DIA-NN 1.8 (Data-Independent Acquisition by Neural Networks)
Compiled on Jun 28 2021 14:55:31
Current date and time: Wed Jan 15 17:01:37 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 24 --verbose 1 --out D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_1.8_default\report.tsv --qvalue 0.01 --matrices --out-lib C:\DIA-NN\1.8\report-lib.tsv --gen-spec-lib --predictor --fasta D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta --fasta-search --min-fr-mz 50 --max-fr-mz 2000 --met-excision --cut K*,R* --missed-cleavages 1 --min-pep-len 6 --max-pep-len 30 --min-pr-mz 400 --max-pr-mz 1000 --min-pr-charge 1 --max-pr-charge 4 --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --monitor-mod UniMod:1 --reanalyse --smart-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
Library-free search enabled
Min fragment m/z set to 50
Max fragment m/z set to 2000
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
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
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
A spectral library will be created from the DIA runs and used to reanalyse them; .quant files will only be saved to disk during the first step
When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones
DIA-NN will optimise the mass accuracy automatically using the first run in the experiment. This is useful primarily for quick initial analyses, when it is not yet known which mass accuracy setting works best for a particular acquisition scheme.
The following variable modifications will be scored: UniMod:1 

6 files will be processed
[0:00] Loading FASTA D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[0:03] Processing FASTA
[0:10] Assembling elution groups
[0:15] 4880109 precursors generated
[0:15] Protein names missing for some isoforms
[0:15] Gene names missing for some isoforms
[0:15] Library contains 31676 proteins, and 0 genes
[0:15] [0:20] [15:02] [17:54] [17:59] [18:01] Saving the library to C:\DIA-NN\1.8\report-lib.predicted.speclib
[18:07] Initialising library

[18:08] First pass: generating a spectral library from DIA data
[18:08] File #1/6
[18:08] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
For most diaPASEF datasets it is better to manually fix both the MS1 and MS2 mass accuracies to 10 ppm.
[19:50] 4880109 library precursors are potentially detectable
[19:50] Processing...
[22:42] RT window set to 2.38556
[22:42] Ion mobility window set to 0.071124
[22:42] Peak width: 4.084
[22:42] Scan window radius set to 8
[22:42] Recommended MS1 mass accuracy setting: 14.3141 ppm
[27:08] Optimised mass accuracy: 12.1831 ppm
[56:05] Removing low confidence identifications
[56:05] Searching PTM decoys
[56:23] Removing interfering precursors
[56:28] Training neural networks: 140526 targets, 101385 decoys
[56:33] Number of IDs at 0.01 FDR: 76644
[56:34] Calculating protein q-values
[56:34] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[56:34] Quantification
[56:35] Precursors with monitored PTMs at 1% FDR: 502 out of 608
[56:35] Unmodified precursors with monitored PTM sites at 1% FDR: 275 out of 303
[56:36] Quantification information saved to D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d.quant.

[56:43] File #2/6
[56:43] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
[58:15] 4880109 library precursors are potentially detectable
[58:15] Processing...
[61:14] RT window set to 2.32166
[61:14] Ion mobility window set to 0.0739735
[61:15] Recommended MS1 mass accuracy setting: 14.1372 ppm
[86:56] Removing low confidence identifications
[86:56] Searching PTM decoys
[87:22] Removing interfering precursors
[87:31] Training neural networks: 159279 targets, 111999 decoys
[87:40] Number of IDs at 0.01 FDR: 82537
[87:42] Calculating protein q-values
[87:42] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[87:43] Quantification
[87:44] Precursors with monitored PTMs at 1% FDR: 472 out of 553
[87:44] Unmodified precursors with monitored PTM sites at 1% FDR: 311 out of 333
[87:46] Quantification information saved to D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d.quant.

