
DIA-NN 2.2.0 Academia  (Data-Independent Acquisition by Neural Networks)
Compiled on May 29 2025 21:29:29
Current date and time: Sun Jul 13 20:34:25 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\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d  --f D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d  --f D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d  --f D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d  --f D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d  --f D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d  --lib  --threads 20 --verbose 1 --out D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_2.2.0_default\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 --peptidoforms --reanalyse --rt-profiling 

Thread number set to 20
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
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
[0:08] 5116700 precursors generated
[0:08] Protein names missing for some isoforms
[0:08] Gene names missing for some isoforms
[0:08] Library contains 31685 proteins, and 0 genes
[0:11] [0:16] [12:15] [14:01] [14:06] [14:07] Saving the library to C:\DIA-NN\2.2.0\report-lib.predicted.speclib
[14:15] Initialising library
[14:30] Loading spectral library C:\DIA-NN\2.2.0\report-lib.predicted.speclib
[14:36] Library annotated with sequence database(s): D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[14:37] Spectral library loaded: 31837 protein isoforms, 51765 protein groups and 5116700 precursors in 2716671 elution groups.
[14:37] Loading protein annotations from FASTA D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[14:38] Annotating library proteins with information from the FASTA database
[14:38] Protein names missing for some isoforms
[14:38] Gene names missing for some isoforms
[14:38] Library contains 31685 proteins, and 0 genes
[14:43] Initialising library

First pass: generating a spectral library from DIA data

[14:58] File #1/6
[14:58] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
WARNING: for the vast majority of timsTOF datasets it is better to manually fix both the MS1 and MS2 mass accuracies to 15 ppm
[16:26] Pre-processing...
[16:33] 4348 MS1 and 104340 MS2 scans in 4348 (inferred) and 4348 (encoded) cycles, 5116700 precursors in range
[16:34] Calibrating with mass accuracies 24 (MS1), 25 (MS2)
[19:29] RT window set to 2.70388
[19:29] IM window set to 0.0436106
[19:29] Peak width: 3.972
[19:29] Scan window radius set to 8
[19:29] Recommended MS1 mass accuracy setting: 11 ppm
[23:29] Optimised mass accuracy: 12 ppm
[24:38] Searching decoys
[40:40] Main search
[71:37] Removing low confidence identifications
[72:20] Removing interfering precursors
[72:24] Training neural networks on 193635 target and 125212 decoy PSMs
[74:02] Training neural networks on 193635 target and 119594 decoy PSMs
[75:51] Number of IDs at 0.01 FDR: 99562
[75:52] Precursors at 1% peptidoform FDR: 94145
[75:52] Calculating protein q-values
[75:53] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[75:53] Quantification
[76:04] Precursors with scored PTMs at 1% FDR: 1604 out of 1861 considered
[76:04] Precursors with all scored PTM sites unoccupied at 1% FDR: 92541
[76:04] Precursors with PTMs localised (when required) with > 90% confidence: 1577 out of 1604
[76:05] Quantification information saved to D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d.quant

[76:05] File #2/6
[76:05] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
[77:26] Pre-processing...
[77:32] 4348 MS1 and 104340 MS2 scans in 4348 (inferred) and 4348 (encoded) cycles, 5116700 precursors in range
[77:32] Calibrating with mass accuracies 24 (MS1), 25 (MS2)
[80:21] RT window set to 2.39056
[80:21] IM window set to 0.042486
[80:21] Recommended MS1 mass accuracy setting: 12 ppm
[81:10] Searching decoys
[92:50] Main search
[117:11] Removing low confidence identifications
[117:55] Removing interfering precursors
[118:00] Training neural networks on 197920 target and 128667 decoy PSMs
[119:42] Training neural networks on 197920 target and 122992 decoy PSMs
[121:19] Number of IDs at 0.01 FDR: 101903
[121:19] Precursors at 1% peptidoform FDR: 96431
[121:20] Calculating protein q-values
[121:20] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[121:20] Quantification
[121:31] Precursors with scored PTMs at 1% FDR: 1214 out of 1451 considered
[121:31] Precursors with all scored PTM sites unoccupied at 1% FDR: 95217
[121:31] Precursors with PTMs localised (when required) with > 90% confidence: 1196 out of 1214
[121:32] Quantification information saved to D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d.quant

