DIA-NN 1.7.16 (Data-Independent Acquisition by Neural Networks)
Compiled on Mar 27 2021 21:34:06
Current date and time: Sun May  4 11:32:20 2025
CPU: GenuineIntel 13th Gen Intel(R) Core(TM) i9-13900F
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 
Logical CPU cores: 32
diann.exe --f D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.mzML  --f D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.mzML  --f D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.mzML  --f D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.mzML  --f D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.mzML  --f D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.mzML  --lib  --threads 12 --verbose 1 --out D:\Proteobench_manuscript_data\run_output_Astral\diann_1.7.2_default\report.tsv --qvalue 0.01 --matrices --out-lib C:\DIA-NN\1.7.16\report-lib.tsv --gen-spec-lib --predictor --fasta D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta --fasta-search --min-fr-mz 50 --max-fr-mz 2000 --met-excision --cut K*,R* --missed-cleavages 1 --min-pep-len 6 --max-pep-len 30 --min-pr-mz 200 --max-pr-mz 1000 --unimod4 --var-mods 1 --unimod35 --reanalyse --smart-profiling 

Thread number set to 12
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
A spectral library will be generated
Deep learning will be used to generate a new in silico spectral library from peptides provided
Library-free search enabled
Min fragment m/z set to 50
Max fragment m/z set to 2000
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
Min peptide length set to 6
Max peptide length set to 30
Min precursor m/z set to 200
Max precursor m/z set to 1000
Cysteine carbamidomethylation enabled as a fixed modification
Maximum number of variable modifications set to 1
Methionine oxidation enabled as a variable modification
A spectral library will be created from the DIA runs and used to reanalyse them; .quant files will only be saved to disk during the first step
When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones
DIA-NN will optimise the mass accuracy automatically using the first run in the experiment. This is useful primarily for quick initial analyses, when it is not yet known which mass accuracy setting works best for a particular acquisition scheme.
Exclusion of fragments shared between heavy and light peptides from quantification is not supported in library-free mode - disabled

6 files will be processed
[0:00] Loading FASTA D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[0:03] Processing FASTA
[0:10] Assembling elution groups
[0:19] 6620457 precursors generated
[0:19] Protein names missing for some isoforms
[0:19] Gene names missing for some isoforms
[0:19] Library contains 31676 proteins, and 0 genes
[0:20] [0:30] [26:42] [35:30] [35:37] [35:41] Saving the library to C:\DIA-NN\1.7.16\report-lib.predicted.speclib
[35:52] Initialising library

[35:54] First pass: generating a spectral library from DIA data
[35:54] File #1/6
[35:54] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.mzML
[37:40] 4883512 library precursors are potentially detectable
[37:40] Processing...
[39:34] RT window set to 1.44342
[39:34] Peak width: 2.94
[39:34] Scan window radius set to 6
[39:35] Recommended MS1 mass accuracy setting: 2.78001 ppm
[46:15] Optimised mass accuracy: 5.62001 ppm
[83:06] Removing low confidence identifications
[83:06] Removing interfering precursors
[84:04] Training the neural network: 192754 targets, 140717 decoys
[84:16] Number of IDs at 0.01 FDR: 95746
[84:18] Calculating protein q-values
[84:18] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[84:19] Quantification
[84:39] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.mzML.quant.

[84:43] File #2/6
[84:43] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.mzML
[86:29] 4883512 library precursors are potentially detectable
[86:29] Processing...
[88:19] RT window set to 1.68628
[88:20] Recommended MS1 mass accuracy setting: 2.68082 ppm
[126:42] Removing low confidence identifications
[126:42] Removing interfering precursors
[127:40] Training the neural network: 192315 targets, 140362 decoys
[127:53] Number of IDs at 0.01 FDR: 97260
[127:54] Calculating protein q-values
[127:55] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[127:55] Quantification
[128:17] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.mzML.quant.

[128:20] File #3/6
[128:20] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.mzML
[130:05] 4883512 library precursors are potentially detectable
[130:05] Processing...
[131:55] RT window set to 1.46593
[131:55] Recommended MS1 mass accuracy setting: 2.77254 ppm
[169:34] Removing low confidence identifications
[169:34] Removing interfering precursors
[170:33] Training the neural network: 194967 targets, 141646 decoys
[170:47] Number of IDs at 0.01 FDR: 98320
[170:48] Calculating protein q-values
[170:49] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[170:49] Quantification
[171:10] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.mzML.quant.

