
DIA-NN 2.1.0 Academia  (Data-Independent Acquisition by Neural Networks)
Compiled on Mar 25 2025 10:59:54
Current date and time: Sun Mar  8 00:16:41 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\260306_Asto309_ML_IAADMSO\Asto309_m109_s009_ML_2ME_3_3uL_DIA_T60.raw  --f Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m108_s008_ML_2ME_2_3uL_DIA_T60.raw  --f Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m107_s007_ML_2ME_1_3uL_DIA_T60.raw  --f Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m106_s006_ML_IAADMSO_3_3uL_DIA_T60.raw  --f Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m105_s005_ML_IAADMSO_2_3uL_DIA_T60.raw  --f Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m104_s004_ML_IAADMSO_1_3uL_DIA_T60.raw  --f Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m103_s003_ML_IAA_3_3uL_DIA_T60.raw  --f Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m102_s002_ML_IAA_2_3uL_DIA_T60.raw  --f Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m101_s001_ML_IAA_1_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\260306_Asto309_ML_IAADMSO\260306_Asto309_ML_IAADMSO\report.parquet --qvalue 0.01 --matrices --fasta Z:\Database\2025\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 

9 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
[0:03] 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 Z:\Database\2025\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 #1/9
[0:22] Loading run Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m109_s009_ML_2ME_3_3uL_DIA_T60.raw
[0:32] Pre-processing...
[0:33] 974 MS1 and 29196 MS2 scans in 974 (inferred) and 974 (encoded) cycles, 3543027 precursors in range
[0:35] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[1:24] RT window set to 3.50664
[1:24] Peak width: 3.064
[1:24] Scan window radius set to 6
[1:24] Recommended MS1 mass accuracy setting: 35 ppm
[2:06] Searching decoys
[2:43] Main search
[4:02] Removing low confidence identifications
[4:14] Removing interfering precursors
[4:22] Training neural networks on 65707 target and 41884 decoy PSMs
[5:11] Training neural networks on 65707 target and 39315 decoy PSMs
[5:52] Number of IDs at 0.01 FDR: 30877
[5:53] Precursors at 1% peptidoform FDR: 27165
[5:54] Calculating protein q-values
[5:54] Number of genes identified at 1% FDR: 4888 (precursor-level), 4438 (protein-level) (inference performed using proteotypic peptides only)
[5:54] Quantification
[5:55] Precursors with scored PTMs at 1% FDR: 4981 out of 6104 considered
[5:55] Precursors with all scored PTM sites unoccupied at 1% FDR: 22184
[5:55] Precursors with PTMs localised (when required) with > 90% confidence: 4931 out of 4981
[5:57] Quantification information saved to Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m109_s009_ML_2ME_3_3uL_DIA_T60.raw.quant

[5:57] File #2/9
[5:57] Loading run Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m108_s008_ML_2ME_2_3uL_DIA_T60.raw
[6:05] Pre-processing...
[6:06] 972 MS1 and 29150 MS2 scans in 972 (inferred) and 972 (encoded) cycles, 3543027 precursors in range
[6:09] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[6:58] RT window set to 3.48207
[6:58] Recommended MS1 mass accuracy setting: 35 ppm
[7:40] Searching decoys
[8:17] Main search
[9:34] Removing low confidence identifications
[9:46] Removing interfering precursors
[9:53] Training neural networks on 66001 target and 41783 decoy PSMs
[10:41] Training neural networks on 66001 target and 39342 decoy PSMs
[11:22] Number of IDs at 0.01 FDR: 31185
[11:22] Precursors at 1% peptidoform FDR: 27408
[11:24] Calculating protein q-values
[11:24] Number of genes identified at 1% FDR: 4895 (precursor-level), 4347 (protein-level) (inference performed using proteotypic peptides only)
[11:24] Quantification
[11:24] Precursors with scored PTMs at 1% FDR: 5018 out of 6153 considered
[11:24] Precursors with all scored PTM sites unoccupied at 1% FDR: 22390
[11:24] Precursors with PTMs localised (when required) with > 90% confidence: 4968 out of 5018
[11:27] Quantification information saved to Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m108_s008_ML_2ME_2_3uL_DIA_T60.raw.quant

