DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks)
Compiled on Dec  1 2022 14:47:06
Current date and time: Fri Oct 10 11:21:36 2025
Logical CPU cores: 128
/usr/diann/1.8.2_beta_8/linux/diann-1.8.1.8 --threads 64 --qvalue 0.01 --matrices --predictor --met-excision --cut K*,R* --min-pep-len 6 --max-pep-len 30 --smart-profiling --fasta-search --fasta /misc/fasta/p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta --var-mods 1 --var-mod UniMod:35,15.994915,M --min-pr-charge 2 --max-pr-charge 3 --min-pr-mz 400 --max-pr-mz 1500 --min-fr-mz 200 --max-fr-mz 1800 --use-quant --verbose 1 --unimod4 --missed-cleavages 1 --mass-acc 20 --mass-acc-ms1 15 --reanalyse --pg-level 0 --f /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.mzML --f /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.mzML --f /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.mzML --f /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.mzML --f /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.mzML --f /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.mzML --out-lib /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report-lib.tsv --out-lib-copy --temp /scratch/DIANN_A362/WU335004/temp-2025-10-10/ --out /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report.tsv 

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
Deep learning will be used to generate a new in silico spectral library from peptides provided
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Min peptide length set to 6
Max peptide length set to 30
When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones
Library-free search enabled
Maximum number of variable modifications set to 1
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
Min precursor charge set to 2
Max precursor charge set to 3
Min precursor m/z set to 400
Max precursor m/z set to 1500
Min fragment m/z set to 200
Max fragment m/z set to 1800
Existing .quant files will be used
Cysteine carbamidomethylation enabled as a fixed modification
Maximum number of missed cleavages set to 1
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
Implicit protein grouping: isoform IDs; this determines which peptides are considered 'proteotypic' and thus affects protein FDR calculation
Copies of the spectral library and the FASTA database will be saved along with the final report
Mass accuracy will be fixed to 2e-05 (MS2) and 1.5e-05 (MS1)
Exclusion of fragments shared between heavy and light peptides from quantification is not supported in FASTA digest mode - disabled; to enable, generate an in silico predicted spectral library and analyse with this library

6 files will be processed
[0:00] Loading FASTA /misc/fasta/p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
[0:04] Processing FASTA
[0:12] Assembling elution groups
[0:17] 3635480 precursors generated
[0:17] Gene names missing for some isoforms
[0:17] Library contains 27290 proteins, and 0 genes
[0:20] [0:26] [5:02] [5:43] [7:13] [7:15] Saving the library to /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report-lib.predicted.speclib
[7:19] Initialising library

[7:24] First pass: generating a spectral library from DIA data
[7:24] File #1/6
[7:24] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.mzML
[7:37] 2167193 library precursors are potentially detectable
[7:37] Processing...
[8:38] RT window set to 1.7957
[8:38] Peak width: 3.08
[8:38] Scan window radius set to 6
[8:38] Recommended MS1 mass accuracy setting: 2.56732 ppm
[11:16] Removing low confidence identifications
[11:16] Removing interfering precursors
[11:18] Training neural networks: 69488 targets, 50153 decoys
[11:21] Number of IDs at 0.01 FDR: 32474
[11:22] Calculating protein q-values
[11:22] Number of protein isoforms identified at 1% FDR: 7203 (precursor-level), 6709 (protein-level) (inference performed using proteotypic peptides only)
[11:22] Quantification
[11:23] Quantification information saved to /scratch/DIANN_A362/WU335004/temp-2025-10-10/_scratch_DIANN_A362_WU335004_20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1_mzML.quant.

[11:24] File #2/6
[11:24] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.mzML
[11:37] 2167193 library precursors are potentially detectable
[11:37] Processing...
[12:42] RT window set to 1.66072
[12:42] Recommended MS1 mass accuracy setting: 2.68498 ppm
[15:50] Removing low confidence identifications
[15:50] Removing interfering precursors
[15:54] Training neural networks: 71788 targets, 52875 decoys
[15:57] Number of IDs at 0.01 FDR: 34402
[15:58] Calculating protein q-values
[15:58] Number of protein isoforms identified at 1% FDR: 7418 (precursor-level), 6882 (protein-level) (inference performed using proteotypic peptides only)
[15:58] Quantification
[15:59] Quantification information saved to /scratch/DIANN_A362/WU335004/temp-2025-10-10/_scratch_DIANN_A362_WU335004_20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2_mzML.quant.

[15:59] File #3/6
[15:59] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.mzML
[16:13] 2167193 library precursors are potentially detectable
[16:14] Processing...
[17:18] RT window set to 1.68079
[17:18] Recommended MS1 mass accuracy setting: 2.90588 ppm
[20:38] Removing low confidence identifications
[20:38] Removing interfering precursors
[20:42] Training neural networks: 72799 targets, 52194 decoys
[20:45] Number of IDs at 0.01 FDR: 33722
[20:45] Calculating protein q-values
[20:46] Number of protein isoforms identified at 1% FDR: 7387 (precursor-level), 6803 (protein-level) (inference performed using proteotypic peptides only)
[20:46] Quantification
[20:46] Quantification information saved to /scratch/DIANN_A362/WU335004/temp-2025-10-10/_scratch_DIANN_A362_WU335004_20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3_mzML.quant.