[171:13] File #4/6
[171:13] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.mzML
[172:59] 4883512 library precursors are potentially detectable
[172:59] Processing...
[174:46] RT window set to 1.40236
[174:46] Recommended MS1 mass accuracy setting: 2.40634 ppm
[214:02] Removing low confidence identifications
[214:02] Removing interfering precursors
[215:01] Training the neural network: 196982 targets, 141812 decoys
[215:14] Number of IDs at 0.01 FDR: 98165
[215:15] Calculating protein q-values
[215:16] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[215:16] Quantification
[215:37] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.mzML.quant.

[215:41] File #5/6
[215:41] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.mzML
[217:26] 4883512 library precursors are potentially detectable
[217:26] Processing...
[218:57] RT window set to 1.69655
[218:57] Recommended MS1 mass accuracy setting: 2.6977 ppm
[256:23] Removing low confidence identifications
[256:23] Removing interfering precursors
[257:21] Training the neural network: 195713 targets, 143257 decoys
[257:34] Number of IDs at 0.01 FDR: 98984
[257:35] Calculating protein q-values
[257:36] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[257:36] Quantification
[257:58] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.mzML.quant.

[258:00] File #6/6
[258:00] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.mzML
[259:46] 4883512 library precursors are potentially detectable
[259:46] Processing...
[261:33] RT window set to 1.61666
[261:33] Recommended MS1 mass accuracy setting: 2.86203 ppm
[299:23] Removing low confidence identifications
[299:23] Removing interfering precursors
[300:21] Training the neural network: 193547 targets, 141940 decoys
[300:33] Number of IDs at 0.01 FDR: 98926
[300:35] Calculating protein q-values
[300:36] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[300:36] Quantification
[300:57] Quantification information saved to D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.mzML.quant.

[301:00] Cross-run analysis
[301:00] Reading quantification information: 6 files
[301:01] Quantifying peptides
[301:09] Assembling protein groups
[301:13] Quantifying proteins
[301:13] Calculating q-values for protein and gene groups
[301:15] Writing report
[301:38] Report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_1.7.2_default\report-first-pass.tsv.
[301:38] Saving precursor levels matrix
[301:39] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_1.7.2_default\report-first-pass.pr_matrix.tsv.
[301:39] Saving protein group levels matrix
[301:39] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_1.7.2_default\report-first-pass.pg_matrix.tsv.
[301:39] Saving gene group levels matrix
[301:39] Gene groups levels matrix (1% precursor FDR and gene group FDR) saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_1.7.2_default\report-first-pass.gg_matrix.tsv.
[301:39] Saving unique genes levels matrix
[301:39] Unique genes levels matrix (1% precursor FDR and unique protein FDR) saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_1.7.2_default\report-first-pass.unique_genes_matrix.tsv.
[301:39] Stats report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_1.7.2_default\report-first-pass.stats.tsv
[301:39] Generating spectral library:
[301:39] Reading quantification information: 6 files
[301:40] Assembling protein groups
[301:45] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.mzML
[303:29] 4883512 library precursors are potentially detectable
[303:31] 26304 precursors added to the library
[303:34] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.mzML
[305:14] 4883512 library precursors are potentially detectable
[305:16] 10401 precursors added to the library
[305:18] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.mzML
[306:57] 4883512 library precursors are potentially detectable
[306:58] 8406 precursors added to the library
[307:01] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.mzML
[308:41] 4883512 library precursors are potentially detectable
[308:42] 12608 precursors added to the library
[308:45] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.mzML
[310:23] 4883512 library precursors are potentially detectable
[310:24] 8130 precursors added to the library
[310:27] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.mzML
[312:05] 4883512 library precursors are potentially detectable
[312:08] 30016 precursors added to the library
[312:11] Saving spectral library to C:\DIA-NN\1.7.16\report-lib.tsv
[312:27] 130559 precursors saved
[312:27] Loading the generated library and saving it in the .speclib format
[312:27] Loading spectral library C:\DIA-NN\1.7.16\report-lib.tsv
[312:33] Spectral library loaded: 14032 protein isoforms, 14631 protein groups and 130559 precursors in 119546 elution groups.
[312:33] Loading protein annotations from FASTA D:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta
[312:34] Gene names missing for some isoforms
[312:34] Library contains 13986 proteins, and 0 genes
[312:34] Saving the library to C:\DIA-NN\1.7.16\report-lib.tsv.speclib

