DIA-NN 1.9.1 (Data-Independent Acquisition by Neural Networks)
Compiled on Jul 15 2024 09:42:01
Current date and time: Tue Jun 23 20:09:15 2026
Logical CPU cores: 128
/home/robbe/bin/diann-1.9.1/diann-linux --f /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d --f /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d --f /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d --f /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d --f /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d --f /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d --f /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d --f /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d --f /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d --f /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d --f /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d --f /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d --fasta /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta --out /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/report.tsv --temp /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1 --threads 15 --missed-cleavages 1 --min-pep-len 6 --max-pep-len 30 --mass-acc 20 --mass-acc-ms1 20 --qvalue 0.01 --protein-qvalue 0.01 --min-pr-charge 1 --max-pr-charge 5 --min-pr-mz 400 --max-pr-mz 1200 --min-fr-mz 200 --max-fr-mz 2000 --cut K*,R* --unimod4 --var-mod UniMod:35,15.994915,M --var-mods 1 --gen-spec-lib --fasta-search --reanalyse 

Thread number set to 15
Maximum number of missed cleavages set to 1
Min peptide length set to 6
Max peptide length set to 30
Output will be filtered at 0.01 FDR
Output will be filtered at 0.01 protein-level FDR
Min precursor charge set to 1
Max precursor charge set to 5
Min precursor m/z set to 400
Max precursor m/z set to 1200
Min fragment m/z set to 200
Max fragment m/z set to 2000
In silico digest will involve cuts at K*,R*
Cysteine carbamidomethylation enabled as a fixed modification
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
Maximum number of variable modifications set to 1
A spectral library will be generated
DIA-NN will carry out FASTA digest for in silico lib generation
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
Mass accuracy will be fixed to 2e-05 (MS2) and 2e-05 (MS1)
WARNING: FASTA digest mode enabled and raw data are provided, turning on deep learning spectra/RT/IM prediction
WARNING: it is strongly recommended to first generate an in silico-predicted library in a separate pipeline step and then use it to process the raw data, now without activating FASTA digest
WARNING: peptidoform scoring enabled because variable modifications have been declared; to disable, use --no-peptidoforms
The following variable modifications will be scored: UniMod:35 

12 files will be processed
[0:00] Loading FASTA /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
[0:04] Processing FASTA
[0:09] Assembling elution groups
[0:16] 5697771 precursors generated
[0:16] Protein names missing for some isoforms
[0:16] Gene names missing for some isoforms
[0:16] Library contains 31685 proteins, and 0 genes
[0:20] [0:34] [9:28] [10:28] [10:33] [10:39] Saving the library to report-lib.predicted.speclib
[10:51] Initialising library
[11:03] Loading spectral library report-lib.predicted.speclib
[11:08] Library annotated with sequence database(s): /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
[11:10] Spectral library loaded: 31837 protein isoforms, 51483 protein groups and 5697771 precursors in 2602499 elution groups.
[11:10] Loading protein annotations from FASTA /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
[11:10] Annotating library proteins with information from the FASTA database
[11:10] Protein names missing for some isoforms
[11:10] Gene names missing for some isoforms
[11:10] Library contains 31685 proteins, and 0 genes
[11:16] [11:26] [18:46] [19:39] [19:43] [19:46] Saving the library to report-lib.predicted.speclib
[20:01] Initialising library