[121:32] File #3/6
[121:32] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
[122:55] Pre-processing...
[123:01] 4348 MS1 and 104340 MS2 scans in 4348 (inferred) and 4348 (encoded) cycles, 5116700 precursors in range
[123:01] Calibrating with mass accuracies 24 (MS1), 25 (MS2)
[125:51] RT window set to 2.54426
[125:51] IM window set to 0.042306
[125:51] Recommended MS1 mass accuracy setting: 11 ppm
[126:45] Searching decoys
[139:33] Main search
[169:01] Removing low confidence identifications
[169:55] Removing interfering precursors
[170:03] Training neural networks on 200641 target and 129122 decoy PSMs
[172:24] Training neural networks on 200641 target and 124029 decoy PSMs
[174:40] Number of IDs at 0.01 FDR: 102142
[174:41] Precursors at 1% peptidoform FDR: 96599
[174:42] Calculating protein q-values
[174:42] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[174:42] Quantification
[174:56] Precursors with scored PTMs at 1% FDR: 1522 out of 1714 considered
[174:56] Precursors with all scored PTM sites unoccupied at 1% FDR: 95077
[174:56] Precursors with PTMs localised (when required) with > 90% confidence: 1497 out of 1522
[174:58] Quantification information saved to D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d.quant

[174:58] File #4/6
[174:58] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
[176:30] Pre-processing...
[176:37] 4348 MS1 and 104340 MS2 scans in 4348 (inferred) and 4348 (encoded) cycles, 5116700 precursors in range
[176:37] Calibrating with mass accuracies 24 (MS1), 25 (MS2)
[180:01] RT window set to 2.56747
[180:01] IM window set to 0.042025
[180:02] Recommended MS1 mass accuracy setting: 11 ppm
[181:07] Searching decoys
[195:20] Main search
[224:02] Removing low confidence identifications
[224:52] Removing interfering precursors
[224:59] Training neural networks on 195062 target and 128656 decoy PSMs
[227:20] Training neural networks on 195062 target and 122531 decoy PSMs
[229:33] Number of IDs at 0.01 FDR: 98970
[229:34] Precursors at 1% peptidoform FDR: 93759
[229:35] Calculating protein q-values
[229:35] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[229:35] Quantification
[229:39] Precursors with scored PTMs at 1% FDR: 1308 out of 1587 considered
[229:39] Precursors with all scored PTM sites unoccupied at 1% FDR: 92451
[229:39] Precursors with PTMs localised (when required) with > 90% confidence: 1290 out of 1308
[229:42] Quantification information saved to D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d.quant

[229:42] File #5/6
[229:42] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
[231:09] Pre-processing...
[231:15] 4348 MS1 and 104340 MS2 scans in 4348 (inferred) and 4348 (encoded) cycles, 5116700 precursors in range
[231:16] Calibrating with mass accuracies 24 (MS1), 25 (MS2)
[234:38] RT window set to 2.56078
[234:38] IM window set to 0.0434684
[234:38] Recommended MS1 mass accuracy setting: 11 ppm
[235:42] Searching decoys
[250:10] Main search
[279:25] Removing low confidence identifications
[280:19] Removing interfering precursors
[280:27] Training neural networks on 198712 target and 128517 decoy PSMs
[282:49] Training neural networks on 198712 target and 123201 decoy PSMs
[285:09] Number of IDs at 0.01 FDR: 100565
[285:10] Precursors at 1% peptidoform FDR: 95205
[285:10] Calculating protein q-values
[285:11] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[285:11] Quantification
[285:15] Precursors with scored PTMs at 1% FDR: 1329 out of 1604 considered
[285:15] Precursors with all scored PTM sites unoccupied at 1% FDR: 93876
[285:15] Precursors with PTMs localised (when required) with > 90% confidence: 1306 out of 1329
[285:18] Quantification information saved to D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d.quant

