
DIA-NN 2.1.0 Academia  (Data-Independent Acquisition by Neural Networks)
Compiled on Mar 25 2025 10:59:54
Current date and time: Tue Mar 17 14:43:12 2026
CPU: GenuineIntel Intel(R) Core(TM) i9-10980XE CPU @ 3.00GHz
SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 
Logical CPU cores: 36
diann.exe --f Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_001_ML_IAA_1_3uL_DIA_T60.raw  --f Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_002_ML_IAA_2_3uL_DIA_T60.raw  --f Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_003_ML_IAA_3_3uL_DIA_T60.raw  --f Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_007_ML_2ME_1_3uL_DIA_T60.raw  --f Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_008_ML_2ME_2_3uL_DIA_T60.raw  --f Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_009_ML_2ME_3_3uL_DIA_T60.raw  --lib C:\DIA-NN\2.1.0\predlib\Mouse\250410_Mouse_UP000000589_E21755_mc1_vmod2_length7_45_z2_4_mz495_775_varmod_2MEIAA_.predicted.predicted.speclib --threads 18 --verbose 1 --out Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\NN210_260313_Asto310_ML_SP3_IAA2ME\report.parquet --qvalue 0.01 --matrices --fasta W:\Database\230303_ok\250318_Mouse_UP000000589_E21755.fasta --met-excision --cut K*,R* --missed-cleavages 1 --var-mods 2 --var-mod UniMod:35,15.994915,M --mass-acc 10 --mass-acc-ms1 10 --rt-profiling --direct-quant --var-mod UniMod:303,75.9982, C  --var-mod UniMod:4,57.021464, C 

Thread number set to 18
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
Maximum number of variable modifications set to 2
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
The spectral library (if generated) will retain the original spectra but will include empirically-aligned RTs
Legacy (direct) quantification mode
Modification UniMod:303 with mass delta 75.9982 at  C will be considered as variable
Modification UniMod:4 with mass delta 57.0215 at  C will be considered as variable
Mass accuracy will be fixed to 1e-05 (MS2) and 1e-05 (MS1)
WARNING: peptidoform scoring enabled because variable modifications have been declared; to disable, use --no-peptidoforms
The following variable modifications will be localised: UniMod:35 UniMod:303 UniMod:4 

6 files will be processed
[0:00] Loading spectral library C:\DIA-NN\2.1.0\predlib\Mouse\250410_Mouse_UP000000589_E21755_mc1_vmod2_length7_45_z2_4_mz495_775_varmod_2MEIAA_.predicted.predicted.speclib
[0:02] Library annotated with sequence database(s): W:\Database\230303_ok\250318_Mouse_UP000000589_E21755.fasta
[0:03] Spectral library loaded: 21720 protein isoforms, 29870 protein groups and 3657378 precursors in 3058692 elution groups.
[0:03] Loading protein annotations from FASTA W:\Database\230303_ok\250318_Mouse_UP000000589_E21755.fasta
[0:04] Annotating library proteins with information from the FASTA database
[0:04] Gene names missing for some isoforms
[0:04] Library contains 21720 proteins, and 21399 genes
[0:07] Initialising library
WARNING: it is strongly recommended to enable MBR when analysing with a large library, if this is a quantitative analysis

[0:22] File #1/6
[0:22] Loading run Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_001_ML_IAA_1_3uL_DIA_T60.raw
[0:31] Pre-processing...
[0:32] 986 MS1 and 29576 MS2 scans in 986 (inferred) and 986 (encoded) cycles, 3543027 precursors in range
[0:34] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[1:16] RT window set to 3.01156
[1:16] Peak width: 3.208
[1:16] Scan window radius set to 7
[1:16] Recommended MS1 mass accuracy setting: 35 ppm
[1:51] Searching decoys
[2:25] Main search
[3:36] Removing low confidence identifications
[3:49] Removing interfering precursors
[3:56] Training neural networks on 70013 target and 43726 decoy PSMs
[4:48] Training neural networks on 70013 target and 42119 decoy PSMs
[5:32] Number of IDs at 0.01 FDR: 36338
[5:33] Precursors at 1% peptidoform FDR: 33116
[5:34] Calculating protein q-values
[5:34] Number of genes identified at 1% FDR: 5496 (precursor-level), 5048 (protein-level) (inference performed using proteotypic peptides only)
[5:35] Quantification
[5:35] Precursors with scored PTMs at 1% FDR: 3026 out of 3802 considered
[5:35] Precursors with all scored PTM sites unoccupied at 1% FDR: 30090
[5:35] Precursors with PTMs localised (when required) with > 90% confidence: 2998 out of 3026
[5:37] Quantification information saved to Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_001_ML_IAA_1_3uL_DIA_T60.raw.quant