First pass: generating a spectral library from DIA data

[20:10] File #1/12
[20:10] Loading run /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
WARNING: for most Slice/DIA-PASEF datasets it is better to manually fix both the MS1 and MS2 mass accuracies to values in the range 10-15 ppm
[20:15] 5543758 library precursors are potentially detectable
[20:16] Processing...
[26:55] RT window set to 1.83689
[26:55] Ion mobility window set to 0.0371556
[26:55] Peak width: 3.292
[26:55] Scan window radius set to 7
[26:55] Recommended MS1 mass accuracy setting: 12.5729 ppm
[35:22] Removing low confidence identifications
[37:44] Precursors at 1% peptidoform FDR: 7233
[37:45] Removing interfering precursors
[37:48] Training neural networks: 24272 targets, 13944 decoys
[37:50] Number of IDs at 0.01 FDR: 14785
[37:51] Precursors at 1% peptidoform FDR: 9093
[37:52] Calculating protein q-values
[37:52] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[37:52] Quantification
[37:53] Precursors with monitored PTMs at 1% FDR: 55 out of 4961 considered
[37:53] Unmodified precursors with monitored PTM sites at 1% FDR: 1492
[37:53] Precursors with PTMs localised (when required) with > 90% confidence: 55 out of 55
[37:53] Quantification information saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/_public_local_ProteoBench_PYE_diaPASEF_A9_G_DIA_nLC_tTOF_R1_d.quant

[37:53] File #2/12
[37:53] Loading run /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
[37:58] 5543758 library precursors are potentially detectable
[37:59] Processing...
[45:09] RT window set to 1.742
[45:09] Ion mobility window set to 0.0382085
[45:10] Recommended MS1 mass accuracy setting: 12.4912 ppm
[53:55] Removing low confidence identifications
[56:15] Precursors at 1% peptidoform FDR: 8619
[56:16] Removing interfering precursors
[56:21] Training neural networks: 26913 targets, 15548 decoys
[56:23] Number of IDs at 0.01 FDR: 16221
[56:25] Precursors at 1% peptidoform FDR: 11174
[56:25] Calculating protein q-values
[56:26] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[56:26] Quantification
[56:26] Precursors with monitored PTMs at 1% FDR: 58 out of 5653 considered
[56:26] Unmodified precursors with monitored PTM sites at 1% FDR: 1898
[56:26] Precursors with PTMs localised (when required) with > 90% confidence: 57 out of 58
[56:26] Quantification information saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/_public_local_ProteoBench_PYE_diaPASEF_A9_G_DIA_nLC_tTOF_R2_d.quant

[56:26] File #3/12
[56:26] Loading run /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
[56:33] 5543758 library precursors are potentially detectable
[56:33] Processing...
[62:59] RT window set to 1.45512
[62:59] Ion mobility window set to 0.036908
[62:59] Recommended MS1 mass accuracy setting: 12.1362 ppm
[69:58] Removing low confidence identifications
[72:03] Precursors at 1% peptidoform FDR: 7910
[72:03] Removing interfering precursors
[72:07] Training neural networks: 26495 targets, 15319 decoys
[72:09] Number of IDs at 0.01 FDR: 15384
[72:10] Precursors at 1% peptidoform FDR: 10146
[72:11] Calculating protein q-values
[72:11] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[72:11] Quantification
[72:12] Precursors with monitored PTMs at 1% FDR: 71 out of 5270 considered
[72:12] Unmodified precursors with monitored PTM sites at 1% FDR: 1631
[72:12] Precursors with PTMs localised (when required) with > 90% confidence: 69 out of 71
[72:12] Quantification information saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/_public_local_ProteoBench_PYE_diaPASEF_A9_G_DIA_nLC_tTOF_R3_d.quant

[72:12] File #4/12
[72:12] Loading run /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
[72:18] 5543758 library precursors are potentially detectable
[72:19] Processing...
[79:52] RT window set to 1.63014
[79:52] Ion mobility window set to 0.0385417
[79:53] Recommended MS1 mass accuracy setting: 12.0866 ppm
[88:48] Removing low confidence identifications
[91:17] Precursors at 1% peptidoform FDR: 8860
[91:18] Removing interfering precursors
[91:22] Training neural networks: 27645 targets, 15786 decoys
[91:25] Number of IDs at 0.01 FDR: 16707
[91:27] Precursors at 1% peptidoform FDR: 11497
[91:28] Calculating protein q-values
[91:29] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[91:29] Quantification
[91:29] Precursors with monitored PTMs at 1% FDR: 23 out of 5793 considered
[91:29] Unmodified precursors with monitored PTM sites at 1% FDR: 1877
[91:29] Precursors with PTMs localised (when required) with > 90% confidence: 22 out of 23
[91:29] Quantification information saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/_public_local_ProteoBench_PYE_diaPASEF_A9_G_DIA_nLC_tTOF_R4_d.quant

