
DIA-NN 2.2.0 Academia  (Data-Independent Acquisition by Neural Networks)
Compiled on May 29 2025 21:29:29
Current date and time: Thu Jul 17 11:25:25 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.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-reprocessing-all-mods\report.parquet --qvalue 0.01 --matrices --out-lib C:\DIA-NN\2.2.0\report-lib.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 5 --cut K*,R* --missed-cleavages 1 --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --var-mod UniMod:21,79.966331,STY --var-mod UniMod:121,114.042927,K --no-cut-after-mod UniMod:121 --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 5
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
Modification UniMod:21 with mass delta 79.9663 at STY will be considered as variable
Modification UniMod:121 with mass delta 114.043 at K 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 UniMod:21 UniMod:121 
In silico cuts after the following modifications will not be considered: UniMod:121 

6 files will be processed
[0:00] Loading FASTA D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[0:04] Processing FASTA
[0:15] Assembling elution groups
[0:37] 15444153 precursors generated
[0:37] Protein names missing for some isoforms
[0:37] Gene names missing for some isoforms
[0:37] Library contains 31685 proteins, and 0 genes
[0:53] [1:30] [26:24] [30:01] [30:13] [30:15] Saving the library to C:\DIA-NN\2.2.0\report-lib.predicted.speclib
[30:27] Initialising library
[30:54] Loading spectral library C:\DIA-NN\2.2.0\report-lib.predicted.speclib
[31:02] Library annotated with sequence database(s): D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[31:04] Spectral library loaded: 31837 protein isoforms, 51765 protein groups and 15444153 precursors in 8032704 elution groups.
[31:04] Loading protein annotations from FASTA D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[31:04] Annotating library proteins with information from the FASTA database
[31:04] Protein names missing for some isoforms
[31:04] Gene names missing for some isoforms
[31:04] Library contains 31685 proteins, and 0 genes
[31:13] Initialising library

First pass: generating a spectral library from DIA data

[31:40] File #1/6
[31:40] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
[32:31] Pre-processing...
[32:34] 2931 MS1 and 293271 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 15130621 precursors in range
[32:35] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[33:29] RT window set to 1.14156
[33:29] Peak width: 2.764
[33:29] Scan window radius set to 6
[33:29] Recommended MS1 mass accuracy setting: 2.5 ppm
[34:24] Optimised mass accuracy: 6 ppm
[34:40] Searching decoys
[36:20] Main search
[39:24] Removing low confidence identifications
[39:42] Removing interfering precursors
[39:52] Training neural networks on 201502 target and 126443 decoy PSMs
[41:29] Training neural networks on 201502 target and 123437 decoy PSMs
[42:57] Number of IDs at 0.01 FDR: 102668
[42:58] Precursors at 1% peptidoform FDR: 99847
[42:59] Calculating protein q-values
[42:59] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[43:00] Quantification
[43:00] Precursors with scored PTMs at 1% FDR: 3338 out of 3693 considered
[43:00] Precursors with all scored PTM sites unoccupied at 1% FDR: 96509
[43:00] Precursors with PTMs localised (when required) with > 90% confidence: 3071 out of 3338
[43:02] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw.quant

[43:02] File #2/6
[43:02] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
[43:53] Pre-processing...
[43:56] 2933 MS1 and 293433 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 15130621 precursors in range
[43:57] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[44:51] RT window set to 1.24739
[44:51] Recommended MS1 mass accuracy setting: 2.5 ppm
[45:10] Searching decoys
[46:56] Main search
[50:11] Removing low confidence identifications
[50:30] Removing interfering precursors
[50:40] Training neural networks on 206798 target and 130158 decoy PSMs
[52:18] Training neural networks on 206798 target and 126695 decoy PSMs
[53:52] Number of IDs at 0.01 FDR: 105614
[53:53] Precursors at 1% peptidoform FDR: 102896
[53:53] Calculating protein q-values
[53:54] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[53:54] Quantification
[53:55] Precursors with scored PTMs at 1% FDR: 3643 out of 4013 considered
[53:55] Precursors with all scored PTM sites unoccupied at 1% FDR: 99253
[53:55] Precursors with PTMs localised (when required) with > 90% confidence: 3351 out of 3643
[53:56] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw.quant