[11:27] File #3/9
[11:27] Loading run Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m107_s007_ML_2ME_1_3uL_DIA_T60.raw
[11:36] Pre-processing...
[11:36] 968 MS1 and 29010 MS2 scans in 967 (inferred) and 967 (encoded) cycles, 3543027 precursors in range
[11:39] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[12:27] RT window set to 3.55919
[12:27] Recommended MS1 mass accuracy setting: 36 ppm
[13:09] Searching decoys
[13:45] Main search
[15:02] Removing low confidence identifications
[15:14] Removing interfering precursors
[15:21] Training neural networks on 66011 target and 42097 decoy PSMs
[16:09] Training neural networks on 66011 target and 39633 decoy PSMs
[16:50] Number of IDs at 0.01 FDR: 30889
[16:51] Precursors at 1% peptidoform FDR: 27281
[16:52] Calculating protein q-values
[16:52] Number of genes identified at 1% FDR: 4907 (precursor-level), 4443 (protein-level) (inference performed using proteotypic peptides only)
[16:53] Quantification
[16:53] Precursors with scored PTMs at 1% FDR: 4997 out of 6089 considered
[16:53] Precursors with all scored PTM sites unoccupied at 1% FDR: 22284
[16:53] Precursors with PTMs localised (when required) with > 90% confidence: 4952 out of 4997
[16:56] Quantification information saved to Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m107_s007_ML_2ME_1_3uL_DIA_T60.raw.quant

[16:56] File #4/9
[16:56] Loading run Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m106_s006_ML_IAADMSO_3_3uL_DIA_T60.raw
[17:04] Pre-processing...
[17:05] 970 MS1 and 29086 MS2 scans in 970 (inferred) and 970 (encoded) cycles, 3543027 precursors in range
[17:08] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[18:06] RT window set to 2.87517
[18:06] Recommended MS1 mass accuracy setting: 39 ppm
[18:58] Searching decoys
[19:31] Main search
[20:39] Removing low confidence identifications
[20:51] Removing interfering precursors
[20:57] Training neural networks on 57304 target and 35552 decoy PSMs
[21:39] Training neural networks on 57304 target and 33206 decoy PSMs
[22:15] Number of IDs at 0.01 FDR: 25132
[22:15] Precursors at 1% peptidoform FDR: 21713
[22:16] Calculating protein q-values
[22:17] Number of genes identified at 1% FDR: 4336 (precursor-level), 3887 (protein-level) (inference performed using proteotypic peptides only)
[22:17] Quantification
[22:17] Precursors with scored PTMs at 1% FDR: 3900 out of 5026 considered
[22:17] Precursors with all scored PTM sites unoccupied at 1% FDR: 17813
[22:17] Precursors with PTMs localised (when required) with > 90% confidence: 3876 out of 3900
[22:19] Quantification information saved to Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m106_s006_ML_IAADMSO_3_3uL_DIA_T60.raw.quant

[22:19] File #5/9
[22:19] Loading run Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m105_s005_ML_IAADMSO_2_3uL_DIA_T60.raw
[22:28] Pre-processing...
[22:29] 962 MS1 and 28853 MS2 scans in 962 (inferred) and 962 (encoded) cycles, 3543027 precursors in range
[22:31] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[23:29] RT window set to 2.9753
[23:29] Recommended MS1 mass accuracy setting: 39 ppm
[24:18] Searching decoys
[24:51] Main search
[26:03] Removing low confidence identifications
[26:14] Removing interfering precursors
[26:21] Training neural networks on 58094 target and 36612 decoy PSMs
[27:04] Training neural networks on 58094 target and 34277 decoy PSMs
[27:40] Number of IDs at 0.01 FDR: 24843
[27:40] Precursors at 1% peptidoform FDR: 21619
[27:41] Calculating protein q-values
[27:42] Number of genes identified at 1% FDR: 4263 (precursor-level), 3849 (protein-level) (inference performed using proteotypic peptides only)
[27:42] Quantification
[27:42] Precursors with scored PTMs at 1% FDR: 3935 out of 4950 considered
[27:42] Precursors with all scored PTM sites unoccupied at 1% FDR: 17684
[27:42] Precursors with PTMs localised (when required) with > 90% confidence: 3911 out of 3935
[27:44] Quantification information saved to Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m105_s005_ML_IAADMSO_2_3uL_DIA_T60.raw.quant