[87:56] File #3/6
[87:56] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
[89:36] 4880109 library precursors are potentially detectable
[89:37] Processing...
[93:55] RT window set to 2.35589
[93:55] Ion mobility window set to 0.0761797
[93:56] Recommended MS1 mass accuracy setting: 14.25 ppm
[123:49] Removing low confidence identifications
[123:49] Searching PTM decoys
[124:07] Removing interfering precursors
[124:13] Training neural networks: 160548 targets, 112616 decoys
[124:18] Number of IDs at 0.01 FDR: 82788
[124:19] Calculating protein q-values
[124:19] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[124:19] Quantification
[124:20] Precursors with monitored PTMs at 1% FDR: 542 out of 571
[124:20] Unmodified precursors with monitored PTM sites at 1% FDR: 318 out of 330
[124:21] Quantification information saved to D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d.quant.

[124:28] File #4/6
[124:28] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
[126:04] 4880109 library precursors are potentially detectable
[126:05] Processing...
[128:53] RT window set to 2.42111
[128:53] Ion mobility window set to 0.0750899
[128:53] Recommended MS1 mass accuracy setting: 13.7167 ppm
[153:04] Removing low confidence identifications
[153:04] Searching PTM decoys
[153:22] Removing interfering precursors
[153:27] Training neural networks: 146208 targets, 106516 decoys
[153:32] Number of IDs at 0.01 FDR: 79810
[153:32] Calculating protein q-values
[153:33] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[153:33] Quantification
[153:33] Precursors with monitored PTMs at 1% FDR: 466 out of 561
[153:33] Unmodified precursors with monitored PTM sites at 1% FDR: 330 out of 390
[153:34] Quantification information saved to D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d.quant.

[153:41] File #5/6
[153:41] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
[155:15] 4880109 library precursors are potentially detectable
[155:16] Processing...
[158:08] RT window set to 2.39336
[158:08] Ion mobility window set to 0.0773038
[158:09] Recommended MS1 mass accuracy setting: 13.7552 ppm
[184:58] Removing low confidence identifications
[184:58] Searching PTM decoys
[185:17] Removing interfering precursors
[185:22] Training neural networks: 159272 targets, 112050 decoys
[185:28] Number of IDs at 0.01 FDR: 81560
[185:29] Calculating protein q-values
[185:29] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[185:29] Quantification
[185:30] Precursors with monitored PTMs at 1% FDR: 390 out of 509
[185:30] Unmodified precursors with monitored PTM sites at 1% FDR: 328 out of 387
[185:31] Quantification information saved to D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d.quant.

[185:38] File #6/6
[185:38] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
[187:20] 4880109 library precursors are potentially detectable
[187:20] Processing...
[190:18] RT window set to 2.37072
[190:18] Ion mobility window set to 0.0753819
[190:19] Recommended MS1 mass accuracy setting: 14.1609 ppm
[214:52] Removing low confidence identifications
[214:52] Searching PTM decoys
[215:10] Removing interfering precursors
[215:16] Training neural networks: 156167 targets, 111498 decoys
[215:21] Number of IDs at 0.01 FDR: 82839
[215:22] Calculating protein q-values
[215:22] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[215:22] Quantification
[215:23] Precursors with monitored PTMs at 1% FDR: 525 out of 536
[215:23] Unmodified precursors with monitored PTM sites at 1% FDR: 381 out of 384
[215:24] Quantification information saved to D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d.quant.