[53:56] File #3/6
[53:56] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
[54:54] Pre-processing...
[54:56] 2932 MS1 and 293358 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 15130621 precursors in range
[54:57] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[55:51] RT window set to 1.27393
[55:51] Recommended MS1 mass accuracy setting: 2.5 ppm
[56:09] Searching decoys
[57:53] Main search
[61:09] Removing low confidence identifications
[61:27] Removing interfering precursors
[61:38] Training neural networks on 205781 target and 128466 decoy PSMs
[63:16] Training neural networks on 205781 target and 125432 decoy PSMs
[64:46] Number of IDs at 0.01 FDR: 105650
[64:47] Precursors at 1% peptidoform FDR: 102785
[64:48] Calculating protein q-values
[64:48] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[64:48] Quantification
[64:49] Precursors with scored PTMs at 1% FDR: 3512 out of 3913 considered
[64:49] Precursors with all scored PTM sites unoccupied at 1% FDR: 99273
[64:49] Precursors with PTMs localised (when required) with > 90% confidence: 3222 out of 3512
[64:50] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw.quant

[64:51] File #4/6
[64:51] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
[65:51] Pre-processing...
[65:54] 2933 MS1 and 293382 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 15130621 precursors in range
[65:55] Calibrating with mass accuracies 22 (MS1), 25 (MS2)
[66:49] RT window set to 1.1236
[66:49] Recommended MS1 mass accuracy setting: 2.7 ppm
[67:01] Searching decoys
[68:37] Main search
[71:35] Removing low confidence identifications
[71:53] Removing interfering precursors
[72:04] Training neural networks on 209831 target and 133059 decoy PSMs
[73:45] Training neural networks on 209831 target and 129276 decoy PSMs
[75:18] Number of IDs at 0.01 FDR: 105248
[75:19] Precursors at 1% peptidoform FDR: 102830
[75:20] Calculating protein q-values
[75:20] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[75:20] Quantification
[75:21] Precursors with scored PTMs at 1% FDR: 4065 out of 4531 considered
[75:21] Precursors with all scored PTM sites unoccupied at 1% FDR: 98765
[75:21] Precursors with PTMs localised (when required) with > 90% confidence: 3740 out of 4065
[75:22] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw.quant

[75:22] File #5/6
[75:22] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
[76:20] Pre-processing...
[76:22] 2933 MS1 and 293330 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 15130621 precursors in range
[76:24] Calibrating with mass accuracies 22 (MS1), 25 (MS2)
[77:18] RT window set to 1.16
[77:18] Recommended MS1 mass accuracy setting: 2.5 ppm
[77:31] Searching decoys
[79:09] Main search
[82:55] Removing low confidence identifications
[83:27] Removing interfering precursors
[83:45] Training neural networks on 209228 target and 131940 decoy PSMs
[85:41] Training neural networks on 209228 target and 128325 decoy PSMs
[88:07] Number of IDs at 0.01 FDR: 105009
[88:09] Precursors at 1% peptidoform FDR: 102641
[88:11] Calculating protein q-values
[88:12] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[88:12] Quantification
[88:13] Precursors with scored PTMs at 1% FDR: 4164 out of 4514 considered
[88:13] Precursors with all scored PTM sites unoccupied at 1% FDR: 98477
[88:13] Precursors with PTMs localised (when required) with > 90% confidence: 3872 out of 4164
[88:16] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw.quant

[88:16] File #6/6
[88:16] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
[89:17] Pre-processing...
[89:21] 2934 MS1 and 293446 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 15130621 precursors in range
[89:23] Calibrating with mass accuracies 22 (MS1), 25 (MS2)
[90:44] RT window set to 1.12798
[90:44] Recommended MS1 mass accuracy setting: 2.7 ppm
[91:11] Searching decoys
[93:28] Main search
[97:38] Removing low confidence identifications
[98:08] Removing interfering precursors
[98:26] Training neural networks on 207604 target and 130950 decoy PSMs
[100:58] Training neural networks on 207604 target and 126793 decoy PSMs
[103:15] Number of IDs at 0.01 FDR: 105110
[103:17] Precursors at 1% peptidoform FDR: 102489
[103:18] 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
[103:21] Precursors with scored PTMs at 1% FDR: 4124 out of 4545 considered
[103:21] Precursors with all scored PTM sites unoccupied at 1% FDR: 98365
[103:21] Precursors with PTMs localised (when required) with > 90% confidence: 3809 out of 4124
[103:23] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw.quant

