DIA-NN 1.9.2 (Data-Independent Acquisition by Neural Networks)
Compiled on Oct 31 2024 04:27:44
Current date and time: Wed Apr 22 12:25:19 2026
Logical CPU cores: 128
/home/robbe/bin/diann-1.9.2/diann-linux --f /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d --f /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d --f /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d --f /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d --f /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d --f /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d --fasta /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta --out /home/robbe/PB_output/results/test_run/HYE_diaPASEF/diann_v1.9.2/report.tsv --threads 32 --missed-cleavages 2 --min-pep-len 7 --max-pep-len 30 --mass-acc 20 --mass-acc-ms1 20 --qvalue 0.01 --protein-qvalue 0.01 --min-pr-charge 2 --max-pr-charge 4 --min-pr-mz 400 --max-pr-mz 1200 --min-fr-mz 200 --max-fr-mz 2000 --unimod4 --var-mod UniMod:35,15.994915,M --gen-spec-lib --fasta-search 

Thread number set to 32
Maximum number of missed cleavages set to 2
Min peptide length set to 7
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 2
Max precursor charge set to 4
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
Cysteine carbamidomethylation enabled as a fixed modification
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
A spectral library will be generated
DIA-NN will carry out FASTA digest for in silico lib generation
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 

6 files will be processed
[0:00] Loading FASTA /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
[0:07] Processing FASTA
[0:15] Assembling elution groups
[0:23] 8103720 precursors generated
[0:23] Protein names missing for some isoforms
[0:23] Gene names missing for some isoforms
[0:23] Library contains 31680 proteins, and 0 genes
[0:29] [0:44] [6:31] [7:14] [7:17] [7:20] Saving the library to /home/robbe/PB_output/results/test_run/HYE_diaPASEF/diann_v1.9.2/report-lib.predicted.speclib
[7:31] Initialising library
[7:47] Loading spectral library /home/robbe/PB_output/results/test_run/HYE_diaPASEF/diann_v1.9.2/report-lib.predicted.speclib
[7:51] Library annotated with sequence database(s): /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
[7:53] Spectral library loaded: 31832 protein isoforms, 43199 protein groups and 8103720 precursors in 3825450 elution groups.
[7:53] Loading protein annotations from FASTA /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
[7:53] Annotating library proteins with information from the FASTA database
[7:53] Protein names missing for some isoforms
[7:53] Gene names missing for some isoforms
[7:53] Library contains 31680 proteins, and 0 genes
[7:59] Initialising library
WARNING: it is strongly recommended to enable MBR when analysing with a large library, if this is a quantitative analysis

[8:18] File #1/6
[8:18] Loading run /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.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
[9:02] 7127359 library precursors are potentially detectable
[9:03] Calibrating with mass accuracies 20 (MS1), 20 (MS2)
[11:22] RT window set to 2.50233
[11:22] Ion mobility window set to 0.0437635
[11:22] Peak width: 4.116
[11:22] Scan window radius set to 9
[11:22] Recommended MS1 mass accuracy setting: 14.2711 ppm
[26:21] Removing low confidence identifications
[33:37] Precursors at 1% peptidoform FDR: 62634
[33:38] Removing interfering precursors
[33:43] Training neural networks on 229112 PSMs
[33:48] Number of IDs at 0.01 FDR: 86360
[33:50] Precursors at 1% peptidoform FDR: 71787
[33:51] Calculating protein q-values
[33:51] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[33:51] Quantification
[33:52] Precursors with monitored PTMs at 1% FDR: 62 out of 16862 considered
[33:52] Unmodified precursors with monitored PTM sites at 1% FDR: 14195
[33:52] Precursors with PTMs localised (when required) with > 90% confidence: 41 out of 62
[33:54] Quantification information saved to /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d.quant

[33:54] File #2/6
[33:54] Loading run /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
[34:38] 7127359 library precursors are potentially detectable
[34:39] Calibrating with mass accuracies 20 (MS1), 20 (MS2)
[36:57] RT window set to 2.19858
[36:57] Ion mobility window set to 0.0423974
[36:57] Recommended MS1 mass accuracy setting: 13.425 ppm
[50:38] Removing low confidence identifications
[57:17] Precursors at 1% peptidoform FDR: 64985
[57:19] Removing interfering precursors
[57:24] Training neural networks on 234165 PSMs
[57:29] Number of IDs at 0.01 FDR: 88674
[57:31] Precursors at 1% peptidoform FDR: 74329
[57:32] Calculating protein q-values
[57:33] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[57:33] Quantification
[57:33] Precursors with monitored PTMs at 1% FDR: 42 out of 17774 considered
[57:33] Unmodified precursors with monitored PTM sites at 1% FDR: 14606
[57:33] Precursors with PTMs localised (when required) with > 90% confidence: 25 out of 42
[57:35] Quantification information saved to /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d.quant