[91:29] File #5/12
[91:29] Loading run /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
[91:36] 5543758 library precursors are potentially detectable
[91:37] Processing...
[97:57] RT window set to 1.84544
[97:57] Ion mobility window set to 0.0367174
[97:57] Recommended MS1 mass accuracy setting: 11.9703 ppm
[106:31] Removing low confidence identifications
[109:00] Precursors at 1% peptidoform FDR: 8446
[109:01] Removing interfering precursors
[109:04] Training neural networks: 27362 targets, 15495 decoys
[109:06] Number of IDs at 0.01 FDR: 16624
[109:08] Precursors at 1% peptidoform FDR: 10899
[109:08] Calculating protein q-values
[109:09] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[109:09] Quantification
[109:09] Precursors with monitored PTMs at 1% FDR: 72 out of 5674 considered
[109:09] Unmodified precursors with monitored PTM sites at 1% FDR: 1783
[109:09] Precursors with PTMs localised (when required) with > 90% confidence: 71 out of 72
[109:10] Quantification information saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/_public_local_ProteoBench_PYE_diaPASEF_A9_G_DIA_nLC_tTOF_R5_d.quant

[109:10] File #6/12
[109:10] Loading run /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
[109:16] 5543758 library precursors are potentially detectable
[109:17] Processing...
[115:40] RT window set to 1.64615
[115:40] Ion mobility window set to 0.0376381
[115:40] Recommended MS1 mass accuracy setting: 12.4164 ppm
[123:49] Removing low confidence identifications
[126:09] Precursors at 1% peptidoform FDR: 8472
[126:10] Removing interfering precursors
[126:13] Training neural networks: 27324 targets, 15394 decoys
[126:15] Number of IDs at 0.01 FDR: 16351
[126:17] Precursors at 1% peptidoform FDR: 10510
[126:17] Calculating protein q-values
[126:18] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[126:18] Quantification
[126:18] Precursors with monitored PTMs at 1% FDR: 83 out of 5487 considered
[126:18] Unmodified precursors with monitored PTM sites at 1% FDR: 1695
[126:18] Precursors with PTMs localised (when required) with > 90% confidence: 83 out of 83
[126:18] Quantification information saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/_public_local_ProteoBench_PYE_diaPASEF_A9_G_DIA_nLC_tTOF_R6_d.quant

[126:18] File #7/12
[126:18] Loading run /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
[126:24] 5543758 library precursors are potentially detectable
[126:25] Processing...
[133:28] RT window set to 1.57136
[133:28] Ion mobility window set to 0.0370608
[133:28] Recommended MS1 mass accuracy setting: 12.0159 ppm
[141:33] Removing low confidence identifications
[143:40] Precursors at 1% peptidoform FDR: 8221
[143:41] Removing interfering precursors
[143:44] Training neural networks: 26337 targets, 14991 decoys
[143:47] Number of IDs at 0.01 FDR: 16035
[143:49] Precursors at 1% peptidoform FDR: 10748
[143:50] Calculating protein q-values
[143:50] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[143:50] Quantification
[143:50] Precursors with monitored PTMs at 1% FDR: 65 out of 5229 considered
[143:50] Unmodified precursors with monitored PTM sites at 1% FDR: 1583
[143:50] Precursors with PTMs localised (when required) with > 90% confidence: 65 out of 65
[143:51] Quantification information saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/_public_local_ProteoBench_PYE_diaPASEF_B9_G_DIA_nLC_tTOF_R1_d.quant