[103:23] Cross-run analysis
[103:23] Reading quantification information: 6 files
[104:15] Quantifying peptides
[107:54] Assembling protein groups
[107:58] Quantifying proteins
[107:58] Calculating q-values for protein and gene groups
[108:04] Calculating global q-values for protein and gene groups
[108:05] Protein groups with global q-value <= 0.01: 11519
[108:10] Compressed report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann-reprocessing-all-mods\report-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[108:10] Site report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann-reprocessing-all-mods\report-first-pass.site_report.parquet
[108:10] Saving precursor levels matrix
[108:11] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_Astral\diann-reprocessing-all-mods\report-first-pass.pr_matrix.tsv.
[108:11] Manifest saved to D:\Proteobench_manuscript_data\run_output_Astral\diann-reprocessing-all-mods\report-first-pass.manifest.txt
[108:11] Stats report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann-reprocessing-all-mods\report-first-pass.stats.tsv
[108:13] Generating spectral library:
[108:17] 135634 target and 1383 decoy precursors saved
[108:17] Spectral library saved to C:\DIA-NN\2.2.0\report-lib.parquet

[108:19] Loading spectral library C:\DIA-NN\2.2.0\report-lib.parquet
[108:21] Spectral library loaded: 13362 protein isoforms, 13210 protein groups and 137017 precursors in 127984 elution groups.
[108:21] Loading protein annotations from FASTA D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[108:21] Annotating library proteins with information from the FASTA database
[108:21] Gene names missing for some isoforms
[108:21] Library contains 13351 proteins, and 0 genes
[108:22] Initialising library
[108:23] Saving the library to C:\DIA-NN\2.2.0\report-lib.parquet.skyline.speclib


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

[108:24] File #1/6
[108:24] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
[109:21] Pre-processing...
[109:22] 2931 MS1 and 293271 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 135634 precursors in range
[109:22] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[109:23] RT window set to 0.452813
[109:23] Recommended MS1 mass accuracy setting: 3.6 ppm
[109:24] Searching decoys
[109:25] Main search
[109:28] Removing low confidence identifications
[109:34] Removing interfering precursors
[109:37] Training neural networks on 118854 target and 57948 decoy PSMs
[110:37] Training neural networks on 118808 target and 63514 decoy PSMs
[111:40] Number of IDs at 0.01 FDR: 115047
[111:41] Precursors at 1% peptidoform FDR: 112814
[111:41] Calculating protein q-values
[111:41] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[111:41] Quantification
[111:42] Precursors with scored PTMs at 1% FDR: 4372 out of 4487 considered
[111:42] Precursors with all scored PTM sites unoccupied at 1% FDR: 108442
[111:42] Precursors with PTMs localised (when required) with > 90% confidence: 4030 out of 4372

[111:43] File #2/6
[111:43] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
[112:40] Pre-processing...
[112:41] 2933 MS1 and 293433 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 135634 precursors in range
[112:41] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[112:42] RT window set to 0.443923
[112:42] Recommended MS1 mass accuracy setting: 3.1 ppm
[112:43] Searching decoys
[112:44] Main search
[112:47] Removing low confidence identifications
[112:53] Removing interfering precursors
[112:55] Training neural networks on 119140 target and 58176 decoy PSMs
[113:57] Training neural networks on 119084 target and 63634 decoy PSMs
[115:01] Number of IDs at 0.01 FDR: 116023
[115:02] Precursors at 1% peptidoform FDR: 114302
[115:02] Calculating protein q-values
[115:02] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[115:02] Quantification
[115:03] Precursors with scored PTMs at 1% FDR: 4501 out of 4582 considered
[115:03] Precursors with all scored PTM sites unoccupied at 1% FDR: 109801
[115:03] Precursors with PTMs localised (when required) with > 90% confidence: 4133 out of 4501

[115:04] File #3/6
[115:04] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
[116:04] Pre-processing...
[116:05] 2932 MS1 and 293358 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 135634 precursors in range
[116:05] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[116:06] RT window set to 0.445936
[116:06] Recommended MS1 mass accuracy setting: 2.9 ppm
[116:06] Searching decoys
[116:07] Main search
[116:10] Removing low confidence identifications
[116:17] Removing interfering precursors
[116:19] Training neural networks on 119168 target and 58284 decoy PSMs
[117:20] Training neural networks on 119126 target and 63843 decoy PSMs
[118:24] Number of IDs at 0.01 FDR: 116333
[118:25] Precursors at 1% peptidoform FDR: 114469
[118:25] Calculating protein q-values
[118:25] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[118:25] Quantification
[118:26] Precursors with scored PTMs at 1% FDR: 4473 out of 4580 considered
[118:26] Precursors with all scored PTM sites unoccupied at 1% FDR: 109996
[118:26] Precursors with PTMs localised (when required) with > 90% confidence: 4100 out of 4473

