
DIA-NN 2.0 Academia  (Data-Independent Acquisition by Neural Networks)
Compiled on Jan 28 2025 11:23:41
Current date and time: Fri Apr 18 12:41:45 2025
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.mzML  --f D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.mzML  --f D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.mzML  --f D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.mzML  --f D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.mzML  --f D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.mzML  --lib  --threads 24 --verbose 1 --out D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\report.parquet --qvalue 0.01 --matrices --out-lib D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\speclib.parquet --gen-spec-lib --predictor --fasta D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta --fasta-search --min-fr-mz 50 --max-fr-mz 2000 --met-excision --min-pep-len 6 --max-pep-len 30 --min-pr-mz 400 --max-pr-mz 1000 --min-pr-charge 1 --max-pr-charge 4 --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
Min fragment m/z set to 50
Max fragment m/z set to 2000
N-terminal methionine excision enabled
Min peptide length set to 6
Max peptide length set to 30
Min precursor m/z set to 400
Max precursor m/z set to 1000
Min precursor charge set to 1
Max precursor charge set to 4
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
[0:09] 5116692 precursors generated
[0:09] Protein names missing for some isoforms
[0:09] Gene names missing for some isoforms
[0:09] Library contains 31685 proteins, and 0 genes
[0:13] [0:22] [11:22] [12:28] [12:32] [12:32] Saving the library to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\speclib.predicted.speclib
[12:36] Initialising library
[12:52] Loading spectral library D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\speclib.predicted.speclib
[12:54] Library annotated with sequence database(s): D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[12:55] Spectral library loaded: 31837 protein isoforms, 51765 protein groups and 5116692 precursors in 2716663 elution groups.
[12:55] Loading protein annotations from FASTA D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[12:55] Annotating library proteins with information from the FASTA database
[12:55] Protein names missing for some isoforms
[12:55] Gene names missing for some isoforms
[12:55] Library contains 31685 proteins, and 0 genes
[12:58] Initialising library

First pass: generating a spectral library from DIA data

[13:12] File #1/6
[13:12] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.mzML
[14:16] Pre-processing...
[14:19] 2931 MS1 and 293271 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 5020855 precursors in range
[14:22] Calibrating with mass accuracies 30 (MS1), 20 (MS2)
[14:45] RT window set to 1.26347
[14:45] Peak width: 2.632
[14:45] Scan window radius set to 5
[14:45] Recommended MS1 mass accuracy setting: 2.6 ppm
[15:21] Optimised mass accuracy: 8 ppm
[15:34] Searching decoys
[16:13] Main search
[17:30] Removing low confidence identifications
[17:42] Removing interfering precursors
[17:49] Training neural networks on 200282 target and 124871 decoy PSMs
[19:35] Training neural networks on 200282 target and 124905 decoy PSMs
[21:18] Number of IDs at 0.01 FDR: 102100
[21:19] Precursors at 1% peptidoform FDR: 99583
[21:19] Calculating protein q-values
[21:19] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[21:19] Quantification
[21:21] Precursors with scored PTMs at 1% FDR: 3374 out of 3552 considered
[21:21] Precursors with all scored PTM sites unoccupied at 1% FDR: 96209
[21:21] Precursors with PTMs localised (when required) with > 90% confidence: 2321 out of 3374
[21:21] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.mzML.quant

[21:21] File #2/6
[21:21] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.mzML
[22:29] Pre-processing...
[22:32] 2933 MS1 and 293433 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5020855 precursors in range
[22:36] Calibrating with mass accuracies 30 (MS1), 18 (MS2)
[22:58] RT window set to 1.15339
[22:58] Recommended MS1 mass accuracy setting: 2.8 ppm
[23:12] Searching decoys
[23:49] Main search
[25:02] Removing low confidence identifications
[25:15] Removing interfering precursors
[25:22] Training neural networks on 207895 target and 130980 decoy PSMs
[27:08] Training neural networks on 207895 target and 130584 decoy PSMs
[28:50] Number of IDs at 0.01 FDR: 103545
[28:50] Precursors at 1% peptidoform FDR: 100639
[28:51] Calculating protein q-values
[28:51] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[28:51] Quantification
[28:52] Precursors with scored PTMs at 1% FDR: 3517 out of 3734 considered
[28:52] Precursors with all scored PTM sites unoccupied at 1% FDR: 97122
[28:52] Precursors with PTMs localised (when required) with > 90% confidence: 2436 out of 3517
[28:53] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.mzML.quant