[143:51] File #8/12
[143:51] Loading run /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
[143:56] 5543758 library precursors are potentially detectable
[143:57] Processing...
[150:33] RT window set to 1.55499
[150:33] Ion mobility window set to 0.0391279
[150:34] Recommended MS1 mass accuracy setting: 11.7653 ppm
[158:02] Removing low confidence identifications
[160:03] Precursors at 1% peptidoform FDR: 8521
[160:04] Removing interfering precursors
[160:08] Training neural networks: 28381 targets, 16287 decoys
[160:10] Number of IDs at 0.01 FDR: 16353
[160:12] Precursors at 1% peptidoform FDR: 11196
[160:12] Calculating protein q-values
[160:13] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[160:13] Quantification
[160:13] Precursors with monitored PTMs at 1% FDR: 93 out of 5392 considered
[160:13] Unmodified precursors with monitored PTM sites at 1% FDR: 1741
[160:13] Precursors with PTMs localised (when required) with > 90% confidence: 92 out of 93
[160:13] Quantification information saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/_public_local_ProteoBench_PYE_diaPASEF_B9_G_DIA_nLC_tTOF_R2_d.quant

[160:13] File #9/12
[160:13] Loading run /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
[160:19] 5543758 library precursors are potentially detectable
[160:20] Processing...
[166:44] RT window set to 1.84165
[166:44] Ion mobility window set to 0.0387315
[166:44] Recommended MS1 mass accuracy setting: 12.0203 ppm
[175:19] Removing low confidence identifications
[177:42] Precursors at 1% peptidoform FDR: 8952
[177:43] Removing interfering precursors
[177:46] Training neural networks: 29047 targets, 16455 decoys
[177:49] Number of IDs at 0.01 FDR: 17551
[177:51] Precursors at 1% peptidoform FDR: 10987
[177:52] Calculating protein q-values
[177:52] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[177:52] Quantification
[177:52] Precursors with monitored PTMs at 1% FDR: 76 out of 5726 considered
[177:52] Unmodified precursors with monitored PTM sites at 1% FDR: 1633
[177:52] Precursors with PTMs localised (when required) with > 90% confidence: 75 out of 76
[177:53] Quantification information saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/_public_local_ProteoBench_PYE_diaPASEF_B9_G_DIA_nLC_tTOF_R3_d.quant

[177:53] File #10/12
[177:53] Loading run /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
[177:59] 5543758 library precursors are potentially detectable
[178:00] Processing...
[184:08] RT window set to 1.86829
[184:08] Ion mobility window set to 0.0386003
[184:08] Recommended MS1 mass accuracy setting: 12.4206 ppm
[193:01] Removing low confidence identifications
[195:35] Precursors at 1% peptidoform FDR: 9332
[195:36] Removing interfering precursors
[195:41] Training neural networks: 29792 targets, 16834 decoys
[195:43] Number of IDs at 0.01 FDR: 17630
[195:45] Precursors at 1% peptidoform FDR: 11044
[195:45] Calculating protein q-values
[195:46] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[195:46] Quantification
[195:46] Precursors with monitored PTMs at 1% FDR: 47 out of 5781 considered
[195:46] Unmodified precursors with monitored PTM sites at 1% FDR: 1666
[195:46] Precursors with PTMs localised (when required) with > 90% confidence: 47 out of 47
[195:47] Quantification information saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/_public_local_ProteoBench_PYE_diaPASEF_B9_G_DIA_nLC_tTOF_R4_d.quant

[195:47] File #11/12
[195:47] Loading run /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
[195:53] 5543758 library precursors are potentially detectable
[195:54] Processing...
[201:57] RT window set to 1.77475
[201:57] Ion mobility window set to 0.037235
[201:57] Recommended MS1 mass accuracy setting: 13.471 ppm
[210:01] Removing low confidence identifications
[212:31] Precursors at 1% peptidoform FDR: 8779
[212:32] Removing interfering precursors
[212:37] Training neural networks: 29367 targets, 16733 decoys
[212:39] Number of IDs at 0.01 FDR: 17484
[212:41] Precursors at 1% peptidoform FDR: 11316
[212:42] Calculating protein q-values
[212:42] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[212:42] Quantification
[212:43] Precursors with monitored PTMs at 1% FDR: 86 out of 5837 considered
[212:43] Unmodified precursors with monitored PTM sites at 1% FDR: 1694
[212:43] Precursors with PTMs localised (when required) with > 90% confidence: 85 out of 86
[212:43] Quantification information saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/_public_local_ProteoBench_PYE_diaPASEF_B9_G_DIA_nLC_tTOF_R5_d.quant