[57:35] File #3/6
[57:35] Loading run /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
[58:22] 7127359 library precursors are potentially detectable
[58:23] Calibrating with mass accuracies 20 (MS1), 20 (MS2)
[60:43] RT window set to 1.97333
[60:43] Ion mobility window set to 0.0416377
[60:43] Recommended MS1 mass accuracy setting: 14.2005 ppm
[73:17] Removing low confidence identifications
[79:25] Precursors at 1% peptidoform FDR: 64437
[79:26] Removing interfering precursors
[79:31] Training neural networks on 236628 PSMs
[79:36] Number of IDs at 0.01 FDR: 88671
[79:39] Precursors at 1% peptidoform FDR: 75046
[79:39] Calculating protein q-values
[79:40] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[79:40] Quantification
[79:41] Precursors with monitored PTMs at 1% FDR: 53 out of 17596 considered
[79:41] Unmodified precursors with monitored PTM sites at 1% FDR: 14759
[79:41] Precursors with PTMs localised (when required) with > 90% confidence: 36 out of 53
[79:43] Quantification information saved to /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d.quant

[79:43] File #4/6
[79:43] Loading run /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
[80:28] 7127359 library precursors are potentially detectable
[80:29] Calibrating with mass accuracies 20 (MS1), 20 (MS2)
[82:16] RT window set to 2.26756
[82:16] Ion mobility window set to 0.0416596
[82:16] Recommended MS1 mass accuracy setting: 14.4084 ppm
[95:51] Removing low confidence identifications
[102:28] Precursors at 1% peptidoform FDR: 62890
[102:29] Removing interfering precursors
[102:34] Training neural networks on 227901 PSMs
[102:40] Number of IDs at 0.01 FDR: 86855
[102:42] Precursors at 1% peptidoform FDR: 73470
[102:43] Calculating protein q-values
[102:43] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[102:43] Quantification
[102:44] Precursors with monitored PTMs at 1% FDR: 64 out of 17643 considered
[102:44] Unmodified precursors with monitored PTM sites at 1% FDR: 14583
[102:44] Precursors with PTMs localised (when required) with > 90% confidence: 44 out of 64
[102:46] Quantification information saved to /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d.quant

[102:46] File #5/6
[102:46] Loading run /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
[103:31] 7127359 library precursors are potentially detectable
[103:32] Calibrating with mass accuracies 20 (MS1), 20 (MS2)
[105:20] RT window set to 2.49161
[105:20] Ion mobility window set to 0.0420663
[105:20] Recommended MS1 mass accuracy setting: 14.2978 ppm
[119:56] Removing low confidence identifications
[127:06] Precursors at 1% peptidoform FDR: 64017
[127:07] Removing interfering precursors
[127:12] Training neural networks on 232239 PSMs
[127:18] Number of IDs at 0.01 FDR: 87769
[127:20] Precursors at 1% peptidoform FDR: 74517
[127:21] Calculating protein q-values
[127:21] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[127:21] Quantification
[127:22] Precursors with monitored PTMs at 1% FDR: 255 out of 17741 considered
[127:22] Unmodified precursors with monitored PTM sites at 1% FDR: 14911
[127:22] Precursors with PTMs localised (when required) with > 90% confidence: 244 out of 255
[127:24] Quantification information saved to /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d.quant

[127:24] File #6/6
[127:24] Loading run /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
[128:09] 7127359 library precursors are potentially detectable
[128:10] Calibrating with mass accuracies 20 (MS1), 20 (MS2)
[129:58] RT window set to 2.21479
[129:58] Ion mobility window set to 0.0416689
[129:59] Recommended MS1 mass accuracy setting: 14.4291 ppm
[143:32] Removing low confidence identifications
[150:09] Precursors at 1% peptidoform FDR: 64362
[150:10] Removing interfering precursors
[150:15] Training neural networks on 233248 PSMs
[150:20] Number of IDs at 0.01 FDR: 89272
[150:23] Precursors at 1% peptidoform FDR: 74810
[150:23] Calculating protein q-values
[150:24] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[150:24] Quantification
[150:24] Precursors with monitored PTMs at 1% FDR: 68 out of 17720 considered
[150:24] Unmodified precursors with monitored PTM sites at 1% FDR: 14911
[150:24] Precursors with PTMs localised (when required) with > 90% confidence: 51 out of 68
[150:26] Quantification information saved to /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d.quant

[150:26] Cross-run analysis
[150:26] Reading quantification information: 6 files
[150:31] Quantifying peptides
[151:28] Quantification parameters: 0.334915, 0.00151565, 0.00310335, 0.122251, 0.151864, 0.140001, 0.206161, 0.0140794, 0.0253369, 0.121622, 0.0921102, 0.102673, 0.169336, 0.0830954, 0.0904021, 0.0123376
[151:34] Assembling protein groups
[151:36] Quantifying proteins
[151:36] Calculating q-values for protein and gene groups
[151:38] Calculating global q-values for protein and gene groups
[151:38] Protein groups with global q-value <= 0.01: 12704
[151:41] Compressed report saved to /home/robbe/PB_output/results/test_run/HYE_diaPASEF/diann_v1.9.2/report.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[151:41] Writing report
[151:47] Report saved to /home/robbe/PB_output/results/test_run/HYE_diaPASEF/diann_v1.9.2/report.tsv.
[151:47] Stats report saved to /home/robbe/PB_output/results/test_run/HYE_diaPASEF/diann_v1.9.2/report.stats.tsv
[151:47] Generating spectral library:
[151:48] 108480 target and 1064 decoy precursors saved
WARNING: 412 precursors without any fragments annotated were skipped
[151:48] Spectral library saved to /home/robbe/PB_output/results/test_run/HYE_diaPASEF/diann_v1.9.2/report-lib.parquet

