
DIA-NN 2.1.0 Academia  (Data-Independent Acquisition by Neural Networks)
Compiled on Mar 25 2025 10:59:54
Current date and time: Mon Apr 21 11:39:08 2025
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 W:\Exploris240_Data\2025\m04\250404_Asto232_tML\Asto232_m023_s002_ML_IAA_4uL_DIA_T60.raw.dia  --f W:\Exploris240_Data\2025\m04\250404_Asto232_tML\Asto232_m024_s009_ML_2ME_300mM_4uL_DIA_T60.raw.dia  --f W:\Exploris240_Data\2025\m04\250404_Asto233_tML\Asto233_m017_s002_ML_IAA_4uL_DIA_T60.raw.dia  --f W:\Exploris240_Data\2025\m04\250404_Asto233_tML\Asto233_m018_s009_ML_2ME_300mM_4uL_DIA_T60.raw.dia  --f W:\Exploris240_Data\2025\m04\250408_Asto234_tML\Asto234_m022_s002_ML_IAA_4uL_DIA_T60.raw.dia  --f W:\Exploris240_Data\2025\m04\250408_Asto234_tML\Asto234_m023_s009_ML_2ME_300mM_4uL_DIA_T60.raw.dia  --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 W:\Exploris240_Data\2025\m04\250408_Asto234_tML\NN210_250421_tML_IAA_2ME_T60\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
[0:03] 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 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 W:\Exploris240_Data\2025\m04\250404_Asto232_tML\Asto232_m023_s002_ML_IAA_4uL_DIA_T60.raw.dia
[0:25] Pre-processing...
[0:26] 999 MS1 and 29952 MS2 scans in 999 (inferred) and 999 (encoded) cycles, 3543027 precursors in range
[0:28] Calibrating with mass accuracies 25 (MS1), 21 (MS2)
[1:14] RT window set to 2.41308
[1:14] Peak width: 3.216
[1:14] Scan window radius set to 7
[1:14] Recommended MS1 mass accuracy setting: 39 ppm
[1:49] Searching decoys
[2:14] Main search
[3:10] Removing low confidence identifications
[3:21] Removing interfering precursors
[3:28] Training neural networks on 62006 target and 37584 decoy PSMs
[4:11] Training neural networks on 62006 target and 36194 decoy PSMs
[4:48] Number of IDs at 0.01 FDR: 30182
[4:49] Precursors at 1% peptidoform FDR: 27989
[4:50] Calculating protein q-values
[4:50] Number of genes identified at 1% FDR: 5299 (precursor-level), 4921 (protein-level) (inference performed using proteotypic peptides only)
[4:50] Quantification
[4:51] Precursors with scored PTMs at 1% FDR: 4158 out of 4749 considered
[4:51] Precursors with all scored PTM sites unoccupied at 1% FDR: 23831
[4:51] Precursors with PTMs localised (when required) with > 90% confidence: 4133 out of 4158
[4:53] Quantification information saved to W:\Exploris240_Data\2025\m04\250404_Asto232_tML\Asto232_m023_s002_ML_IAA_4uL_DIA_T60.raw.dia.quant

[4:53] File #2/6
[4:53] Loading run W:\Exploris240_Data\2025\m04\250404_Asto232_tML\Asto232_m024_s009_ML_2ME_300mM_4uL_DIA_T60.raw.dia
[4:56] Pre-processing...
[4:57] 1021 MS1 and 30612 MS2 scans in 1021 (inferred) and 1021 (encoded) cycles, 3543027 precursors in range
[4:59] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[5:40] RT window set to 3.17228
[5:40] Recommended MS1 mass accuracy setting: 39 ppm
[6:17] Searching decoys
[6:52] Main search
[8:05] Removing low confidence identifications
[8:17] Removing interfering precursors
[8:24] Training neural networks on 71822 target and 45119 decoy PSMs
[9:15] Training neural networks on 71822 target and 43022 decoy PSMs
[9:58] Number of IDs at 0.01 FDR: 34740
[9:58] Precursors at 1% peptidoform FDR: 31864
[10:00] Calculating protein q-values
[10:00] Number of genes identified at 1% FDR: 5480 (precursor-level), 4983 (protein-level) (inference performed using proteotypic peptides only)
[10:00] Quantification
[10:00] Precursors with scored PTMs at 1% FDR: 5445 out of 6460 considered
[10:00] Precursors with all scored PTM sites unoccupied at 1% FDR: 26419
[10:00] Precursors with PTMs localised (when required) with > 90% confidence: 5416 out of 5445
[10:04] Quantification information saved to W:\Exploris240_Data\2025\m04\250404_Asto232_tML\Asto232_m024_s009_ML_2ME_300mM_4uL_DIA_T60.raw.dia.quant

