DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks)
Compiled on Apr 14 2022 15:31:19
Current date and time: Thu Apr 11 15:51:10 2024
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:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C1_rep1.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C1_rep2.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C1_rep3.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C2_rep1.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C2_rep2.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C2_rep3.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T1_rep1.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T1_rep2.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T1_rep3.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T2_rep1.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T2_rep2.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T2_rep3.raw  --lib  --threads 18 --verbose 1 --out W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\report.pr_matrix.tsv --qvalue 0.01 --matrices --out-lib W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\lib.tsv --gen-spec-lib --predictor --fasta W:\personal\KI\FASTA_Files_Libraries\uniprotkb_proteome_UP000005640_human 2024_02_07_SP_TB_canonical_isoform.fasta --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --met-excision --cut K*,R* --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --unimod4 --reanalyse --relaxed-prot-inf --smart-profiling --peak-center --no-ifs-removal --protein-qvalue 0.01  --peak-translation  --mass-acc-cal 10  --relaxed-prot-inf  --matrix-qvalue 0.01  --matrix-spec-q  --top 4   

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
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 200
Max fragment m/z set to 1800
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 7
Max peptide length set to 30
Min precursor m/z set to 300
Max precursor m/z set to 1800
Min precursor charge set to 1
Max precursor charge set to 4
Cysteine carbamidomethylation enabled as a fixed 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
Highly heuristic protein grouping will be used, to reduce the number of protein groups obtained; this mode is recommended for benchmarking protein ID numbers; use with caution for anything else
When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones
Fixed-width center of each elution peak will be used for quantification
Interference removal from fragment elution curves disabled
Output will be filtered at 0.01 protein-level FDR
Translation of retention times between peptides within the same elution group enabled
Calibration mass accuracy set to 1e-05
Highly heuristic protein grouping will be used, to reduce the number of protein groups obtained; this mode is recommended for benchmarking protein ID numbers; use with caution for anything else
Precursor/protein x sample matrices will be filtered at 0.01 precursor & protein-level FDR
Protein x sample matrices will be also filtered using run-specific protein q-value
Top 4 precursors will be used for protein quantification in each run
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 FASTA digest mode - disabled; to enable, generate an in silico predicted spectral library and analyse with this library

12 files will be processed
[0:00] Loading FASTA W:\personal\KI\FASTA_Files_Libraries\uniprotkb_proteome_UP000005640_human 2024_02_07_SP_TB_canonical_isoform.fasta
[0:14] Processing FASTA
[0:22] Assembling elution groups
[0:40] 5202593 precursors generated
[0:40] Gene names missing for some isoforms
[0:40] Library contains 82078 proteins, and 20536 genes
[0:41] [0:50] [16:29] [23:54] [24:01] [24:05] Saving the library to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\lib.predicted.speclib
[33:41] Initialising library

[33:45] First pass: generating a spectral library from DIA data
[33:45] File #1/12
[33:45] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C1_rep1.raw
[34:42] 1351384 library precursors are potentially detectable
[34:42] Processing...
[35:10] RT window set to 2.48152
[35:10] Peak width: 2.748
[35:10] Scan window radius set to 6
[35:10] Recommended MS1 mass accuracy setting: 3.22824 ppm
[35:34] Optimised mass accuracy: 5.48439 ppm
[36:01] Removing low confidence identifications
[36:01] Removing interfering precursors
[36:02] Training neural networks: 42765 targets, 27200 decoys
[36:04] Number of IDs at 0.01 FDR: 22918
[36:04] Translating peaks within elution groups
[36:05] Number of IDs at 0.01 FDR: 23039
[36:05] Calculating protein q-values
[36:05] Number of genes identified at 1% FDR: 5799 (precursor-level), 5474 (protein-level) (inference performed using proteotypic peptides only)
[36:05] Quantification
[36:12] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C1_rep1.raw.quant.