[20:47] File #4/6
[20:47] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.mzML
[21:00] 2167193 library precursors are potentially detectable
[21:00] Processing...
[22:16] RT window set to 1.62453
[22:16] Recommended MS1 mass accuracy setting: 2.40588 ppm
[25:18] Removing low confidence identifications
[25:18] Removing interfering precursors
[25:20] Training neural networks: 64771 targets, 47055 decoys
[25:23] Number of IDs at 0.01 FDR: 30935
[25:24] Calculating protein q-values
[25:24] Number of protein isoforms identified at 1% FDR: 6548 (precursor-level), 6150 (protein-level) (inference performed using proteotypic peptides only)
[25:24] Quantification
[25:25] Quantification information saved to /scratch/DIANN_A362/WU335004/temp-2025-10-10/_scratch_DIANN_A362_WU335004_20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1_mzML.quant.

[25:27] File #5/6
[25:27] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.mzML
[25:39] 2167193 library precursors are potentially detectable
[25:39] Processing...
[26:40] RT window set to 1.41512
[26:41] Recommended MS1 mass accuracy setting: 2.72951 ppm
[28:55] Removing low confidence identifications
[28:55] Removing interfering precursors
[28:58] Training neural networks: 67323 targets, 48588 decoys
[29:01] Number of IDs at 0.01 FDR: 31567
[29:01] Calculating protein q-values
[29:01] Number of protein isoforms identified at 1% FDR: 6736 (precursor-level), 6259 (protein-level) (inference performed using proteotypic peptides only)
[29:01] Quantification
[29:02] Quantification information saved to /scratch/DIANN_A362/WU335004/temp-2025-10-10/_scratch_DIANN_A362_WU335004_20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2_mzML.quant.

[29:03] File #6/6
[29:03] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.mzML
[29:15] 2167193 library precursors are potentially detectable
[29:15] Processing...
[30:12] RT window set to 1.66873
[30:12] Recommended MS1 mass accuracy setting: 2.68599 ppm
[32:26] Removing low confidence identifications
[32:26] Removing interfering precursors
[32:29] Training neural networks: 66532 targets, 48529 decoys
[32:32] Number of IDs at 0.01 FDR: 31474
[32:33] Calculating protein q-values
[32:33] Number of protein isoforms identified at 1% FDR: 6688 (precursor-level), 6289 (protein-level) (inference performed using proteotypic peptides only)
[32:33] Quantification
[32:34] Quantification information saved to /scratch/DIANN_A362/WU335004/temp-2025-10-10/_scratch_DIANN_A362_WU335004_20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3_mzML.quant.

[32:35] Cross-run analysis
[32:35] Reading quantification information: 6 files
[32:35] Quantifying peptides
[32:38] Assembling protein groups
[32:40] Quantifying proteins
[32:40] Calculating q-values for protein and gene groups
[32:40] Calculating global q-values for protein and gene groups
[32:40] Writing report
[32:47] Report saved to /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report-first-pass.tsv.
[32:47] Saving precursor levels matrix
[32:47] Precursor levels matrix (1% precursor and protein group FDR) saved to /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report-first-pass.pr_matrix.tsv.
[32:47] Saving protein group levels matrix
[32:47] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report-first-pass.pg_matrix.tsv.
[32:47] Saving gene group levels matrix
[32:47] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report-first-pass.gg_matrix.tsv.
[32:47] Saving unique genes levels matrix
[32:47] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report-first-pass.unique_genes_matrix.tsv.
[32:47] Stats report saved to /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report-first-pass.stats.tsv
[32:47] Generating spectral library:
[32:47] 43366 precursors passing the FDR threshold are to be extracted
[32:47] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.mzML
[33:01] 2167193 library precursors are potentially detectable
[33:01] 4907 spectra added to the library
[33:02] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.mzML
[33:15] 2167193 library precursors are potentially detectable
[33:16] 4968 spectra added to the library
[33:16] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.mzML
[33:30] 2167193 library precursors are potentially detectable
[33:31] 4325 spectra added to the library
[33:31] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.mzML
[33:43] 2167193 library precursors are potentially detectable
[33:44] 6873 spectra added to the library
[33:44] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.mzML
[33:56] 2167193 library precursors are potentially detectable
[33:56] 2104 spectra added to the library
[33:56] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.mzML
[34:10] 2167193 library precursors are potentially detectable
[34:11] 10526 spectra added to the library
[34:11] Saving spectral library to /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report-lib.tsv
[34:14] 43366 precursors saved
[34:14] Loading the generated library and saving it in the .speclib format
[34:14] Loading spectral library /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report-lib.tsv
[34:15] Spectral library loaded: 9777 protein isoforms, 9744 protein groups and 43366 precursors in 42619 elution groups.
[34:15] Loading protein annotations from FASTA /misc/fasta/p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
[34:15] Gene names missing for some isoforms
[34:15] Library contains 9726 proteins, and 0 genes
[34:15] Saving the library to /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report-lib.tsv.speclib