[28:53] File #3/6
[28:53] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.mzML
[29:57] Pre-processing...
[30:00] 2932 MS1 and 293358 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5020855 precursors in range
[30:03] Calibrating with mass accuracies 30 (MS1), 18 (MS2)
[30:25] RT window set to 1.20795
[30:25] Recommended MS1 mass accuracy setting: 2.7 ppm
[30:38] Searching decoys
[31:14] Main search
[32:24] Removing low confidence identifications
[32:36] Removing interfering precursors
[32:42] Training neural networks on 206415 target and 129600 decoy PSMs
[34:27] Training neural networks on 206415 target and 128721 decoy PSMs
[36:12] Number of IDs at 0.01 FDR: 104055
[36:13] Precursors at 1% peptidoform FDR: 101339
[36:13] Calculating protein q-values
[36:13] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[36:13] Quantification
[36:14] Precursors with scored PTMs at 1% FDR: 3472 out of 3683 considered
[36:14] Precursors with all scored PTM sites unoccupied at 1% FDR: 97867
[36:14] Precursors with PTMs localised (when required) with > 90% confidence: 2404 out of 3472
[36:15] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.mzML.quant

[36:15] File #4/6
[36:15] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.mzML
[37:31] Pre-processing...
[37:34] 2933 MS1 and 293382 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5020855 precursors in range
[37:37] Calibrating with mass accuracies 30 (MS1), 18 (MS2)
[37:59] RT window set to 1.26284
[37:59] Recommended MS1 mass accuracy setting: 2.6 ppm
[38:14] Searching decoys
[38:54] Main search
[40:10] Removing low confidence identifications
[40:22] Removing interfering precursors
[40:28] Training neural networks on 208980 target and 132900 decoy PSMs
[42:15] Training neural networks on 208980 target and 131248 decoy PSMs
[43:58] Number of IDs at 0.01 FDR: 103915
[43:59] Precursors at 1% peptidoform FDR: 101069
[43:59] Calculating protein q-values
[43:59] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[43:59] Quantification
[44:00] Precursors with scored PTMs at 1% FDR: 4038 out of 4329 considered
[44:00] Precursors with all scored PTM sites unoccupied at 1% FDR: 97031
[44:00] Precursors with PTMs localised (when required) with > 90% confidence: 2962 out of 4038
[44:01] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.mzML.quant

[44:01] File #5/6
[44:01] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.mzML
[45:19] Pre-processing...
[45:22] 2933 MS1 and 293330 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5020855 precursors in range
[45:25] Calibrating with mass accuracies 30 (MS1), 19 (MS2)
[45:47] RT window set to 1.16961
[45:47] Recommended MS1 mass accuracy setting: 2.4 ppm
[46:01] Searching decoys
[46:35] Main search
[47:43] Removing low confidence identifications
[47:54] Removing interfering precursors
[48:00] Training neural networks on 208725 target and 131788 decoy PSMs
[49:45] Training neural networks on 208725 target and 130896 decoy PSMs
[51:27] Number of IDs at 0.01 FDR: 103536
[51:27] Precursors at 1% peptidoform FDR: 101141
[51:28] Calculating protein q-values
[51:28] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[51:28] Quantification
[51:29] Precursors with scored PTMs at 1% FDR: 4125 out of 4367 considered
[51:29] Precursors with all scored PTM sites unoccupied at 1% FDR: 97016
[51:29] Precursors with PTMs localised (when required) with > 90% confidence: 3017 out of 4125
[51:30] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.mzML.quant

[51:30] File #6/6
[51:30] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.mzML
[52:46] Pre-processing...
[52:49] 2934 MS1 and 293446 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 5020855 precursors in range
[52:52] Calibrating with mass accuracies 30 (MS1), 19 (MS2)
[53:14] RT window set to 1.22941
[53:14] Recommended MS1 mass accuracy setting: 2.6 ppm
[53:28] Searching decoys
[54:05] Main search
[55:18] Removing low confidence identifications
[55:30] Removing interfering precursors
[55:37] Training neural networks on 206140 target and 129559 decoy PSMs
[57:20] Training neural networks on 206140 target and 128812 decoy PSMs
[59:00] Number of IDs at 0.01 FDR: 104140
[59:00] Precursors at 1% peptidoform FDR: 101039
[59:01] Calculating protein q-values
[59:01] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[59:01] Quantification
[59:02] Precursors with scored PTMs at 1% FDR: 4102 out of 4390 considered
[59:02] Precursors with all scored PTM sites unoccupied at 1% FDR: 96937
[59:02] Precursors with PTMs localised (when required) with > 90% confidence: 2974 out of 4102
[59:03] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.mzML.quant