[36:12] File #2/12
[36:12] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C1_rep2.raw
[39:12] 1351384 library precursors are potentially detectable
[39:12] Processing...
[39:39] RT window set to 2.54361
[39:39] Recommended MS1 mass accuracy setting: 3.24498 ppm
[40:11] Removing low confidence identifications
[40:11] Removing interfering precursors
[40:12] Training neural networks: 43016 targets, 27000 decoys
[40:15] Number of IDs at 0.01 FDR: 22523
[40:15] Translating peaks within elution groups
[40:15] Number of IDs at 0.01 FDR: 22654
[40:15] Calculating protein q-values
[40:16] Number of genes identified at 1% FDR: 5726 (precursor-level), 5365 (protein-level) (inference performed using proteotypic peptides only)
[40:16] Quantification
[40:25] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C1_rep2.raw.quant.

[40:25] File #3/12
[40:25] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C1_rep3.raw
[41:32] 1351384 library precursors are potentially detectable
[41:32] Processing...
[42:07] RT window set to 2.72068
[42:07] Recommended MS1 mass accuracy setting: 4.46045 ppm
[42:39] Removing low confidence identifications
[42:39] Removing interfering precursors
[42:40] Training neural networks: 28843 targets, 17488 decoys
[42:41] Number of IDs at 0.01 FDR: 15260
[42:41] Translating peaks within elution groups
[42:42] Number of IDs at 0.01 FDR: 15422
[42:42] Calculating protein q-values
[42:42] Number of genes identified at 1% FDR: 4815 (precursor-level), 4552 (protein-level) (inference performed using proteotypic peptides only)
[42:43] Quantification
[42:52] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C1_rep3.raw.quant.

[42:52] File #4/12
[42:52] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C2_rep1.raw
[46:16] 1351384 library precursors are potentially detectable
[46:17] Processing...
[46:39] RT window set to 2.49239
[46:39] Recommended MS1 mass accuracy setting: 3.25402 ppm
[47:17] Removing low confidence identifications
[47:17] Removing interfering precursors
[47:19] Training neural networks: 59742 targets, 37569 decoys
[47:22] Number of IDs at 0.01 FDR: 32447
[47:22] Translating peaks within elution groups
[47:23] Number of IDs at 0.01 FDR: 32827
[47:23] Calculating protein q-values
[47:23] Number of genes identified at 1% FDR: 6976 (precursor-level), 6661 (protein-level) (inference performed using proteotypic peptides only)
[47:23] Quantification
[50:25] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C2_rep1.raw.quant.

[50:25] File #5/12
[50:25] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C2_rep2.raw
[51:58] 1351384 library precursors are potentially detectable
[51:58] Processing...
[52:21] RT window set to 2.63244
[52:21] Recommended MS1 mass accuracy setting: 3.24904 ppm
[53:02] Removing low confidence identifications
[53:02] Removing interfering precursors
[53:04] Training neural networks: 58720 targets, 36357 decoys
[53:07] Number of IDs at 0.01 FDR: 31567
[53:07] Translating peaks within elution groups
[53:08] Number of IDs at 0.01 FDR: 31918
[53:08] Calculating protein q-values
[53:08] Number of genes identified at 1% FDR: 6959 (precursor-level), 6601 (protein-level) (inference performed using proteotypic peptides only)
[53:08] Quantification
[56:16] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C2_rep2.raw.quant.

[56:16] File #6/12
[56:16] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C2_rep3.raw
[57:37] 1351384 library precursors are potentially detectable
[57:37] Processing...
[58:02] RT window set to 2.76934
[58:02] Recommended MS1 mass accuracy setting: 4.1478 ppm
[58:42] Removing low confidence identifications
[58:43] Removing interfering precursors
[58:44] Training neural networks: 52221 targets, 32279 decoys
[58:47] Number of IDs at 0.01 FDR: 27567
[58:47] Translating peaks within elution groups
[58:47] Number of IDs at 0.01 FDR: 27834
[58:47] Calculating protein q-values
[58:48] Number of genes identified at 1% FDR: 6449 (precursor-level), 6087 (protein-level) (inference performed using proteotypic peptides only)
[58:48] Quantification
[61:11] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C2_rep3.raw.quant.