[215:31] Cross-run analysis
[215:31] Reading quantification information: 6 files
[215:32] Quantifying peptides
[215:34] Assembling protein groups
[215:36] Quantifying proteins
[215:36] Calculating q-values for protein and gene groups
[215:37] Calculating global q-values for protein and gene groups
[215:37] Writing report
[215:52] Report saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_1.8_default\report-first-pass.tsv.
[215:52] Saving precursor levels matrix
[215:52] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_1.8_default\report-first-pass.pr_matrix.tsv.
[215:52] Saving protein group levels matrix
[215:52] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_1.8_default\report-first-pass.pg_matrix.tsv.
[215:52] Saving gene group levels matrix
[215:52] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_1.8_default\report-first-pass.gg_matrix.tsv.
[215:52] Saving unique genes levels matrix
[215:52] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_1.8_default\report-first-pass.unique_genes_matrix.tsv.
[215:52] Stats report saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_1.8_default\report-first-pass.stats.tsv
[215:52] Generating spectral library:
[215:52] Reading quantification information: 6 files
[215:53] Assembling protein groups
[215:56] 104377 precursors passing the FDR threshold are to be extracted
[215:56] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
[217:38] 4880109 library precursors are potentially detectable
[217:40] 14338 spectra added to the library
[217:46] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
[219:18] 4880109 library precursors are potentially detectable
[219:19] 11635 spectra added to the library
[219:26] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
[221:01] 4880109 library precursors are potentially detectable
[221:03] 17107 spectra added to the library
[221:10] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
[222:44] 4880109 library precursors are potentially detectable
[222:46] 15461 spectra added to the library
[222:53] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
[224:26] 4880109 library precursors are potentially detectable
[224:28] 12631 spectra added to the library
[224:34] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
[226:16] 4880109 library precursors are potentially detectable
[226:17] 10994 spectra added to the library
[226:24] Saving spectral library to C:\DIA-NN\1.8\report-lib.tsv
[226:32] 104377 precursors saved
[226:32] Loading the generated library and saving it in the .speclib format
[226:32] Loading spectral library C:\DIA-NN\1.8\report-lib.tsv
[226:34] Spectral library loaded: 13082 protein isoforms, 13526 protein groups and 104377 precursors in 94931 elution groups.
[226:34] Loading protein annotations from FASTA D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[226:34] Gene names missing for some isoforms
[226:34] Library contains 13030 proteins, and 0 genes
[226:35] Saving the library to C:\DIA-NN\1.8\report-lib.tsv.speclib

[226:36] Second pass: using the newly created spectral library to reanalyse the data
[226:36] File #1/6
[226:36] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
[228:11] 104377 library precursors are potentially detectable
[228:11] Processing...
[228:13] RT window set to 0.938328
[228:13] Ion mobility window set to 0.04
[228:13] Recommended MS1 mass accuracy setting: 14.4897 ppm
[228:28] Removing low confidence identifications
[228:28] Searching PTM decoys
[228:28] Removing interfering precursors
[228:30] Training neural networks: 100573 targets, 103295 decoys
[228:34] Number of IDs at 0.01 FDR: 89748
[228:35] Calculating protein q-values
[228:35] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[228:35] Quantification
[228:36] Precursors with monitored PTMs at 1% FDR: 561 out of 628
[228:36] Unmodified precursors with monitored PTM sites at 1% FDR: 334 out of 370

[228:43] File #2/6
[228:43] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
[230:11] 104377 library precursors are potentially detectable
[230:11] Processing...
[230:13] RT window set to 0.938706
[230:13] Ion mobility window set to 0.04
[230:13] Recommended MS1 mass accuracy setting: 14.2755 ppm
[230:28] Removing low confidence identifications
[230:28] Searching PTM decoys
[230:28] Removing interfering precursors
[230:31] Training neural networks: 102674 targets, 103908 decoys
[230:35] Number of IDs at 0.01 FDR: 97699
[230:36] Calculating protein q-values
[230:36] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[230:36] Quantification
[230:36] Precursors with monitored PTMs at 1% FDR: 611 out of 640
[230:36] Unmodified precursors with monitored PTM sites at 1% FDR: 366 out of 404