[10:04] File #3/6
[10:04] Loading run W:\Exploris240_Data\2025\m04\250404_Asto233_tML\Asto233_m017_s002_ML_IAA_4uL_DIA_T60.raw.dia
[10:07] Pre-processing...
[10:08] 1010 MS1 and 30275 MS2 scans in 1010 (inferred) and 1010 (encoded) cycles, 3543027 precursors in range
[10:10] Calibrating with mass accuracies 25 (MS1), 21 (MS2)
[10:57] RT window set to 2.61744
[10:57] Recommended MS1 mass accuracy setting: 38 ppm
[11:34] Searching decoys
[12:04] Main search
[13:07] Removing low confidence identifications
[13:19] Removing interfering precursors
[13:26] Training neural networks on 64700 target and 39376 decoy PSMs
[14:11] Training neural networks on 64700 target and 37891 decoy PSMs
[14:50] Number of IDs at 0.01 FDR: 29864
[14:51] Precursors at 1% peptidoform FDR: 27401
[14:52] Calculating protein q-values
[14:52] Number of genes identified at 1% FDR: 5264 (precursor-level), 4861 (protein-level) (inference performed using proteotypic peptides only)
[14:52] Quantification
[14:53] Precursors with scored PTMs at 1% FDR: 3717 out of 4300 considered
[14:53] Precursors with all scored PTM sites unoccupied at 1% FDR: 23684
[14:53] Precursors with PTMs localised (when required) with > 90% confidence: 3692 out of 3717
[14:55] Quantification information saved to W:\Exploris240_Data\2025\m04\250404_Asto233_tML\Asto233_m017_s002_ML_IAA_4uL_DIA_T60.raw.dia.quant

[14:55] File #4/6
[14:55] Loading run W:\Exploris240_Data\2025\m04\250404_Asto233_tML\Asto233_m018_s009_ML_2ME_300mM_4uL_DIA_T60.raw.dia
[14:58] Pre-processing...
[14:59] 995 MS1 and 29843 MS2 scans in 995 (inferred) and 995 (encoded) cycles, 3543027 precursors in range
[15:01] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[15:41] RT window set to 3.67334
[15:41] Recommended MS1 mass accuracy setting: 38 ppm
[16:19] Searching decoys
[16:55] Main search
[18:12] Removing low confidence identifications
[18:24] Removing interfering precursors
[18:31] Training neural networks on 66317 target and 41331 decoy PSMs
[19:18] Training neural networks on 66317 target and 39228 decoy PSMs
[19:58] Number of IDs at 0.01 FDR: 33841
[19:58] Precursors at 1% peptidoform FDR: 31208
[19:59] Calculating protein q-values
[20:00] Number of genes identified at 1% FDR: 5270 (precursor-level), 4764 (protein-level) (inference performed using proteotypic peptides only)
[20:00] Quantification
[20:00] Precursors with scored PTMs at 1% FDR: 5502 out of 6443 considered
[20:00] Precursors with all scored PTM sites unoccupied at 1% FDR: 25706
[20:00] Precursors with PTMs localised (when required) with > 90% confidence: 5465 out of 5502
[20:03] Quantification information saved to W:\Exploris240_Data\2025\m04\250404_Asto233_tML\Asto233_m018_s009_ML_2ME_300mM_4uL_DIA_T60.raw.dia.quant

[20:03] File #5/6
[20:03] Loading run W:\Exploris240_Data\2025\m04\250408_Asto234_tML\Asto234_m022_s002_ML_IAA_4uL_DIA_T60.raw.dia
[20:05] Pre-processing...
[20:06] 981 MS1 and 29409 MS2 scans in 981 (inferred) and 981 (encoded) cycles, 3543027 precursors in range
[20:09] Calibrating with mass accuracies 25 (MS1), 21 (MS2)
[20:52] RT window set to 2.56398
[20:53] Recommended MS1 mass accuracy setting: 40 ppm
[21:28] Searching decoys
[21:52] Main search
[22:43] Removing low confidence identifications
[22:54] Removing interfering precursors
[23:01] Training neural networks on 57633 target and 35252 decoy PSMs
[23:42] Training neural networks on 57633 target and 34127 decoy PSMs
[24:17] Number of IDs at 0.01 FDR: 29274
[24:17] Precursors at 1% peptidoform FDR: 27605
[24:19] Calculating protein q-values
[24:19] Number of genes identified at 1% FDR: 5325 (precursor-level), 4838 (protein-level) (inference performed using proteotypic peptides only)
[24:19] Quantification
[24:19] Precursors with scored PTMs at 1% FDR: 4649 out of 5132 considered
[24:19] Precursors with all scored PTM sites unoccupied at 1% FDR: 22956
[24:19] Precursors with PTMs localised (when required) with > 90% confidence: 4618 out of 4649
[24:22] Quantification information saved to W:\Exploris240_Data\2025\m04\250408_Asto234_tML\Asto234_m022_s002_ML_IAA_4uL_DIA_T60.raw.dia.quant