[61:11] File #7/12
[61:11] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T1_rep1.raw
[62:30] 1351384 library precursors are potentially detectable
[62:30] Processing...
[63:01] RT window set to 2.51756
[63:01] Recommended MS1 mass accuracy setting: 2.97922 ppm
[63:38] Removing low confidence identifications
[63:38] Removing interfering precursors
[63:39] Training neural networks: 49136 targets, 30796 decoys
[63:42] Number of IDs at 0.01 FDR: 26561
[63:42] Translating peaks within elution groups
[63:42] Number of IDs at 0.01 FDR: 26776
[63:42] Calculating protein q-values
[63:43] Number of genes identified at 1% FDR: 6163 (precursor-level), 5769 (protein-level) (inference performed using proteotypic peptides only)
[63:43] Quantification
[66:08] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T1_rep1.raw.quant.

[66:08] File #8/12
[66:08] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T1_rep2.raw
[67:21] 1351384 library precursors are potentially detectable
[67:22] Processing...
[67:51] RT window set to 2.49867
[67:51] Recommended MS1 mass accuracy setting: 2.91869 ppm
[68:25] Removing low confidence identifications
[68:25] Removing interfering precursors
[68:26] Training neural networks: 45316 targets, 28012 decoys
[68:29] Number of IDs at 0.01 FDR: 23811
[68:29] Translating peaks within elution groups
[68:29] Number of IDs at 0.01 FDR: 23969
[68:29] Calculating protein q-values
[68:30] Number of genes identified at 1% FDR: 5846 (precursor-level), 5515 (protein-level) (inference performed using proteotypic peptides only)
[68:30] Quantification
[70:47] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T1_rep2.raw.quant.

[70:48] File #9/12
[70:48] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T1_rep3.raw
[72:14] 1351384 library precursors are potentially detectable
[72:14] Processing...
[72:41] RT window set to 2.53135
[72:42] Recommended MS1 mass accuracy setting: 3.18105 ppm
[73:18] Removing low confidence identifications
[73:18] Removing interfering precursors
[73:19] Training neural networks: 53472 targets, 33689 decoys
[73:22] Number of IDs at 0.01 FDR: 28777
[73:22] Translating peaks within elution groups
[73:23] Number of IDs at 0.01 FDR: 29043
[73:23] Calculating protein q-values
[73:24] Number of genes identified at 1% FDR: 6287 (precursor-level), 5893 (protein-level) (inference performed using proteotypic peptides only)
[73:24] Quantification
[77:57] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T1_rep3.raw.quant.

[77:58] File #10/12
[77:58] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T2_rep1.raw
[80:52] 1351384 library precursors are potentially detectable
[80:52] Processing...
[81:17] RT window set to 2.54856
[81:17] Recommended MS1 mass accuracy setting: 3.10817 ppm
[82:02] Removing low confidence identifications
[82:02] Removing interfering precursors
[82:04] Training neural networks: 65848 targets, 40740 decoys
[82:07] Number of IDs at 0.01 FDR: 35375
[82:07] Translating peaks within elution groups
[82:08] Number of IDs at 0.01 FDR: 35766
[82:08] Calculating protein q-values
[82:09] Number of genes identified at 1% FDR: 7275 (precursor-level), 6916 (protein-level) (inference performed using proteotypic peptides only)
[82:09] Quantification
[85:22] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T2_rep1.raw.quant.

[85:22] File #11/12
[85:22] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T2_rep2.raw
[87:00] 1351384 library precursors are potentially detectable
[87:00] Processing...
[87:24] RT window set to 2.54898
[87:24] Recommended MS1 mass accuracy setting: 2.97982 ppm
[88:05] Removing low confidence identifications
[88:05] Removing interfering precursors
[88:06] Training neural networks: 56861 targets, 35441 decoys
[88:09] Number of IDs at 0.01 FDR: 31385
[88:10] Translating peaks within elution groups
[88:10] Number of IDs at 0.01 FDR: 31729
[88:10] Calculating protein q-values
[88:11] Number of genes identified at 1% FDR: 6785 (precursor-level), 6412 (protein-level) (inference performed using proteotypic peptides only)
[88:11] Quantification
[90:40] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T2_rep2.raw.quant.

[90:40] File #12/12
[90:40] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T2_rep3.raw
[92:14] 1351384 library precursors are potentially detectable
[92:15] Processing...
[92:38] RT window set to 2.5112
[92:39] Recommended MS1 mass accuracy setting: 3.64717 ppm
[93:18] Removing low confidence identifications
[93:18] Removing interfering precursors
[93:20] Training neural networks: 60759 targets, 37934 decoys
[93:23] Number of IDs at 0.01 FDR: 33369
[93:23] Translating peaks within elution groups
[93:23] Number of IDs at 0.01 FDR: 33719
[93:23] Calculating protein q-values
[93:24] Number of genes identified at 1% FDR: 6985 (precursor-level), 6590 (protein-level) (inference performed using proteotypic peptides only)
[93:24] Quantification
[93:59] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T2_rep3.raw.quant.