[312:38] Second pass: using the newly created spectral library to reanalyse the data
[312:38] File #1/6
[312:38] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.mzML
[314:02] 130559 library precursors are potentially detectable
[314:02] Processing...
[314:04] RT window set to 0.443107
[314:04] Recommended MS1 mass accuracy setting: 2.56776 ppm
[315:00] Removing low confidence identifications
[315:00] Removing interfering precursors
[315:25] Training the neural network: 121162 targets, 55207 decoys
[315:30] Number of IDs at 0.01 FDR: 113871
[315:32] Calculating protein q-values
[315:32] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[315:32] Quantification

[315:57] File #2/6
[315:57] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.mzML
[317:21] 130559 library precursors are potentially detectable
[317:21] Processing...
[317:24] RT window set to 0.444117
[317:24] Recommended MS1 mass accuracy setting: 2.66388 ppm
[318:19] Removing low confidence identifications
[318:19] Removing interfering precursors
[318:43] Training the neural network: 122170 targets, 55497 decoys
[318:49] Number of IDs at 0.01 FDR: 115685
[318:51] Calculating protein q-values
[318:51] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[318:51] Quantification

[319:16] File #3/6
[319:16] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.mzML
[320:40] 130559 library precursors are potentially detectable
[320:40] Processing...
[320:42] RT window set to 0.436047
[320:42] Recommended MS1 mass accuracy setting: 2.49129 ppm
[321:38] Removing low confidence identifications
[321:38] Removing interfering precursors
[322:03] Training the neural network: 122020 targets, 55022 decoys
[322:09] Number of IDs at 0.01 FDR: 115413
[322:10] Calculating protein q-values
[322:10] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[322:10] Quantification

[322:35] File #4/6
[322:35] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.mzML
[324:01] 130559 library precursors are potentially detectable
[324:01] Processing...
[324:03] RT window set to 0.455964
[324:03] Recommended MS1 mass accuracy setting: 2.81375 ppm
[324:59] Removing low confidence identifications
[324:59] Removing interfering precursors
[325:24] Training the neural network: 122852 targets, 56691 decoys
[325:30] Number of IDs at 0.01 FDR: 116290
[325:31] Calculating protein q-values
[325:31] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[325:31] Quantification

[325:57] File #5/6
[325:57] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.mzML
[327:22] 130559 library precursors are potentially detectable
[327:22] Processing...
[327:25] RT window set to 0.453763
[327:25] Recommended MS1 mass accuracy setting: 2.91215 ppm
[328:23] Removing low confidence identifications
[328:23] Removing interfering precursors
[328:48] Training the neural network: 122834 targets, 56309 decoys
[328:54] Number of IDs at 0.01 FDR: 116325
[328:55] Calculating protein q-values
[328:55] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[328:55] Quantification

[329:21] File #6/6
[329:21] Loading run D:\Proteobench_manuscript_data\Astral_raw\LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.mzML
[330:45] 130559 library precursors are potentially detectable
[330:45] Processing...
[330:48] RT window set to 0.463955
[330:48] Recommended MS1 mass accuracy setting: 3.094 ppm
[331:43] Removing low confidence identifications
[331:43] Removing interfering precursors
[332:09] Training the neural network: 122982 targets, 57339 decoys
[332:14] Number of IDs at 0.01 FDR: 116515
[332:16] Calculating protein q-values
[332:16] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[332:16] Quantification

[332:41] Cross-run analysis
[332:41] Reading quantification information: 6 files
[332:42] Quantifying peptides
[332:51] Quantifying proteins
[332:52] Calculating q-values for protein and gene groups
[332:53] Writing report
[333:20] Report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_1.7.2_default\report.tsv.
[333:20] Saving precursor levels matrix
[333:20] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_1.7.2_default\report.pr_matrix.tsv.
[333:20] Saving protein group levels matrix
[333:20] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_1.7.2_default\report.pg_matrix.tsv.
[333:20] Saving gene group levels matrix
[333:20] Gene groups levels matrix (1% precursor FDR and gene group FDR) saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_1.7.2_default\report.gg_matrix.tsv.
[333:20] Saving unique genes levels matrix
[333:20] Unique genes levels matrix (1% precursor FDR and unique protein FDR) saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_1.7.2_default\report.unique_genes_matrix.tsv.
[333:20] Stats report saved to D:\Proteobench_manuscript_data\run_output_Astral\diann_1.7.2_default\report.stats.tsv