[212:43] File #12/12
[212:43] Loading run /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
[212:50] 5543758 library precursors are potentially detectable
[212:51] Processing...
[219:09] RT window set to 1.67202
[219:09] Ion mobility window set to 0.0378728
[219:09] Recommended MS1 mass accuracy setting: 12.4477 ppm
[227:02] Removing low confidence identifications
[229:24] Precursors at 1% peptidoform FDR: 8743
[229:25] Removing interfering precursors
[229:29] Training neural networks: 28908 targets, 16458 decoys
[229:31] Number of IDs at 0.01 FDR: 17600
[229:33] Precursors at 1% peptidoform FDR: 11961
[229:34] Calculating protein q-values
[229:34] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[229:34] Quantification
[229:34] Precursors with monitored PTMs at 1% FDR: 96 out of 5608 considered
[229:34] Unmodified precursors with monitored PTM sites at 1% FDR: 1774
[229:34] Precursors with PTMs localised (when required) with > 90% confidence: 95 out of 96
[229:35] Quantification information saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/_public_local_ProteoBench_PYE_diaPASEF_B9_G_DIA_nLC_tTOF_R6_d.quant

[229:35] Cross-run analysis
[229:35] Reading quantification information: 12 files
[229:38] Quantifying peptides
[229:44] Assembling protein groups
[229:46] Quantifying proteins
[229:46] Calculating q-values for protein and gene groups
[229:49] Calculating global q-values for protein and gene groups
[229:49] Protein groups with global q-value <= 0.01: 16216
[229:50] Compressed report saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/report-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[229:50] Writing report
[229:52] Report saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/report-first-pass.tsv.
[229:52] Stats report saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/report-first-pass.stats.tsv
[229:52] Generating spectral library:
[229:53] 43049 target and 400 decoy precursors saved
WARNING: 2038 precursors without any fragments annotated were skipped
[229:53] Spectral library saved to report-lib.parquet

[229:54] Loading spectral library report-lib.parquet
[229:54] Spectral library loaded: 15885 protein isoforms, 15983 protein groups and 43449 precursors in 42317 elution groups.
[229:54] Loading protein annotations from FASTA /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
[229:54] Annotating library proteins with information from the FASTA database
[229:54] Protein names missing for some isoforms
[229:54] Gene names missing for some isoforms
[229:54] Library contains 15835 proteins, and 0 genes
[229:54] Initialising library
[229:54] Saving the library to report-lib.parquet.skyline.speclib


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

[229:55] File #1/12
[229:55] Loading run /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R1.d
[229:59] 43049 library precursors are potentially detectable
[229:59] Processing...
[230:02] RT window set to 0.661144
[230:02] Ion mobility window set to 0.0128284
[230:02] Recommended MS1 mass accuracy setting: 16.1776 ppm
[230:05] Removing low confidence identifications
[230:05] Precursors at 1% peptidoform FDR: 4871
[230:06] Removing interfering precursors
[230:06] Training neural networks: 34990 targets, 18489 decoys
[230:07] Number of IDs at 0.01 FDR: 17105
[230:08] Precursors at 1% peptidoform FDR: 11239
[230:08] Calculating protein q-values
[230:08] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[230:08] Quantification
[230:08] Precursors with monitored PTMs at 1% FDR: 64 out of 6490 considered
[230:08] Unmodified precursors with monitored PTM sites at 1% FDR: 1894
[230:08] Precursors with PTMs localised (when required) with > 90% confidence: 63 out of 64