[93:59] Cross-run analysis
[93:59] Reading quantification information: 12 files
[94:24] Quantifying peptides
[94:27] Assembling protein groups
[94:33] Quantifying proteins
[94:34] Calculating q-values for protein and gene groups
[94:35] Calculating global q-values for protein and gene groups
[94:35] Writing report
[96:10] Report saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\report.pr_matrix-first-pass.tsv.
[96:10] Saving precursor levels matrix
[96:14] Precursor levels matrix (1% precursor and protein group FDR) saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\report.pr_matrix-first-pass.pr_matrix.tsv.
[96:14] Saving protein group levels matrix
[96:15] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\report.pr_matrix-first-pass.pg_matrix.tsv.
[96:15] Saving gene group levels matrix
[96:15] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\report.pr_matrix-first-pass.gg_matrix.tsv.
[96:15] Saving unique genes levels matrix
[96:16] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\report.pr_matrix-first-pass.unique_genes_matrix.tsv.
[96:16] Stats report saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\report.pr_matrix-first-pass.stats.tsv
[96:16] Generating spectral library:
[96:16] 41131 precursors passing the FDR threshold are to be extracted
[96:16] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C1_rep1.raw
[97:13] 1351384 library precursors are potentially detectable
[97:13] 1132 spectra added to the library
[97:14] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C1_rep2.raw
[100:05] 1351384 library precursors are potentially detectable
[100:06] 472 spectra added to the library
[100:07] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C1_rep3.raw
[101:12] 1351384 library precursors are potentially detectable
[101:13] 807 spectra added to the library
[101:13] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C2_rep1.raw
[102:34] 1351384 library precursors are potentially detectable
[102:35] 12288 spectra added to the library
[102:35] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C2_rep2.raw
[104:29] 1351384 library precursors are potentially detectable
[104:29] 821 spectra added to the library
[104:32] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C2_rep3.raw
[106:08] 1351384 library precursors are potentially detectable
[106:08] 996 spectra added to the library
[106:08] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T1_rep1.raw
[107:19] 1351384 library precursors are potentially detectable
[107:19] 2851 spectra added to the library
[107:20] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T1_rep2.raw
[108:24] 1351384 library precursors are potentially detectable
[108:25] 643 spectra added to the library
[108:25] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T1_rep3.raw
[109:40] 1351384 library precursors are potentially detectable
[109:40] 812 spectra added to the library
[109:40] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T2_rep1.raw
[111:24] 1351384 library precursors are potentially detectable
[111:25] 7194 spectra added to the library
[111:25] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T2_rep2.raw
[112:54] 1351384 library precursors are potentially detectable
[112:54] 2093 spectra added to the library
[112:55] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T2_rep3.raw
[114:28] 1351384 library precursors are potentially detectable
[114:28] 3224 spectra added to the library
[114:29] Saving spectral library to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\lib.tsv
[115:13] 41131 precursors saved
[115:13] Loading the generated library and saving it in the .speclib format
[115:13] Loading spectral library W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\lib.tsv
[115:34] Spectral library loaded: 42675 protein isoforms, 18767 protein groups and 41131 precursors in 40209 elution groups.
[115:34] Loading protein annotations from FASTA W:\personal\KI\FASTA_Files_Libraries\uniprotkb_proteome_UP000005640_human 2024_02_07_SP_TB_canonical_isoform.fasta
[115:47] Gene names missing for some isoforms
[115:47] Library contains 32209 proteins, and 8853 genes
[115:47] Saving the library to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\lib.tsv.speclib