[59:03] Cross-run analysis
[59:03] Reading quantification information: 6 files
[59:15] Quantifying peptides
[60:38] Assembling protein groups
[60:40] Quantifying proteins
[60:40] Calculating q-values for protein and gene groups
[60:41] Calculating global q-values for protein and gene groups
[60:41] Protein groups with global q-value <= 0.01: 11409
[60:43] Compressed report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\report-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[60:43] Saving precursor levels matrix
[60:43] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\report-first-pass.pr_matrix.tsv.
[60:43] Manifest saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\report-first-pass.manifest.txt
[60:43] Stats report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\report-first-pass.stats.tsv
[60:43] Generating spectral library:
[60:45] 133197 target and 1348 decoy precursors saved
[60:45] Spectral library saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\speclib.parquet

[60:47] Loading spectral library D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\speclib.parquet
[60:48] Spectral library loaded: 13221 protein isoforms, 13073 protein groups and 134545 precursors in 125863 elution groups.
[60:48] Loading protein annotations from FASTA D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[60:48] Annotating library proteins with information from the FASTA database
[60:48] Gene names missing for some isoforms
[60:48] Library contains 13210 proteins, and 0 genes
[60:48] Initialising library
[60:49] Saving the library to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\speclib.parquet.skyline.speclib


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

[60:49] File #1/6
[60:49] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.mzML
[61:51] Pre-processing...
[61:53] 2931 MS1 and 293271 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 133197 precursors in range
[61:53] Calibrating with mass accuracies 30 (MS1), 18 (MS2)
[61:53] RT window set to 0.367045
[61:53] Recommended MS1 mass accuracy setting: 3.3 ppm
[61:54] Searching decoys
[61:54] Main search
[61:56] Removing low confidence identifications
[62:00] Removing interfering precursors
[62:01] Training neural networks on 116446 target and 57081 decoy PSMs
[62:47] Training neural networks on 116408 target and 62737 decoy PSMs
[63:35] Number of IDs at 0.01 FDR: 112311
[63:35] Precursors at 1% peptidoform FDR: 110413
[63:35] Calculating protein q-values
[63:35] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[63:35] Quantification
[63:36] Precursors with scored PTMs at 1% FDR: 3974 out of 4101 considered
[63:36] Precursors with all scored PTM sites unoccupied at 1% FDR: 106439
[63:36] Precursors with PTMs localised (when required) with > 90% confidence: 2775 out of 3974

[63:37] File #2/6
[63:37] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.mzML
[64:39] Pre-processing...
[64:41] 2933 MS1 and 293433 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 133197 precursors in range
[64:41] Calibrating with mass accuracies 30 (MS1), 18 (MS2)
[64:41] RT window set to 0.400392
[64:41] Recommended MS1 mass accuracy setting: 3 ppm
[64:42] Searching decoys
[64:42] Main search
[64:44] Removing low confidence identifications
[64:48] Removing interfering precursors
[64:49] Training neural networks on 116872 target and 58116 decoy PSMs
[65:36] Training neural networks on 116837 target and 63558 decoy PSMs
[66:24] Number of IDs at 0.01 FDR: 113630
[66:25] Precursors at 1% peptidoform FDR: 112185
[66:25] Calculating protein q-values
[66:25] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[66:25] Quantification
[66:26] Precursors with scored PTMs at 1% FDR: 4102 out of 4193 considered
[66:26] Precursors with all scored PTM sites unoccupied at 1% FDR: 108083
[66:26] Precursors with PTMs localised (when required) with > 90% confidence: 2864 out of 4102

[66:26] File #3/6
[66:26] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.mzML
[67:28] Pre-processing...
[67:30] 2932 MS1 and 293358 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 133197 precursors in range
[67:30] Calibrating with mass accuracies 30 (MS1), 17 (MS2)
[67:31] RT window set to 0.403913
[67:31] Recommended MS1 mass accuracy setting: 3.3 ppm
[67:31] Searching decoys
[67:32] Main search
[67:34] Removing low confidence identifications
[67:38] Removing interfering precursors
[67:39] Training neural networks on 116772 target and 58135 decoy PSMs
[68:27] Training neural networks on 116715 target and 63659 decoy PSMs
[69:14] Number of IDs at 0.01 FDR: 113780
[69:14] Precursors at 1% peptidoform FDR: 112005
[69:14] Calculating protein q-values
[69:14] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[69:14] Quantification
[69:15] Precursors with scored PTMs at 1% FDR: 4134 out of 4226 considered
[69:15] Precursors with all scored PTM sites unoccupied at 1% FDR: 107871
[69:15] Precursors with PTMs localised (when required) with > 90% confidence: 2895 out of 4134