[230:08] File #2/12
[230:08] Loading run /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R2.d
[230:13] 43049 library precursors are potentially detectable
[230:13] Processing...
[230:15] RT window set to 0.677037
[230:15] Ion mobility window set to 0.012244
[230:15] Recommended MS1 mass accuracy setting: 14.5004 ppm
[230:18] Removing low confidence identifications
[230:18] Precursors at 1% peptidoform FDR: 6392
[230:19] Removing interfering precursors
[230:19] Training neural networks: 35279 targets, 18626 decoys
[230:20] Number of IDs at 0.01 FDR: 17534
[230:21] Precursors at 1% peptidoform FDR: 11563
[230:21] Calculating protein q-values
[230:21] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[230:21] Quantification
[230:21] Precursors with monitored PTMs at 1% FDR: 67 out of 6528 considered
[230:21] Unmodified precursors with monitored PTM sites at 1% FDR: 1922
[230:21] Precursors with PTMs localised (when required) with > 90% confidence: 66 out of 67

[230:22] File #3/12
[230:22] Loading run /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R3.d
[230:27] 43049 library precursors are potentially detectable
[230:27] Processing...
[230:30] RT window set to 0.66749
[230:30] Ion mobility window set to 0.0119966
[230:30] Recommended MS1 mass accuracy setting: 15.7097 ppm
[230:32] Removing low confidence identifications
[230:33] Precursors at 1% peptidoform FDR: 3254
[230:33] Removing interfering precursors
[230:34] Training neural networks: 35504 targets, 18611 decoys
[230:35] Number of IDs at 0.01 FDR: 17993
[230:36] Precursors at 1% peptidoform FDR: 11454
[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: 70 out of 7135 considered
[230:36] Unmodified precursors with monitored PTM sites at 1% FDR: 1932
[230:36] Precursors with PTMs localised (when required) with > 90% confidence: 69 out of 70

[230:36] File #4/12
[230:36] Loading run /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R4.d
[230:42] 43049 library precursors are potentially detectable
[230:42] Processing...
[230:44] RT window set to 0.677747
[230:44] Ion mobility window set to 0.0116496
[230:44] Recommended MS1 mass accuracy setting: 14.9932 ppm
[230:46] Removing low confidence identifications
[230:47] Precursors at 1% peptidoform FDR: 6524
[230:48] Removing interfering precursors
[230:48] Training neural networks: 35624 targets, 18850 decoys
[230:49] Number of IDs at 0.01 FDR: 19046
[230:50] Precursors at 1% peptidoform FDR: 11733
[230:50] Calculating protein q-values
[230:50] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[230:50] Quantification
[230:50] Precursors with monitored PTMs at 1% FDR: 72 out of 7709 considered
[230:50] Unmodified precursors with monitored PTM sites at 1% FDR: 1919
[230:50] Precursors with PTMs localised (when required) with > 90% confidence: 71 out of 72

[230:50] File #5/12
[230:50] Loading run /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R5.d
[230:56] 43049 library precursors are potentially detectable
[230:56] Processing...
[231:00] RT window set to 0.66172
[231:00] Ion mobility window set to 0.0113631
[231:00] Recommended MS1 mass accuracy setting: 14.6439 ppm
[231:02] Removing low confidence identifications
[231:03] Precursors at 1% peptidoform FDR: 6311
[231:04] Removing interfering precursors
[231:04] Training neural networks: 35524 targets, 18722 decoys
[231:05] Number of IDs at 0.01 FDR: 19630
[231:06] Precursors at 1% peptidoform FDR: 11852
[231:06] Calculating protein q-values
[231:06] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[231:06] Quantification
[231:06] Precursors with monitored PTMs at 1% FDR: 72 out of 8007 considered
[231:06] Unmodified precursors with monitored PTM sites at 1% FDR: 1912
[231:06] Precursors with PTMs localised (when required) with > 90% confidence: 71 out of 72