[117:53] Second pass: using the newly created spectral library to reanalyse the data
[117:53] File #1/12
[117:53] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C1_rep1.raw
[119:44] 41131 library precursors are potentially detectable
[119:44] Processing...
[119:45] RT window set to 1.2203
[119:45] Recommended MS1 mass accuracy setting: 3.13446 ppm
[119:46] Removing low confidence identifications
[119:46] Removing interfering precursors
[119:46] Training neural networks: 30481 targets, 12812 decoys
[119:48] Number of IDs at 0.01 FDR: 28080
[119:48] Translating peaks within elution groups
[119:48] Number of IDs at 0.01 FDR: 28196
[119:48] Calculating protein q-values
[119:48] Number of genes identified at 1% FDR: 6535 (precursor-level), 6111 (protein-level) (inference performed using proteotypic peptides only)
[119:48] Quantification

[119:48] File #2/12
[119:48] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C1_rep2.raw
[121:42] 41131 library precursors are potentially detectable
[121:42] Processing...
[121:43] RT window set to 1.25742
[121:43] Recommended MS1 mass accuracy setting: 3.47893 ppm
[121:44] Removing low confidence identifications
[121:44] Removing interfering precursors
[121:44] Training neural networks: 30424 targets, 13036 decoys
[121:45] Number of IDs at 0.01 FDR: 27702
[121:46] Translating peaks within elution groups
[121:46] Number of IDs at 0.01 FDR: 27807
[121:46] Calculating protein q-values
[121:46] Number of genes identified at 1% FDR: 6488 (precursor-level), 6079 (protein-level) (inference performed using proteotypic peptides only)
[121:46] Quantification

[121:46] File #3/12
[121:46] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C1_rep3.raw
[123:37] 41131 library precursors are potentially detectable
[123:37] Processing...
[123:38] RT window set to 1.08118
[123:38] Recommended MS1 mass accuracy setting: 4.63674 ppm
[123:39] Removing low confidence identifications
[123:39] Removing interfering precursors
[123:39] Training neural networks: 20889 targets, 8890 decoys
[123:40] Number of IDs at 0.01 FDR: 18739
[123:41] Translating peaks within elution groups
[123:41] Number of IDs at 0.01 FDR: 18872
[123:41] Calculating protein q-values
[123:41] Number of genes identified at 1% FDR: 5488 (precursor-level), 5136 (protein-level) (inference performed using proteotypic peptides only)
[123:41] Quantification

[123:41] File #4/12
[123:41] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C2_rep1.raw
[126:17] 41131 library precursors are potentially detectable
[126:17] Processing...
[126:18] RT window set to 1.25629
[126:18] Recommended MS1 mass accuracy setting: 3.22679 ppm
[126:19] Removing low confidence identifications
[126:19] Removing interfering precursors
[126:20] Training neural networks: 38050 targets, 20182 decoys
[126:22] Number of IDs at 0.01 FDR: 36587
[126:22] Translating peaks within elution groups
[126:22] Number of IDs at 0.01 FDR: 36829
[126:22] Calculating protein q-values
[126:22] Number of genes identified at 1% FDR: 7422 (precursor-level), 6825 (protein-level) (inference performed using proteotypic peptides only)
[126:22] Quantification

[126:23] File #5/12
[126:23] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C2_rep2.raw
[129:08] 41131 library precursors are potentially detectable
[129:08] Processing...
[129:09] RT window set to 1.30464
[129:09] Recommended MS1 mass accuracy setting: 3.437 ppm
[129:10] Removing low confidence identifications
[129:10] Removing interfering precursors
[129:10] Training neural networks: 37854 targets, 21403 decoys
[129:12] Number of IDs at 0.01 FDR: 35935
[129:12] Translating peaks within elution groups
[129:12] Number of IDs at 0.01 FDR: 36167
[129:12] Calculating protein q-values
[129:13] Number of genes identified at 1% FDR: 7358 (precursor-level), 6822 (protein-level) (inference performed using proteotypic peptides only)
[129:13] Quantification

[129:13] File #6/12
[129:13] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C2_rep3.raw
[131:37] 41131 library precursors are potentially detectable
[131:37] Processing...
[131:38] RT window set to 1.25487
[131:38] Recommended MS1 mass accuracy setting: 4.11575 ppm
[131:39] Removing low confidence identifications
[131:39] Removing interfering precursors
[131:40] Training neural networks: 35266 targets, 18901 decoys
[131:41] Number of IDs at 0.01 FDR: 32678
[131:42] Translating peaks within elution groups
[131:42] Number of IDs at 0.01 FDR: 32887
[131:42] Calculating protein q-values
[131:42] Number of genes identified at 1% FDR: 7044 (precursor-level), 6475 (protein-level) (inference performed using proteotypic peptides only)
[131:42] Quantification

