
DIA-NN 2.2.0 Academia  (Data-Independent Acquisition by Neural Networks)
Compiled on May 29 2025 21:29:29
Current date and time: Fri Jul 18 14:35:52 2025
CPU: GenuineIntel Intel(R) Xeon(R) Gold 6430
SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 
Logical CPU cores: 128
diann.exe --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw  --f H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw  --lib H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB1\PB1.parquet --threads 64 --verbose 1 --out H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\reportPB4.parquet --qvalue 0.01 --matrices --fasta H:\DELALANDE Frankois\ProteoBench\DIA Astral\ProteoBenchFASTA_MixedSpecies_HYE.fasta --met-excision --cut K*,R* --missed-cleavages 1 --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --window 6 --mass-acc 3.0 --mass-acc-ms1 7.0 --peptidoforms --rt-profiling --pg-level 1 --direct-quant 

Thread number set to 64
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
N-terminal methionine excision enabled
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
Scan window radius set to 6
Peptidoform scoring enabled
The spectral library (if generated) will retain the original spectra but will include empirically-aligned RTs
Implicit protein grouping: protein names; this determines which peptides are considered 'proteotypic' and thus affects protein FDR calculation
Legacy (direct) quantification mode
WARNING: for DIA-NN to switch to the new .raw reader library, please download and install .NET SDK 8.0.407 or later https://dotnet.microsoft.com/en-us/download/dotnet/8.0
Mass accuracy will be fixed to 3e-06 (MS2) and 7e-06 (MS1)
The following variable modifications will be localised: UniMod:35 UniMod:1 

6 files will be processed
[0:00] Loading spectral library H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB1\PB1.parquet
[0:02] Spectral library loaded: 12926 protein isoforms, 12760 protein groups and 130455 precursors in 121948 elution groups.
[0:02] Loading protein annotations from FASTA H:\DELALANDE Frankois\ProteoBench\DIA Astral\ProteoBenchFASTA_MixedSpecies_HYE.fasta
[0:02] Annotating library proteins with information from the FASTA database
[0:02] Gene names missing for some isoforms
[0:02] Library contains 12911 proteins, and 0 genes
[0:02] Initialising library
[0:05] Saving the library to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB1\PB1.parquet.skyline.speclib

[0:18] File #1/6
[0:18] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
[2:29] Pre-processing...
[2:31] 2931 MS1 and 293271 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 129146 precursors in range
[2:31] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[2:31] RT window set to 0.441974
[2:31] Recommended MS1 mass accuracy setting: 3.2 ppm
[2:32] Searching decoys
[2:32] Main search
[2:33] Removing low confidence identifications
[2:37] Removing interfering precursors
[2:38] Training neural networks on 110482 target and 39965 decoy PSMs
[2:59] Training neural networks on 110433 target and 45221 decoy PSMs
[3:20] Number of IDs at 0.01 FDR: 106515
[3:20] Precursors at 1% peptidoform FDR: 104580
[3:20] Calculating protein q-values
[3:20] Number of proteins identified at 1% FDR: 10546 (precursor-level), 9569 (protein-level) (inference performed using proteotypic peptides only)
[3:20] Quantification
[3:21] Precursors with scored PTMs at 1% FDR: 3500 out of 3605 considered
[3:21] Precursors with all scored PTM sites unoccupied at 1% FDR: 101080
[3:21] Precursors with PTMs localised (when required) with > 90% confidence: 3409 out of 3500
[4:14] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw.quant

[4:14] File #2/6
[4:14] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
[5:56] Pre-processing...
[5:57] 2933 MS1 and 293433 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[5:57] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[5:58] RT window set to 0.428373
[5:58] Recommended MS1 mass accuracy setting: 3.3 ppm
[5:58] Searching decoys
[5:58] Main search
[6:00] Removing low confidence identifications
[6:03] Removing interfering precursors
[6:04] Training neural networks on 110681 target and 39019 decoy PSMs
[6:25] Training neural networks on 110646 target and 44117 decoy PSMs
[6:45] Number of IDs at 0.01 FDR: 106617
[6:46] Precursors at 1% peptidoform FDR: 105296
[6:46] Calculating protein q-values
[6:46] Number of proteins identified at 1% FDR: 10484 (precursor-level), 9512 (protein-level) (inference performed using proteotypic peptides only)
[6:46] Quantification
[6:47] Precursors with scored PTMs at 1% FDR: 3562 out of 3623 considered
[6:47] Precursors with all scored PTM sites unoccupied at 1% FDR: 101734
[6:47] Precursors with PTMs localised (when required) with > 90% confidence: 3492 out of 3562
[7:18] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw.quant

[7:18] File #3/6
[7:18] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
[9:08] Pre-processing...
[9:09] 2932 MS1 and 293358 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[9:09] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[9:09] RT window set to 0.438533
[9:09] Recommended MS1 mass accuracy setting: 3 ppm
[9:10] Searching decoys
[9:10] Main search
[9:11] Removing low confidence identifications
[9:15] Removing interfering precursors
[9:16] Training neural networks on 110749 target and 40023 decoy PSMs
[9:37] Training neural networks on 110709 target and 44812 decoy PSMs
[9:58] Number of IDs at 0.01 FDR: 107552
[9:58] Precursors at 1% peptidoform FDR: 105818
[9:58] Calculating protein q-values
[9:58] Number of proteins identified at 1% FDR: 10539 (precursor-level), 9529 (protein-level) (inference performed using proteotypic peptides only)
[9:58] Quantification
[10:00] Precursors with scored PTMs at 1% FDR: 3563 out of 3673 considered
[10:00] Precursors with all scored PTM sites unoccupied at 1% FDR: 102255
[10:00] Precursors with PTMs localised (when required) with > 90% confidence: 3483 out of 3563
[11:12] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw.quant