[24:22] File #6/6
[24:22] Loading run W:\Exploris240_Data\2025\m04\250408_Asto234_tML\Asto234_m023_s009_ML_2ME_300mM_4uL_DIA_T60.raw.dia
[24:25] Pre-processing...
[24:26] 1024 MS1 and 30720 MS2 scans in 1024 (inferred) and 1024 (encoded) cycles, 3543027 precursors in range
[24:29] Calibrating with mass accuracies 25 (MS1), 22 (MS2)
[25:10] RT window set to 3.31191
[25:10] Recommended MS1 mass accuracy setting: 37 ppm
[25:48] Searching decoys
[26:24] Main search
[27:42] Removing low confidence identifications
[27:56] Removing interfering precursors
[28:03] Training neural networks on 73520 target and 45847 decoy PSMs
[28:54] Training neural networks on 73520 target and 43360 decoy PSMs
[29:39] Number of IDs at 0.01 FDR: 36259
[29:39] Precursors at 1% peptidoform FDR: 32930
[29:40] Calculating protein q-values
[29:41] Number of genes identified at 1% FDR: 5608 (precursor-level), 5018 (protein-level) (inference performed using proteotypic peptides only)
[29:41] Quantification
[29:41] Precursors with scored PTMs at 1% FDR: 5651 out of 6827 considered
[29:41] Precursors with all scored PTM sites unoccupied at 1% FDR: 27279
[29:41] Precursors with PTMs localised (when required) with > 90% confidence: 5629 out of 5651
[29:45] Quantification information saved to W:\Exploris240_Data\2025\m04\250408_Asto234_tML\Asto234_m023_s009_ML_2ME_300mM_4uL_DIA_T60.raw.dia.quant

[29:45] Cross-run analysis
[29:45] Reading quantification information: 6 files
[29:57] Quantifying peptides
[30:26] Assembling protein groups
[30:27] Quantifying proteins
[30:27] Calculating q-values for protein and gene groups
[30:29] Calculating global q-values for protein and gene groups
[30:29] Protein groups with global q-value <= 0.01: 5542
[30:33] Compressed report saved to W:\Exploris240_Data\2025\m04\250408_Asto234_tML\NN210_250421_tML_IAA_2ME_T60\report.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[30:34] Saving precursor levels matrix
[30:35] Precursor levels matrix (1% precursor and protein group FDR) saved to W:\Exploris240_Data\2025\m04\250408_Asto234_tML\NN210_250421_tML_IAA_2ME_T60\report.pr_matrix.tsv.
[30:35] Saving protein group levels matrix
[30:35] Protein groups matrix saved to W:\Exploris240_Data\2025\m04\250408_Asto234_tML\NN210_250421_tML_IAA_2ME_T60\report.pg_matrix.tsv.
[30:35] Saving gene group levels matrix
[30:36] Gene groups matrix saved to W:\Exploris240_Data\2025\m04\250408_Asto234_tML\NN210_250421_tML_IAA_2ME_T60\report.gg_matrix.tsv.
[30:36] Saving unique genes levels matrix
[30:36] Unique genes matrix saved to W:\Exploris240_Data\2025\m04\250408_Asto234_tML\NN210_250421_tML_IAA_2ME_T60\report.unique_genes_matrix.tsv.
[30:37] Manifest saved to W:\Exploris240_Data\2025\m04\250408_Asto234_tML\NN210_250421_tML_IAA_2ME_T60\report.manifest.txt
[30:37] Stats report saved to W:\Exploris240_Data\2025\m04\250408_Asto234_tML\NN210_250421_tML_IAA_2ME_T60\report.stats.tsv

