136:46] Precursors at 1% peptidoform FDR: 120124
[136:46] Number of IDs at 0.01 FDR: 125079
[136:46] Calculating protein q-values
[136:46] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[136:46] Quantification
[136:47] Precursors with scored PTMs at 1% FDR: 4634 out of 4769 considered
[136:47] Precursors with all scored PTM sites unoccupied at 1% FDR: 116937
[136:47] Precursors with PTMs localised (when required) with > 90% confidence: 4523 out of 4634

[136:48] File #6/6
[136:48] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
[143:13] Pre-processing...
[143:14] 2934 MS1 and 293446 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 142137 precursors in range
[143:14] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[143:15] RT window set to 0.447276
[143:15] Recommended MS1 mass accuracy setting: 3.3 ppm
[143:15] Searching decoys
[143:16] Main search
[143:20] Removing low confidence identifications
[143:27] Removing interfering precursors
[143:29] Training neural networks on 125346 target and 59410 decoy PSMs
[144:41] Training neural networks on 125283 target and 69718 decoy PSMs
[145:59] IDs at 0.01 FDR: 121882
[145:59] Precursors at 1% peptidoform FDR: 119358
[145:59] Number of IDs at 0.01 FDR: 124837
[145:59] Calculating protein q-values
[145:59] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[145:59] Quantification
[146:01] Precursors with scored PTMs at 1% FDR: 4548 out of 4721 considered
[146:01] Precursors with all scored PTM sites unoccupied at 1% FDR: 116372
[146:01] Precursors with PTMs localised (when required) with > 90% confidence: 4444 out of 4548

[146:02] Cross-run analysis
[146:02] Reading quantification information: 6 files
[146:06] Quantifying peptides
[148:30] Quantification parameters: 0.367043, 0.00133082, 0.00161234, 0.012105, 0.0118261, 0.012017, 0.178318, 0.253171, 0.19508, 0.0133853, 0.0339275, 0.0148482, 0.366513, 0.0530965, 0.0779883, 0.0111365
[148:50] Quantifying proteins
[148:50] Calculating q-values for protein and gene groups
[148:51] Calculating global q-values for protein and gene groups
[148:51] Protein groups with global q-value <= 0.01: 11070
[148:56] Compressed report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\diann_2.3.0_default.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[148:56] Site report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\diann_2.3.0_default.site_report.parquet
[148:56] Saving precursor levels matrix
[148:57] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\diann_2.3.0_default.pr_matrix.tsv.
[148:57] Saving protein group levels matrix
[148:57] Protein groups matrix saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\diann_2.3.0_default.pg_matrix.tsv.
[148:57] Saving gene group levels matrix
[148:57] Gene groups matrix saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\diann_2.3.0_default.gg_matrix.tsv.
[148:57] Saving unique genes levels matrix
[148:57] Unique genes matrix saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\diann_2.3.0_default.unique_genes_matrix.tsv.
[148:57] Manifest saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\diann_2.3.0_default.manifest.txt
[148:57] Stats report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.3.0_default\diann_2.3.0_default.stats.tsv