[230:44] File #3/6
[230:44] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
[232:15] 104377 library precursors are potentially detectable
[232:15] Processing...
[232:18] RT window set to 0.937404
[232:18] Ion mobility window set to 0.04
[232:18] Recommended MS1 mass accuracy setting: 14.0052 ppm
[232:33] Removing low confidence identifications
[232:33] Searching PTM decoys
[232:33] Removing interfering precursors
[232:35] Training neural networks: 102061 targets, 103240 decoys
[232:39] Number of IDs at 0.01 FDR: 93303
[232:40] Calculating protein q-values
[232:40] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[232:40] Quantification
[232:41] Precursors with monitored PTMs at 1% FDR: 575 out of 629
[232:41] Unmodified precursors with monitored PTM sites at 1% FDR: 353 out of 397

[232:49] File #4/6
[232:49] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
[234:20] 104377 library precursors are potentially detectable
[234:20] Processing...
[234:22] RT window set to 0.940822
[234:22] Ion mobility window set to 0.04
[234:22] Recommended MS1 mass accuracy setting: 14.8222 ppm
[234:37] Removing low confidence identifications
[234:37] Searching PTM decoys
[234:37] Removing interfering precursors
[234:40] Training neural networks: 102748 targets, 103822 decoys
[234:43] Number of IDs at 0.01 FDR: 98353
[234:44] Calculating protein q-values
[234:44] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[234:44] Quantification
[234:45] Precursors with monitored PTMs at 1% FDR: 586 out of 636
[234:45] Unmodified precursors with monitored PTM sites at 1% FDR: 408 out of 449

[234:53] File #5/6
[234:53] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
[236:22] 104377 library precursors are potentially detectable
[236:22] Processing...
[236:25] RT window set to 0.936274
[236:25] Ion mobility window set to 0.04
[236:25] Recommended MS1 mass accuracy setting: 14.9256 ppm
[236:40] Removing low confidence identifications
[236:40] Searching PTM decoys
[236:40] Removing interfering precursors
[236:43] Training neural networks: 102797 targets, 103785 decoys
[236:46] Number of IDs at 0.01 FDR: 98863
[236:47] Calculating protein q-values
[236:47] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[236:47] Quantification
[236:48] Precursors with monitored PTMs at 1% FDR: 586 out of 639
[236:48] Unmodified precursors with monitored PTM sites at 1% FDR: 405 out of 452

[236:56] File #6/6
[236:56] Loading run D:\Proteobench_manuscript_data\Raw_diaPASEF\Marie_2025\ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
[238:34] 104377 library precursors are potentially detectable
[238:34] Processing...
[238:37] RT window set to 0.934809
[238:37] Ion mobility window set to 0.04
[238:37] Recommended MS1 mass accuracy setting: 14.5157 ppm
[238:52] Removing low confidence identifications
[238:52] Searching PTM decoys
[238:52] Removing interfering precursors
[238:54] Training neural networks: 102745 targets, 103797 decoys
[238:58] Number of IDs at 0.01 FDR: 98464
[238:59] Calculating protein q-values
[238:59] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[238:59] Quantification
[239:00] Precursors with monitored PTMs at 1% FDR: 593 out of 639
[239:00] Unmodified precursors with monitored PTM sites at 1% FDR: 420 out of 457

[239:08] Cross-run analysis
[239:08] Reading quantification information: 6 files
[239:09] Quantifying peptides
[239:10] Quantifying proteins
[239:10] Calculating q-values for protein and gene groups
[239:11] Calculating global q-values for protein and gene groups
[239:11] Writing report
[239:27] Report saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_1.8_default\report.tsv.
[239:27] Saving precursor levels matrix
[239:27] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_1.8_default\report.pr_matrix.tsv.
[239:27] Saving protein group levels matrix
[239:28] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_1.8_default\report.pg_matrix.tsv.
[239:28] Saving gene group levels matrix
[239:28] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_1.8_default\report.gg_matrix.tsv.
[239:28] Saving unique genes levels matrix
[239:28] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_1.8_default\report.unique_genes_matrix.tsv.
[239:28] Stats report saved to D:\Proteobench_manuscript_data\run_output_diaPASEF\diann_1.8_default\report.stats.tsv