[285:18] File #6/6
[285:18] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
[286:50] Pre-processing...
[286:56] 4348 MS1 and 104343 MS2 scans in 4348 (inferred) and 4348 (encoded) cycles, 5116700 precursors in range
[286:57] Calibrating with mass accuracies 24 (MS1), 25 (MS2)
[290:21] RT window set to 2.55737
[290:21] IM window set to 0.0415447
[290:21] Recommended MS1 mass accuracy setting: 11 ppm
[291:26] Searching decoys
[305:53] Main search
[334:51] Removing low confidence identifications
[335:44] Removing interfering precursors
[335:52] Training neural networks on 198822 target and 128240 decoy PSMs
[338:14] Training neural networks on 198822 target and 123378 decoy PSMs
[340:30] Number of IDs at 0.01 FDR: 101281
[340:31] Precursors at 1% peptidoform FDR: 95616
[340:32] Calculating protein q-values
[340:32] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[340:33] Quantification
[340:37] Precursors with scored PTMs at 1% FDR: 1513 out of 1860 considered
[340:37] Precursors with all scored PTM sites unoccupied at 1% FDR: 94103
[340:37] Precursors with PTMs localised (when required) with > 90% confidence: 1485 out of 1513
[340:39] Quantification information saved to D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d.quant

[340:39] Cross-run analysis
[340:39] Reading quantification information: 6 files
[341:06] Quantifying peptides
[341:54] Assembling protein groups
[341:57] Quantifying proteins
[341:57] Calculating q-values for protein and gene groups
[342:00] Calculating global q-values for protein and gene groups
[342:00] Protein groups with global q-value <= 0.01: 11603
[342:04] Compressed report saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_2.2.0_default\report-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[342:04] Site report saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_2.2.0_default\report-first-pass.site_report.parquet
[342:04] Saving precursor levels matrix
[342:05] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_2.2.0_default\report-first-pass.pr_matrix.tsv.
[342:05] Manifest saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_2.2.0_default\report-first-pass.manifest.txt
[342:05] Stats report saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_2.2.0_default\report-first-pass.stats.tsv
[342:06] Generating spectral library:
[342:09] 125271 target and 1272 decoy precursors saved
[342:09] Spectral library saved to C:\DIA-NN\2.2.0\report-lib.parquet

[342:17] Loading spectral library C:\DIA-NN\2.2.0\report-lib.parquet
[342:18] Spectral library loaded: 13539 protein isoforms, 13348 protein groups and 126543 precursors in 116403 elution groups.
[342:18] Loading protein annotations from FASTA D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[342:19] Annotating library proteins with information from the FASTA database
[342:19] Gene names missing for some isoforms
[342:19] Library contains 13519 proteins, and 0 genes
[342:19] Initialising library
[342:21] 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

[342:21] File #1/6
[342:21] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
[343:48] Pre-processing...
[343:55] 4348 MS1 and 104340 MS2 scans in 4348 (inferred) and 4348 (encoded) cycles, 125271 precursors in range
[343:55] Calibrating with mass accuracies 24 (MS1), 25 (MS2)
[344:00] RT window set to 0.940476
[344:00] IM window set to 0.01
[344:00] Recommended MS1 mass accuracy setting: 11 ppm
[344:01] Searching decoys
[344:12] Main search
[344:33] Removing low confidence identifications
[344:46] Removing interfering precursors
[344:47] Training neural networks on 112901 target and 70678 decoy PSMs
[345:55] Training neural networks on 112873 target and 65764 decoy PSMs
[346:59] Number of IDs at 0.01 FDR: 112587
[346:59] Precursors at 1% peptidoform FDR: 105442
[346:59] Calculating protein q-values
[347:00] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[347:00] Quantification
[347:04] Precursors with scored PTMs at 1% FDR: 1732 out of 1832 considered
[347:04] Precursors with all scored PTM sites unoccupied at 1% FDR: 103710
[347:04] Precursors with PTMs localised (when required) with > 90% confidence: 1718 out of 1732