[5:38] File #2/6
[5:38] Loading run Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_002_ML_IAA_2_3uL_DIA_T60.raw
[5:46] Pre-processing...
[5:47] 983 MS1 and 29465 MS2 scans in 983 (inferred) and 983 (encoded) cycles, 3543027 precursors in range
[5:49] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[6:31] RT window set to 2.94835
[6:31] Recommended MS1 mass accuracy setting: 35 ppm
[7:05] Searching decoys
[7:37] Main search
[8:45] Removing low confidence identifications
[8:58] Removing interfering precursors
[9:05] Training neural networks on 70149 target and 44183 decoy PSMs
[9:57] Training neural networks on 70149 target and 42572 decoy PSMs
[10:42] Number of IDs at 0.01 FDR: 36079
[10:43] Precursors at 1% peptidoform FDR: 32837
[10:44] Calculating protein q-values
[10:44] Number of genes identified at 1% FDR: 5506 (precursor-level), 5035 (protein-level) (inference performed using proteotypic peptides only)
[10:44] Quantification
[10:45] Precursors with scored PTMs at 1% FDR: 2950 out of 3680 considered
[10:45] Precursors with all scored PTM sites unoccupied at 1% FDR: 29887
[10:45] Precursors with PTMs localised (when required) with > 90% confidence: 2922 out of 2950
[10:48] Quantification information saved to Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_002_ML_IAA_2_3uL_DIA_T60.raw.quant

[10:48] File #3/6
[10:48] Loading run Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_003_ML_IAA_3_3uL_DIA_T60.raw
[10:55] Pre-processing...
[10:56] 979 MS1 and 29350 MS2 scans in 979 (inferred) and 979 (encoded) cycles, 3543027 precursors in range
[10:59] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[11:40] RT window set to 3.13089
[11:40] Recommended MS1 mass accuracy setting: 35 ppm
[12:15] Searching decoys
[12:49] Main search
[14:00] Removing low confidence identifications
[14:13] Removing interfering precursors
[14:20] Training neural networks on 71698 target and 46641 decoy PSMs
[15:14] Training neural networks on 71698 target and 44462 decoy PSMs
[16:00] Number of IDs at 0.01 FDR: 35313
[16:00] Precursors at 1% peptidoform FDR: 32008
[16:01] Calculating protein q-values
[16:02] Number of genes identified at 1% FDR: 5425 (precursor-level), 4942 (protein-level) (inference performed using proteotypic peptides only)
[16:02] Quantification
[16:02] Precursors with scored PTMs at 1% FDR: 2475 out of 3203 considered
[16:02] Precursors with all scored PTM sites unoccupied at 1% FDR: 29533
[16:02] Precursors with PTMs localised (when required) with > 90% confidence: 2448 out of 2475
[16:05] Quantification information saved to Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_003_ML_IAA_3_3uL_DIA_T60.raw.quant

[16:05] File #4/6
[16:05] Loading run Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_007_ML_2ME_1_3uL_DIA_T60.raw
[16:13] Pre-processing...
[16:14] 1015 MS1 and 30443 MS2 scans in 1015 (inferred) and 1015 (encoded) cycles, 3543027 precursors in range
[16:17] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[17:00] RT window set to 3.96871
[17:00] Recommended MS1 mass accuracy setting: 35 ppm
[17:40] Searching decoys
[18:25] Main search
[20:00] Removing low confidence identifications
[20:14] Removing interfering precursors
[20:21] Training neural networks on 79533 target and 49250 decoy PSMs
[21:19] Training neural networks on 79533 target and 47090 decoy PSMs
[22:09] Number of IDs at 0.01 FDR: 40273
[22:09] Precursors at 1% peptidoform FDR: 36282
[22:11] Calculating protein q-values
[22:11] Number of genes identified at 1% FDR: 5668 (precursor-level), 5074 (protein-level) (inference performed using proteotypic peptides only)
[22:11] Quantification
[22:11] Precursors with scored PTMs at 1% FDR: 6737 out of 8128 considered
[22:11] Precursors with all scored PTM sites unoccupied at 1% FDR: 29545
[22:11] Precursors with PTMs localised (when required) with > 90% confidence: 6703 out of 6737
[22:15] Quantification information saved to Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_007_ML_2ME_1_3uL_DIA_T60.raw.quant