[34:18] Second pass: using the newly created spectral library to reanalyse the data
[34:18] File #1/6
[34:18] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.mzML
[34:27] 43366 library precursors are potentially detectable
[34:28] Processing...
[34:29] RT window set to 0.457567
[34:29] Recommended MS1 mass accuracy setting: 2.71465 ppm
[34:31] Removing low confidence identifications
[34:31] Removing interfering precursors
[34:32] Training neural networks: 41860 targets, 42029 decoys
[34:34] Number of IDs at 0.01 FDR: 37884
[34:34] Calculating protein q-values
[34:34] Number of protein isoforms identified at 1% FDR: 7757 (precursor-level), 7117 (protein-level) (inference performed using proteotypic peptides only)
[34:34] Quantification

[34:35] File #2/6
[34:35] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.mzML
[34:45] 43366 library precursors are potentially detectable
[34:45] Processing...
[34:46] RT window set to 0.457075
[34:46] Recommended MS1 mass accuracy setting: 2.97394 ppm
[34:48] Removing low confidence identifications
[34:48] Removing interfering precursors
[34:49] Training neural networks: 42142 targets, 42562 decoys
[34:50] Number of IDs at 0.01 FDR: 39257
[34:51] Calculating protein q-values
[34:51] Number of protein isoforms identified at 1% FDR: 7855 (precursor-level), 7232 (protein-level) (inference performed using proteotypic peptides only)
[34:51] Quantification

[34:51] File #3/6
[34:51] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.mzML
[35:01] 43366 library precursors are potentially detectable
[35:01] Processing...
[35:03] RT window set to 0.458691
[35:03] Recommended MS1 mass accuracy setting: 3.04949 ppm
[35:04] Removing low confidence identifications
[35:04] Removing interfering precursors
[35:06] Training neural networks: 41885 targets, 42518 decoys
[35:07] Number of IDs at 0.01 FDR: 37989
[35:08] Calculating protein q-values
[35:08] Number of protein isoforms identified at 1% FDR: 7797 (precursor-level), 7102 (protein-level) (inference performed using proteotypic peptides only)
[35:08] Quantification

[35:08] File #4/6
[35:08] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.mzML
[35:17] 43366 library precursors are potentially detectable
[35:17] Processing...
[35:19] RT window set to 0.459826
[35:19] Recommended MS1 mass accuracy setting: 2.65457 ppm
[35:20] Removing low confidence identifications
[35:20] Removing interfering precursors
[35:22] Training neural networks: 41640 targets, 41512 decoys
[35:23] Number of IDs at 0.01 FDR: 36428
[35:24] Calculating protein q-values
[35:24] Number of protein isoforms identified at 1% FDR: 7247 (precursor-level), 6537 (protein-level) (inference performed using proteotypic peptides only)
[35:24] Quantification

[35:24] File #5/6
[35:24] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.mzML
[35:33] 43366 library precursors are potentially detectable
[35:33] Processing...
[35:34] RT window set to 0.461277
[35:34] Recommended MS1 mass accuracy setting: 2.86493 ppm
[35:36] Removing low confidence identifications
[35:36] Removing interfering precursors
[35:37] Training neural networks: 41817 targets, 41710 decoys
[35:39] Number of IDs at 0.01 FDR: 36910
[35:39] Calculating protein q-values
[35:39] Number of protein isoforms identified at 1% FDR: 7402 (precursor-level), 6707 (protein-level) (inference performed using proteotypic peptides only)
[35:39] Quantification

[35:39] File #6/6
[35:39] Loading run /scratch/DIANN_A362/WU335004/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.mzML
[35:48] 43366 library precursors are potentially detectable
[35:48] Processing...
[35:50] RT window set to 0.465375
[35:50] Recommended MS1 mass accuracy setting: 2.89841 ppm
[35:52] Removing low confidence identifications
[35:52] Removing interfering precursors
[35:53] Training neural networks: 41579 targets, 41672 decoys
[35:55] Number of IDs at 0.01 FDR: 36608
[35:55] Calculating protein q-values
[35:55] Number of protein isoforms identified at 1% FDR: 7380 (precursor-level), 6681 (protein-level) (inference performed using proteotypic peptides only)
[35:55] Quantification

[35:55] Cross-run analysis
[35:55] Reading quantification information: 6 files
[35:56] Quantifying peptides
[35:59] Quantifying proteins
[35:59] Calculating q-values for protein and gene groups
[35:59] Calculating global q-values for protein and gene groups
[35:59] Writing report
[36:06] Report saved to /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report.tsv.
[36:06] Saving precursor levels matrix
[36:06] Precursor levels matrix (1% precursor and protein group FDR) saved to /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report.pr_matrix.tsv.
[36:06] Saving protein group levels matrix
[36:06] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report.pg_matrix.tsv.
[36:06] Saving gene group levels matrix
[36:06] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report.gg_matrix.tsv.
[36:06] Saving unique genes levels matrix
[36:06] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report.unique_genes_matrix.tsv.
[36:06] Stats report saved to /scratch/DIANN_A362/WU335004/out-2025-10-10//WU335004_report.stats.tsv

Finished