[27:44] File #6/9
[27:44] Loading run Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m104_s004_ML_IAADMSO_1_3uL_DIA_T60.raw
[27:53] Pre-processing...
[27:54] 966 MS1 and 28958 MS2 scans in 966 (inferred) and 966 (encoded) cycles, 3543027 precursors in range
[27:57] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[28:54] RT window set to 2.83939
[28:54] Recommended MS1 mass accuracy setting: 37 ppm
[29:43] Searching decoys
[30:16] Main search
[31:25] Removing low confidence identifications
[31:36] Removing interfering precursors
[31:43] Training neural networks on 56593 target and 35067 decoy PSMs
[32:25] Training neural networks on 56593 target and 32817 decoy PSMs
[33:00] Number of IDs at 0.01 FDR: 25457
[33:00] Precursors at 1% peptidoform FDR: 21923
[33:02] Calculating protein q-values
[33:02] Number of genes identified at 1% FDR: 4316 (precursor-level), 3955 (protein-level) (inference performed using proteotypic peptides only)
[33:02] Quantification
[33:02] Precursors with scored PTMs at 1% FDR: 3985 out of 5076 considered
[33:02] Precursors with all scored PTM sites unoccupied at 1% FDR: 17938
[33:02] Precursors with PTMs localised (when required) with > 90% confidence: 3960 out of 3985
[33:04] Quantification information saved to Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m104_s004_ML_IAADMSO_1_3uL_DIA_T60.raw.quant

[33:04] File #7/9
[33:04] Loading run Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m103_s003_ML_IAA_3_3uL_DIA_T60.raw
[33:13] Pre-processing...
[33:14] 978 MS1 and 29334 MS2 scans in 978 (inferred) and 978 (encoded) cycles, 3543027 precursors in range
[33:17] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[34:15] RT window set to 3.06718
[34:15] Recommended MS1 mass accuracy setting: 36 ppm
[34:55] Searching decoys
[35:29] Main search
[36:40] Removing low confidence identifications
[36:52] Removing interfering precursors
[36:59] Training neural networks on 60076 target and 37359 decoy PSMs
[37:43] Training neural networks on 60076 target and 34820 decoy PSMs
[38:20] Number of IDs at 0.01 FDR: 27408
[38:20] Precursors at 1% peptidoform FDR: 24079
[38:22] Calculating protein q-values
[38:22] Number of genes identified at 1% FDR: 4753 (precursor-level), 4348 (protein-level) (inference performed using proteotypic peptides only)
[38:22] Quantification
[38:22] Precursors with scored PTMs at 1% FDR: 4226 out of 5267 considered
[38:22] Precursors with all scored PTM sites unoccupied at 1% FDR: 19853
[38:22] Precursors with PTMs localised (when required) with > 90% confidence: 4202 out of 4226
[38:25] Quantification information saved to Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m103_s003_ML_IAA_3_3uL_DIA_T60.raw.quant