[22:15] File #5/6
[22:15] Loading run Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_008_ML_2ME_2_3uL_DIA_T60.raw
[22:24] Pre-processing...
[22:25] 1015 MS1 and 30440 MS2 scans in 1015 (inferred) and 1015 (encoded) cycles, 3543027 precursors in range
[22:28] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[23:11] RT window set to 3.55351
[23:11] Recommended MS1 mass accuracy setting: 34 ppm
[23:50] Searching decoys
[24:30] Main search
[25:56] Removing low confidence identifications
[26:10] Removing interfering precursors
[26:18] Training neural networks on 81359 target and 51106 decoy PSMs
[27:17] Training neural networks on 81359 target and 48569 decoy PSMs
[28:09] Number of IDs at 0.01 FDR: 41002
[28:09] Precursors at 1% peptidoform FDR: 36678
[28:11] Calculating protein q-values
[28:11] Number of genes identified at 1% FDR: 5764 (precursor-level), 5169 (protein-level) (inference performed using proteotypic peptides only)
[28:11] Quantification
[28:11] Precursors with scored PTMs at 1% FDR: 6729 out of 8164 considered
[28:11] Precursors with all scored PTM sites unoccupied at 1% FDR: 29949
[28:11] Precursors with PTMs localised (when required) with > 90% confidence: 6704 out of 6729
[28:15] Quantification information saved to Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_008_ML_2ME_2_3uL_DIA_T60.raw.quant

[28:15] File #6/6
[28:15] Loading run Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_009_ML_2ME_3_3uL_DIA_T60.raw
[28:23] Pre-processing...
[28:24] 1013 MS1 and 30390 MS2 scans in 1013 (inferred) and 1013 (encoded) cycles, 3543027 precursors in range
[28:26] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[29:10] RT window set to 3.72539
[29:10] Recommended MS1 mass accuracy setting: 33 ppm
[29:48] Searching decoys
[30:31] Main search
[32:00] Removing low confidence identifications
[32:15] Removing interfering precursors
[32:22] Training neural networks on 78784 target and 49071 decoy PSMs
[33:20] Training neural networks on 78784 target and 47189 decoy PSMs
[34:10] Number of IDs at 0.01 FDR: 39987
[34:11] Precursors at 1% peptidoform FDR: 35925
[34:12] Calculating protein q-values
[34:12] Number of genes identified at 1% FDR: 5591 (precursor-level), 5083 (protein-level) (inference performed using proteotypic peptides only)
[34:12] Quantification
[34:13] Precursors with scored PTMs at 1% FDR: 6722 out of 8024 considered
[34:13] Precursors with all scored PTM sites unoccupied at 1% FDR: 29203
[34:13] Precursors with PTMs localised (when required) with > 90% confidence: 6692 out of 6722
[34:16] Quantification information saved to Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\Asto310_009_ML_2ME_3_3uL_DIA_T60.raw.quant

[34:16] Cross-run analysis
[34:16] Reading quantification information: 6 files
[34:27] Quantifying peptides
[34:59] Assembling protein groups
[35:00] Quantifying proteins
[35:01] Calculating q-values for protein and gene groups
[35:03] Calculating global q-values for protein and gene groups
[35:03] Protein groups with global q-value <= 0.01: 5687
[35:05] Compressed report saved to Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\NN210_260313_Asto310_ML_SP3_IAA2ME\report.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[35:05] Saving precursor levels matrix
[35:06] Precursor levels matrix (1% precursor and protein group FDR) saved to Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\NN210_260313_Asto310_ML_SP3_IAA2ME\report.pr_matrix.tsv.
[35:06] Saving protein group levels matrix
[35:06] Protein groups matrix saved to Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\NN210_260313_Asto310_ML_SP3_IAA2ME\report.pg_matrix.tsv.
[35:06] Saving gene group levels matrix
[35:06] Gene groups matrix saved to Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\NN210_260313_Asto310_ML_SP3_IAA2ME\report.gg_matrix.tsv.
[35:06] Saving unique genes levels matrix
[35:06] Unique genes matrix saved to Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\NN210_260313_Asto310_ML_SP3_IAA2ME\report.unique_genes_matrix.tsv.
[35:07] Manifest saved to Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\NN210_260313_Asto310_ML_SP3_IAA2ME\report.manifest.txt
[35:07] Stats report saved to Z:\Exploris240_Data\2026\m03\260313_Asto310_ML_SP3\NN210_260313_Asto310_ML_SP3_IAA2ME\report.stats.tsv