[11:12] File #4/6
[11:12] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
[12:46] Pre-processing...
[12:47] 2933 MS1 and 293382 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[12:47] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[12:47] RT window set to 0.455627
[12:47] Recommended MS1 mass accuracy setting: 3.3 ppm
[12:48] Searching decoys
[12:48] Main search
[12:49] Removing low confidence identifications
[12:53] Removing interfering precursors
[12:55] Training neural networks on 111460 target and 40989 decoy PSMs
[13:16] Training neural networks on 111427 target and 45890 decoy PSMs
[13:38] Number of IDs at 0.01 FDR: 108088
[13:38] Precursors at 1% peptidoform FDR: 106117
[13:38] Calculating protein q-values
[13:38] Number of proteins identified at 1% FDR: 10447 (precursor-level), 9403 (protein-level) (inference performed using proteotypic peptides only)
[13:38] Quantification
[13:39] Precursors with scored PTMs at 1% FDR: 3797 out of 3902 considered
[13:39] Precursors with all scored PTM sites unoccupied at 1% FDR: 102320
[13:39] Precursors with PTMs localised (when required) with > 90% confidence: 3707 out of 3797
[14:31] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw.quant

[14:31] File #5/6
[14:31] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
[16:26] Pre-processing...
[16:27] 2933 MS1 and 293330 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[16:27] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[16:28] RT window set to 0.458947
[16:28] Recommended MS1 mass accuracy setting: 3.2 ppm
[16:28] Searching decoys
[16:28] Main search
[16:30] Removing low confidence identifications
[16:34] Removing interfering precursors
[16:35] Training neural networks on 111577 target and 40952 decoy PSMs
[16:56] Training neural networks on 111544 target and 45832 decoy PSMs
[17:18] Number of IDs at 0.01 FDR: 108234
[17:18] Precursors at 1% peptidoform FDR: 106360
[17:19] Calculating protein q-values
[17:19] Number of proteins identified at 1% FDR: 10530 (precursor-level), 9485 (protein-level) (inference performed using proteotypic peptides only)
[17:19] Quantification
[17:20] Precursors with scored PTMs at 1% FDR: 3854 out of 3936 considered
[17:20] Precursors with all scored PTM sites unoccupied at 1% FDR: 102506
[17:20] Precursors with PTMs localised (when required) with > 90% confidence: 3760 out of 3854
[18:14] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw.quant

[18:14] File #6/6
[18:14] Loading run H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
[20:21] Pre-processing...
[20:22] 2934 MS1 and 293446 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 129146 precursors in range
[20:22] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[20:23] RT window set to 0.456243
[20:23] Recommended MS1 mass accuracy setting: 3.1 ppm
[20:23] Searching decoys
[20:23] Main search
[20:25] Removing low confidence identifications
[20:28] Removing interfering precursors
[20:29] Training neural networks on 111490 target and 40760 decoy PSMs
[20:51] Training neural networks on 111452 target and 45956 decoy PSMs
[21:12] Number of IDs at 0.01 FDR: 108063
[21:13] Precursors at 1% peptidoform FDR: 106286
[21:13] Calculating protein q-values
[21:13] Number of proteins identified at 1% FDR: 10458 (precursor-level), 9482 (protein-level) (inference performed using proteotypic peptides only)
[21:13] Quantification
[21:14] Precursors with scored PTMs at 1% FDR: 3879 out of 3979 considered
[21:14] Precursors with all scored PTM sites unoccupied at 1% FDR: 102407
[21:14] Precursors with PTMs localised (when required) with > 90% confidence: 3783 out of 3879
[21:44] Quantification information saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw.quant

[21:44] Cross-run analysis
[21:44] Reading quantification information: 6 files
[22:02] Quantifying peptides
[24:22] Assembling protein groups
[24:22] Quantifying proteins
[24:23] Calculating q-values for protein and gene groups
[24:23] Calculating global q-values for protein and gene groups
[24:23] Protein groups with global q-value <= 0.01: 10582
[24:29] Compressed report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\reportPB4.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[24:29] Site report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\reportPB4.site_report.parquet
[24:29] Saving precursor levels matrix
[24:32] Precursor levels matrix (1% precursor and protein group FDR) saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\reportPB4.pr_matrix.tsv.
[24:32] Saving protein group levels matrix
[24:32] Protein groups matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\reportPB4.pg_matrix.tsv.
[24:32] Saving gene group levels matrix
[24:33] Gene groups matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\reportPB4.gg_matrix.tsv.
[24:33] Saving unique genes levels matrix
[24:33] Unique genes matrix saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\reportPB4.unique_genes_matrix.tsv.
[24:34] Manifest saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\reportPB4.manifest.txt
[24:34] Stats report saved to H:\DELALANDE Frankois\ProteoBench\DIA Astral\PB4\reportPB4.stats.tsv