[118:27] File #4/6
[118:27] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
[119:29] Pre-processing...
[119:30] 2933 MS1 and 293382 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 135634 precursors in range
[119:30] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[119:31] RT window set to 0.45469
[119:31] Recommended MS1 mass accuracy setting: 3.5 ppm
[119:31] Searching decoys
[119:32] Main search
[119:36] Removing low confidence identifications
[119:42] Removing interfering precursors
[119:44] Training neural networks on 119799 target and 59083 decoy PSMs
[120:46] Training neural networks on 119757 target and 64425 decoy PSMs
[121:50] Number of IDs at 0.01 FDR: 116715
[121:51] Precursors at 1% peptidoform FDR: 114730
[121:51] Calculating protein q-values
[121:51] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[121:51] Quantification
[121:52] Precursors with scored PTMs at 1% FDR: 4705 out of 4802 considered
[121:52] Precursors with all scored PTM sites unoccupied at 1% FDR: 110025
[121:52] Precursors with PTMs localised (when required) with > 90% confidence: 4343 out of 4705

[121:53] File #5/6
[121:53] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
[122:50] Pre-processing...
[122:52] 2933 MS1 and 293330 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 135634 precursors in range
[122:52] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[122:52] RT window set to 0.456055
[122:52] Recommended MS1 mass accuracy setting: 3.2 ppm
[122:53] Searching decoys
[122:54] Main search
[122:57] Removing low confidence identifications
[123:03] Removing interfering precursors
[123:05] Training neural networks on 119863 target and 58814 decoy PSMs
[124:07] Training neural networks on 119813 target and 64482 decoy PSMs
[125:13] Number of IDs at 0.01 FDR: 116974
[125:13] Precursors at 1% peptidoform FDR: 115183
[125:13] Calculating protein q-values
[125:13] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[125:13] Quantification
[125:15] Precursors with scored PTMs at 1% FDR: 4770 out of 4821 considered
[125:15] Precursors with all scored PTM sites unoccupied at 1% FDR: 110413
[125:15] Precursors with PTMs localised (when required) with > 90% confidence: 4415 out of 4770

[125:16] File #6/6
[125:16] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
[125:31] Pre-processing...
[125:32] 2934 MS1 and 293446 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 135634 precursors in range
[125:32] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[125:32] RT window set to 0.451432
[125:32] Recommended MS1 mass accuracy setting: 3.5 ppm
[125:33] Searching decoys
[125:34] Main search
[125:37] Removing low confidence identifications
[125:43] Removing interfering precursors
[125:45] Training neural networks on 119857 target and 58936 decoy PSMs
[126:49] Training neural networks on 119802 target and 64360 decoy PSMs
[127:54] Number of IDs at 0.01 FDR: 116917
[127:55] Precursors at 1% peptidoform FDR: 114858
[127:55] Calculating protein q-values
[127:55] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[127:55] Quantification
[127:56] Precursors with scored PTMs at 1% FDR: 4750 out of 4821 considered
[127:56] Precursors with all scored PTM sites unoccupied at 1% FDR: 110108
[127:56] Precursors with PTMs localised (when required) with > 90% confidence: 4403 out of 4750

[127:57] Cross-run analysis
[127:57] Reading quantification information: 6 files
[128:00] Quantifying peptides
[131:10] Quantification parameters: 0.365535, 0.00137162, 0.00161738, 0.0118865, 0.0111855, 0.012221, 0.177419, 0.253064, 0.194679, 0.0134077, 0.0335087, 0.0140962, 0.379552, 0.0530668, 0.0785842, 0.0108611
[132:22] Quantifying proteins
[132:22] Calculating q-values for protein and gene groups
[132:23] Calculating global q-values for protein and gene groups
[132:23] Protein groups with global q-value <= 0.01: 11048
[132:27] Compressed report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann-reprocessing-all-mods\report.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[132:27] Site report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann-reprocessing-all-mods\report.site_report.parquet
[132:27] Saving precursor levels matrix
[132:28] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_Astral\diann-reprocessing-all-mods\report.pr_matrix.tsv.
[132:28] Saving protein group levels matrix
[132:28] Protein groups matrix saved to D:\Proteobench_manuscript_data\run_output_Astral\diann-reprocessing-all-mods\report.pg_matrix.tsv.
[132:28] Saving gene group levels matrix
[132:28] Gene groups matrix saved to D:\Proteobench_manuscript_data\run_output_Astral\diann-reprocessing-all-mods\report.gg_matrix.tsv.
[132:28] Saving unique genes levels matrix
[132:28] Unique genes matrix saved to D:\Proteobench_manuscript_data\run_output_Astral\diann-reprocessing-all-mods\report.unique_genes_matrix.tsv.
[132:28] Manifest saved to D:\Proteobench_manuscript_data\run_output_Astral\diann-reprocessing-all-mods\report.manifest.txt
[132:28] Stats report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann-reprocessing-all-mods\report.stats.tsv