[347:06] File #2/6
[347:06] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
[348:35] Pre-processing...
[348:41] 4348 MS1 and 104340 MS2 scans in 4348 (inferred) and 4348 (encoded) cycles, 125271 precursors in range
[348:41] Calibrating with mass accuracies 24 (MS1), 25 (MS2)
[348:46] RT window set to 0.942643
[348:46] IM window set to 0.01
[348:46] Recommended MS1 mass accuracy setting: 12 ppm
[348:48] Searching decoys
[348:58] Main search
[349:20] Removing low confidence identifications
[349:33] Removing interfering precursors
[349:35] Training neural networks on 113332 target and 71153 decoy PSMs
[350:43] Training neural networks on 113303 target and 65906 decoy PSMs
[351:48] Number of IDs at 0.01 FDR: 114627
[351:49] Precursors at 1% peptidoform FDR: 107323
[351:49] Calculating protein q-values
[351:49] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[351:49] Quantification
[351:53] Precursors with scored PTMs at 1% FDR: 1758 out of 1859 considered
[351:53] Precursors with all scored PTM sites unoccupied at 1% FDR: 105565
[351:53] Precursors with PTMs localised (when required) with > 90% confidence: 1739 out of 1758

[351:55] File #3/6
[351:55] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
[353:25] Pre-processing...
[353:31] 4348 MS1 and 104340 MS2 scans in 4348 (inferred) and 4348 (encoded) cycles, 125271 precursors in range
[353:31] Calibrating with mass accuracies 24 (MS1), 25 (MS2)
[353:37] RT window set to 0.942636
[353:37] IM window set to 0.01
[353:37] Recommended MS1 mass accuracy setting: 12 ppm
[353:38] Searching decoys
[353:50] Main search
[354:11] Removing low confidence identifications
[354:24] Removing interfering precursors
[354:26] Training neural networks on 113226 target and 71332 decoy PSMs
[355:35] Training neural networks on 113192 target and 66423 decoy PSMs
[356:40] Number of IDs at 0.01 FDR: 114366
[356:41] Precursors at 1% peptidoform FDR: 107467
[356:41] Calculating protein q-values
[356:41] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[356:41] Quantification
[356:45] Precursors with scored PTMs at 1% FDR: 1748 out of 1832 considered
[356:45] Precursors with all scored PTM sites unoccupied at 1% FDR: 105719
[356:45] Precursors with PTMs localised (when required) with > 90% confidence: 1728 out of 1748

[356:47] File #4/6
[356:47] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
[358:15] Pre-processing...
[358:21] 4348 MS1 and 104340 MS2 scans in 4348 (inferred) and 4348 (encoded) cycles, 125271 precursors in range
[358:21] Calibrating with mass accuracies 24 (MS1), 25 (MS2)
[358:26] RT window set to 0.940197
[358:26] IM window set to 0.01
[358:26] Recommended MS1 mass accuracy setting: 11 ppm
[358:28] Searching decoys
[358:38] Main search
[358:59] Removing low confidence identifications
[359:13] Removing interfering precursors
[359:15] Training neural networks on 113045 target and 70897 decoy PSMs
[360:27] Training neural networks on 113020 target and 65584 decoy PSMs
[361:32] Number of IDs at 0.01 FDR: 113897
[361:32] Precursors at 1% peptidoform FDR: 106488
[361:32] Calculating protein q-values
[361:32] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[361:32] Quantification
[361:36] Precursors with scored PTMs at 1% FDR: 1734 out of 1845 considered
[361:36] Precursors with all scored PTM sites unoccupied at 1% FDR: 104754
[361:36] Precursors with PTMs localised (when required) with > 90% confidence: 1724 out of 1734