[69:15] File #4/6
[69:15] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.mzML
[70:17] Pre-processing...
[70:19] 2933 MS1 and 293382 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 133197 precursors in range
[70:19] Calibrating with mass accuracies 30 (MS1), 18 (MS2)
[70:20] RT window set to 0.383538
[70:20] Recommended MS1 mass accuracy setting: 3.3 ppm
[70:20] Searching decoys
[70:21] Main search
[70:23] Removing low confidence identifications
[70:26] Removing interfering precursors
[70:27] Training neural networks on 117189 target and 58162 decoy PSMs
[71:15] Training neural networks on 117147 target and 64000 decoy PSMs
[72:03] Number of IDs at 0.01 FDR: 114412
[72:04] Precursors at 1% peptidoform FDR: 112350
[72:04] Calculating protein q-values
[72:04] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[72:04] Quantification
[72:05] Precursors with scored PTMs at 1% FDR: 4421 out of 4511 considered
[72:05] Precursors with all scored PTM sites unoccupied at 1% FDR: 107929
[72:05] Precursors with PTMs localised (when required) with > 90% confidence: 3183 out of 4421

[72:05] File #5/6
[72:05] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.mzML
[73:07] Pre-processing...
[73:10] 2933 MS1 and 293330 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 133197 precursors in range
[73:10] Calibrating with mass accuracies 30 (MS1), 18 (MS2)
[73:10] RT window set to 0.384615
[73:10] Recommended MS1 mass accuracy setting: 3.1 ppm
[73:10] Searching decoys
[73:11] Main search
[73:13] Removing low confidence identifications
[73:16] Removing interfering precursors
[73:18] Training neural networks on 117209 target and 57998 decoy PSMs
[74:05] Training neural networks on 117159 target and 63756 decoy PSMs
[74:53] Number of IDs at 0.01 FDR: 114018
[74:53] Precursors at 1% peptidoform FDR: 112509
[74:53] Calculating protein q-values
[74:53] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[74:53] Quantification
[74:54] Precursors with scored PTMs at 1% FDR: 4447 out of 4537 considered
[74:54] Precursors with all scored PTM sites unoccupied at 1% FDR: 108062
[74:54] Precursors with PTMs localised (when required) with > 90% confidence: 3213 out of 4447

[74:55] File #6/6
[74:55] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.mzML
[75:57] Pre-processing...
[75:59] 2934 MS1 and 293446 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 133197 precursors in range
[75:59] Calibrating with mass accuracies 30 (MS1), 18 (MS2)
[76:00] RT window set to 0.372732
[76:00] Recommended MS1 mass accuracy setting: 2.9 ppm
[76:00] Searching decoys
[76:00] Main search
[76:02] Removing low confidence identifications
[76:07] Removing interfering precursors
[76:08] Training neural networks on 116638 target and 57160 decoy PSMs
[76:54] Training neural networks on 116601 target and 62938 decoy PSMs
[77:42] Number of IDs at 0.01 FDR: 113385
[77:42] Precursors at 1% peptidoform FDR: 111852
[77:42] Calculating protein q-values
[77:42] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[77:42] Quantification
[77:43] Precursors with scored PTMs at 1% FDR: 4388 out of 4476 considered
[77:43] Precursors with all scored PTM sites unoccupied at 1% FDR: 107464
[77:43] Precursors with PTMs localised (when required) with > 90% confidence: 3129 out of 4388

[77:44] Cross-run analysis
[77:44] Reading quantification information: 6 files
[77:45] Quantifying peptides
[79:31] Quantification parameters: 0.356228, 0.00138548, 0.00159702, 0.0121397, 0.011992, 0.0120048, 0.192168, 0.226966, 0.181161, 0.013719, 0.0356975, 0.0147727, 0.370563, 0.0525835, 0.0750157, 0.0118972
[80:10] Quantifying proteins
[80:10] Calculating q-values for protein and gene groups
[80:10] Calculating global q-values for protein and gene groups
[80:10] Protein groups with global q-value <= 0.01: 11002
[80:12] Compressed report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\report.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[80:12] Saving precursor levels matrix
[80:13] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\report.pr_matrix.tsv.
[80:13] Saving protein group levels matrix
[80:13] Protein groups matrix saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\report.pg_matrix.tsv.
[80:13] Saving gene group levels matrix
[80:13] Gene groups matrix saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\report.gg_matrix.tsv.
[80:13] Saving unique genes levels matrix
[80:13] Unique genes matrix saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\report.unique_genes_matrix.tsv.
[80:13] Manifest saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\report.manifest.txt
[80:13] Stats report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_2.0_default\report.stats.tsv