[38:25] File #8/9
[38:25] Loading run Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m102_s002_ML_IAA_2_3uL_DIA_T60.raw
[38:34] Pre-processing...
[38:35] 977 MS1 and 29297 MS2 scans in 977 (inferred) and 977 (encoded) cycles, 3543027 precursors in range
[38:37] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[39:35] RT window set to 3.21641
[39:35] Recommended MS1 mass accuracy setting: 37 ppm
[40:26] Searching decoys
[41:03] Main search
[42:19] Removing low confidence identifications
[42:30] Removing interfering precursors
[42:37] Training neural networks on 56488 target and 34896 decoy PSMs
[43:18] Training neural networks on 56488 target and 32782 decoy PSMs
[43:53] Number of IDs at 0.01 FDR: 25315
[43:53] Precursors at 1% peptidoform FDR: 22637
[43:55] Calculating protein q-values
[43:55] Number of genes identified at 1% FDR: 4557 (precursor-level), 4193 (protein-level) (inference performed using proteotypic peptides only)
[43:55] Quantification
[43:55] Precursors with scored PTMs at 1% FDR: 3966 out of 4827 considered
[43:55] Precursors with all scored PTM sites unoccupied at 1% FDR: 18671
[43:55] Precursors with PTMs localised (when required) with > 90% confidence: 3943 out of 3966
[43:57] Quantification information saved to Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m102_s002_ML_IAA_2_3uL_DIA_T60.raw.quant

[43:57] File #9/9
[43:57] Loading run Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m101_s001_ML_IAA_1_3uL_DIA_T60.raw
[44:06] Pre-processing...
[44:07] 975 MS1 and 29247 MS2 scans in 975 (inferred) and 975 (encoded) cycles, 3543027 precursors in range
[44:09] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[45:07] RT window set to 3.1309
[45:07] Recommended MS1 mass accuracy setting: 39 ppm
[45:54] Searching decoys
[46:28] Main search
[47:39] Removing low confidence identifications
[47:50] Removing interfering precursors
[47:57] Training neural networks on 59444 target and 37167 decoy PSMs
[48:41] Training neural networks on 59444 target and 34743 decoy PSMs
[49:18] Number of IDs at 0.01 FDR: 26453
[49:19] Precursors at 1% peptidoform FDR: 23322
[49:20] Calculating protein q-values
[49:20] Number of genes identified at 1% FDR: 4677 (precursor-level), 4315 (protein-level) (inference performed using proteotypic peptides only)
[49:20] Quantification
[49:21] Precursors with scored PTMs at 1% FDR: 4158 out of 5155 considered
[49:21] Precursors with all scored PTM sites unoccupied at 1% FDR: 19164
[49:21] Precursors with PTMs localised (when required) with > 90% confidence: 4139 out of 4158
[49:23] Quantification information saved to Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\Asto309_m101_s001_ML_IAA_1_3uL_DIA_T60.raw.quant

[49:23] Cross-run analysis
[49:23] Reading quantification information: 9 files
[49:34] Quantifying peptides
[50:10] Assembling protein groups
[50:11] Quantifying proteins
[50:11] Calculating q-values for protein and gene groups
[50:14] Calculating global q-values for protein and gene groups
[50:14] Protein groups with global q-value <= 0.01: 4952
[50:16] Compressed report saved to Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\260306_Asto309_ML_IAADMSO\report.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[50:16] Saving precursor levels matrix
[50:17] Precursor levels matrix (1% precursor and protein group FDR) saved to Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\260306_Asto309_ML_IAADMSO\report.pr_matrix.tsv.
[50:17] Saving protein group levels matrix
[50:18] Protein groups matrix saved to Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\260306_Asto309_ML_IAADMSO\report.pg_matrix.tsv.
[50:18] Saving gene group levels matrix
[50:18] Gene groups matrix saved to Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\260306_Asto309_ML_IAADMSO\report.gg_matrix.tsv.
[50:18] Saving unique genes levels matrix
[50:18] Unique genes matrix saved to Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\260306_Asto309_ML_IAADMSO\report.unique_genes_matrix.tsv.
[50:19] Manifest saved to Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\260306_Asto309_ML_IAADMSO\report.manifest.txt
[50:19] Stats report saved to Z:\Exploris240_Data\2026\m03\260306_Asto309_ML_IAADMSO\260306_Asto309_ML_IAADMSO\report.stats.tsv