[361:38] File #5/6
[361:38] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
[363:07] Pre-processing...
[363:13] 4348 MS1 and 104340 MS2 scans in 4348 (inferred) and 4348 (encoded) cycles, 125271 precursors in range
[363:13] Calibrating with mass accuracies 24 (MS1), 25 (MS2)
[363:18] RT window set to 0.940522
[363:18] IM window set to 0.01
[363:18] Recommended MS1 mass accuracy setting: 12 ppm
[363:20] Searching decoys
[363:31] Main search
[363:52] Removing low confidence identifications
[364:04] Removing interfering precursors
[364:06] Training neural networks on 112975 target and 71282 decoy PSMs
[365:16] Training neural networks on 112943 target and 65714 decoy PSMs
[366:20] Number of IDs at 0.01 FDR: 114227
[366:21] Precursors at 1% peptidoform FDR: 107265
[366:21] Calculating protein q-values
[366:21] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[366:21] Quantification
[366:25] Precursors with scored PTMs at 1% FDR: 1729 out of 1830 considered
[366:25] Precursors with all scored PTM sites unoccupied at 1% FDR: 105536
[366:25] Precursors with PTMs localised (when required) with > 90% confidence: 1712 out of 1729

[366:27] File #6/6
[366:27] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
[367:57] Pre-processing...
[368:03] 4348 MS1 and 104343 MS2 scans in 4348 (inferred) and 4348 (encoded) cycles, 125271 precursors in range
[368:03] Calibrating with mass accuracies 24 (MS1), 25 (MS2)
[368:08] RT window set to 0.940354
[368:08] IM window set to 0.01
[368:08] Recommended MS1 mass accuracy setting: 11 ppm
[368:10] Searching decoys
[368:21] Main search
[368:42] Removing low confidence identifications
[368:55] Removing interfering precursors
[368:56] Training neural networks on 113017 target and 70758 decoy PSMs
[370:06] Training neural networks on 112982 target and 65858 decoy PSMs
[371:11] Number of IDs at 0.01 FDR: 114253
[371:12] Precursors at 1% peptidoform FDR: 107267
[371:12] Calculating protein q-values
[371:12] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[371:12] Quantification
[371:16] Precursors with scored PTMs at 1% FDR: 1730 out of 1821 considered
[371:16] Precursors with all scored PTM sites unoccupied at 1% FDR: 105537
[371:16] Precursors with PTMs localised (when required) with > 90% confidence: 1712 out of 1730

[371:18] Cross-run analysis
[371:18] Reading quantification information: 6 files
[371:21] Quantifying peptides
[374:28] Quantification parameters: 0.364491, 0.00130596, 0.00412396, 0.0452866, 0.0552398, 0.0566368, 0.201886, 0.0144234, 0.0592795, 0.0493625, 0.0554986, 0.0535301, 0.219115, 0.116442, 0.128653, 0.0119587
[374:48] Quantifying proteins
[374:48] Calculating q-values for protein and gene groups
[374:48] Calculating global q-values for protein and gene groups
[374:48] Protein groups with global q-value <= 0.01: 11349
[374:55] Compressed report saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_2.2.0_default\report.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[374:55] Site report saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_2.2.0_default\report.site_report.parquet
[374:55] Saving precursor levels matrix
[374:56] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_2.2.0_default\report.pr_matrix.tsv.
[374:56] Saving protein group levels matrix
[374:56] Protein groups matrix saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_2.2.0_default\report.pg_matrix.tsv.
[374:56] Saving gene group levels matrix
[374:56] Gene groups matrix saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_2.2.0_default\report.gg_matrix.tsv.
[374:56] Saving unique genes levels matrix
[374:56] Unique genes matrix saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_2.2.0_default\report.unique_genes_matrix.tsv.
[374:56] Manifest saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_2.2.0_default\report.manifest.txt
[374:56] Stats report saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_2.2.0_default\report.stats.tsv