[231:07] File #6/12
[231:07] Loading run /public/local/ProteoBench/PYE_diaPASEF/A9_G_DIA_nLC_tTOF_R6.d
[231:12] 43049 library precursors are potentially detectable
[231:12] Processing...
[231:16] RT window set to 0.660699
[231:16] Ion mobility window set to 0.0120358
[231:16] Recommended MS1 mass accuracy setting: 15.683 ppm
[231:18] Removing low confidence identifications
[231:19] Precursors at 1% peptidoform FDR: 5866
[231:19] Removing interfering precursors
[231:19] Training neural networks: 35353 targets, 18686 decoys
[231:21] Number of IDs at 0.01 FDR: 18824
[231:21] Precursors at 1% peptidoform FDR: 11717
[231:21] Calculating protein q-values
[231:21] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[231:21] Quantification
[231:22] Precursors with monitored PTMs at 1% FDR: 71 out of 7328 considered
[231:22] Unmodified precursors with monitored PTM sites at 1% FDR: 1864
[231:22] Precursors with PTMs localised (when required) with > 90% confidence: 70 out of 71

[231:22] File #7/12
[231:22] Loading run /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R1.d
[231:27] 43049 library precursors are potentially detectable
[231:27] Processing...
[231:29] RT window set to 0.66665
[231:29] Ion mobility window set to 0.010336
[231:29] Recommended MS1 mass accuracy setting: 14.8717 ppm
[231:31] Removing low confidence identifications
[231:32] Precursors at 1% peptidoform FDR: 6245
[231:32] Removing interfering precursors
[231:33] Training neural networks: 34957 targets, 18495 decoys
[231:34] Number of IDs at 0.01 FDR: 17785
[231:35] Precursors at 1% peptidoform FDR: 11739
[231:35] Calculating protein q-values
[231:35] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[231:35] Quantification
[231:35] Precursors with monitored PTMs at 1% FDR: 73 out of 6217 considered
[231:35] Unmodified precursors with monitored PTM sites at 1% FDR: 1867
[231:35] Precursors with PTMs localised (when required) with > 90% confidence: 73 out of 73

[231:35] File #8/12
[231:35] Loading run /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R2.d
[231:40] 43049 library precursors are potentially detectable
[231:40] Processing...
[231:42] RT window set to 0.662256
[231:42] Ion mobility window set to 0.0128722
[231:42] Recommended MS1 mass accuracy setting: 15.1374 ppm
[231:44] Removing low confidence identifications
[231:45] Precursors at 1% peptidoform FDR: 6354
[231:45] Removing interfering precursors
[231:45] Training neural networks: 35117 targets, 18575 decoys
[231:47] Number of IDs at 0.01 FDR: 19163
[231:48] Precursors at 1% peptidoform FDR: 12037
[231:48] Calculating protein q-values
[231:48] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[231:48] Quantification
[231:48] Precursors with monitored PTMs at 1% FDR: 70 out of 7115 considered
[231:48] Unmodified precursors with monitored PTM sites at 1% FDR: 1909
[231:48] Precursors with PTMs localised (when required) with > 90% confidence: 70 out of 70

[231:48] File #9/12
[231:48] Loading run /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R3.d
[231:53] 43049 library precursors are potentially detectable
[231:53] Processing...
[231:57] RT window set to 0.656382
[231:57] Ion mobility window set to 0.0109504
[231:57] Recommended MS1 mass accuracy setting: 15.2061 ppm
[231:59] Removing low confidence identifications
[232:00] Precursors at 1% peptidoform FDR: 6755
[232:00] Removing interfering precursors
[232:00] Training neural networks: 35452 targets, 18710 decoys
[232:01] Number of IDs at 0.01 FDR: 19205
[232:02] Precursors at 1% peptidoform FDR: 12071
[232:02] Calculating protein q-values
[232:02] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[232:02] Quantification
[232:03] Precursors with monitored PTMs at 1% FDR: 72 out of 7072 considered
[232:03] Unmodified precursors with monitored PTM sites at 1% FDR: 1898
[232:03] Precursors with PTMs localised (when required) with > 90% confidence: 71 out of 72

[232:03] File #10/12
[232:03] Loading run /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R4.d
[232:09] 43049 library precursors are potentially detectable
[232:09] Processing...
[232:11] RT window set to 0.668226
[232:11] Ion mobility window set to 0.0102454
[232:11] Recommended MS1 mass accuracy setting: 15.3542 ppm
[232:13] Removing low confidence identifications
[232:14] Precursors at 1% peptidoform FDR: 7080
[232:14] Removing interfering precursors
[232:15] Training neural networks: 35420 targets, 18689 decoys
[232:16] Number of IDs at 0.01 FDR: 19084
[232:17] Precursors at 1% peptidoform FDR: 12023
[232:17] Calculating protein q-values
[232:17] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[232:17] Quantification
[232:17] Precursors with monitored PTMs at 1% FDR: 72 out of 6946 considered
[232:17] Unmodified precursors with monitored PTM sites at 1% FDR: 1880
[232:17] Precursors with PTMs localised (when required) with > 90% confidence: 72 out of 72

[232:17] File #11/12
[232:17] Loading run /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R5.d
[232:23] 43049 library precursors are potentially detectable
[232:23] Processing...
[232:25] RT window set to 0.6666
[232:25] Ion mobility window set to 0.0109866
[232:25] Recommended MS1 mass accuracy setting: 15.7568 ppm
[232:27] Removing low confidence identifications
[232:28] Precursors at 1% peptidoform FDR: 6936
[232:29] Removing interfering precursors
[232:29] Training neural networks: 35341 targets, 18661 decoys
[232:30] Number of IDs at 0.01 FDR: 19113
[232:31] Precursors at 1% peptidoform FDR: 11909
[232:31] Calculating protein q-values
[232:31] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[232:31] Quantification
[232:31] Precursors with monitored PTMs at 1% FDR: 73 out of 7081 considered
[232:31] Unmodified precursors with monitored PTM sites at 1% FDR: 1847
[232:31] Precursors with PTMs localised (when required) with > 90% confidence: 72 out of 73

[232:31] File #12/12
[232:31] Loading run /public/local/ProteoBench/PYE_diaPASEF/B9_G_DIA_nLC_tTOF_R6.d
[232:37] 43049 library precursors are potentially detectable
[232:37] Processing...
[232:39] RT window set to 0.659481
[232:39] Ion mobility window set to 0.010685
[232:39] Recommended MS1 mass accuracy setting: 16.1913 ppm
[232:41] Removing low confidence identifications
[232:42] Precursors at 1% peptidoform FDR: 7277
[232:42] Removing interfering precursors
[232:42] Training neural networks: 35208 targets, 18607 decoys
[232:43] Number of IDs at 0.01 FDR: 19640
[232:44] Precursors at 1% peptidoform FDR: 12090
[232:44] Calculating protein q-values
[232:44] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[232:44] Quantification
[232:44] Precursors with monitored PTMs at 1% FDR: 73 out of 7286 considered
[232:44] Unmodified precursors with monitored PTM sites at 1% FDR: 1871
[232:44] Precursors with PTMs localised (when required) with > 90% confidence: 72 out of 73

[232:45] Cross-run analysis
[232:45] Reading quantification information: 12 files
[232:45] Quantifying peptides
[233:06] Quantification parameters: 0.302011, 0.00268455, 0.0111848, 0.0152014, 0.0423176, 0.0374553, 0.34342, 0.139818, 0.218892, 0.0211793, 0.0867946, 0.0651179, 0.279505, 0.182541, 0.163041, 0.0137813
[233:10] Quantifying proteins
[233:10] Calculating q-values for protein and gene groups
[233:10] Calculating global q-values for protein and gene groups
[233:10] Protein groups with global q-value <= 0.01: 10363
[233:11] Compressed report saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/report.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[233:11] Writing report
[233:13] Report saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/report.tsv.
[233:13] Stats report saved to /home/robbe/PB_output/results/Plasma_Normalization/PYE_diaPASEF/diann_v1.9.1/report.stats.tsv