[131:42] File #7/12
[131:42] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T1_rep1.raw
[133:59] 41131 library precursors are potentially detectable
[133:59] Processing...
[133:59] RT window set to 1.29219
[133:59] Recommended MS1 mass accuracy setting: 3.24461 ppm
[134:00] Removing low confidence identifications
[134:00] Removing interfering precursors
[134:01] Training neural networks: 34124 targets, 15802 decoys
[134:03] Number of IDs at 0.01 FDR: 32053
[134:03] Translating peaks within elution groups
[134:03] Number of IDs at 0.01 FDR: 32239
[134:03] Calculating protein q-values
[134:03] Number of genes identified at 1% FDR: 6877 (precursor-level), 6397 (protein-level) (inference performed using proteotypic peptides only)
[134:03] Quantification

[134:03] File #8/12
[134:03] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T1_rep2.raw
[136:09] 41131 library precursors are potentially detectable
[136:09] Processing...
[136:10] RT window set to 1.21798
[136:10] Recommended MS1 mass accuracy setting: 3.48445 ppm
[136:11] Removing low confidence identifications
[136:11] Removing interfering precursors
[136:11] Training neural networks: 31758 targets, 13346 decoys
[136:13] Number of IDs at 0.01 FDR: 29400
[136:13] Translating peaks within elution groups
[136:13] Number of IDs at 0.01 FDR: 29533
[136:13] Calculating protein q-values
[136:13] Number of genes identified at 1% FDR: 6612 (precursor-level), 6139 (protein-level) (inference performed using proteotypic peptides only)
[136:13] Quantification

[136:13] File #9/12
[136:13] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T1_rep3.raw
[138:38] 41131 library precursors are potentially detectable
[138:38] Processing...
[138:39] RT window set to 1.28572
[138:39] Recommended MS1 mass accuracy setting: 3.26962 ppm
[138:40] Removing low confidence identifications
[138:40] Removing interfering precursors
[138:40] Training neural networks: 35738 targets, 16790 decoys
[138:42] Number of IDs at 0.01 FDR: 33628
[138:42] Translating peaks within elution groups
[138:42] Number of IDs at 0.01 FDR: 33827
[138:42] Calculating protein q-values
[138:42] Number of genes identified at 1% FDR: 6912 (precursor-level), 6366 (protein-level) (inference performed using proteotypic peptides only)
[138:42] Quantification

[138:43] File #10/12
[138:43] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T2_rep1.raw
[142:05] 41131 library precursors are potentially detectable
[142:05] Processing...
[142:06] RT window set to 1.29213
[142:06] Recommended MS1 mass accuracy setting: 3.18383 ppm
[142:07] Removing low confidence identifications
[142:07] Removing interfering precursors
[142:08] Training neural networks: 39450 targets, 23199 decoys
[142:10] Number of IDs at 0.01 FDR: 38177
[142:10] Translating peaks within elution groups
[142:10] Number of IDs at 0.01 FDR: 38438
[142:10] Calculating protein q-values
[142:10] Number of genes identified at 1% FDR: 7505 (precursor-level), 6975 (protein-level) (inference performed using proteotypic peptides only)
[142:10] Quantification

[142:11] File #11/12
[142:11] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T2_rep2.raw
[145:03] 41131 library precursors are potentially detectable
[145:03] Processing...
[145:04] RT window set to 1.28881
[145:04] Recommended MS1 mass accuracy setting: 3.29461 ppm
[145:05] Removing low confidence identifications
[145:05] Removing interfering precursors
[145:06] Training neural networks: 37845 targets, 20057 decoys
[145:08] Number of IDs at 0.01 FDR: 36374
[145:08] Translating peaks within elution groups
[145:08] Number of IDs at 0.01 FDR: 36587
[145:08] Calculating protein q-values
[145:08] Number of genes identified at 1% FDR: 7356 (precursor-level), 6829 (protein-level) (inference performed using proteotypic peptides only)
[145:08] Quantification

[145:09] File #12/12
[145:09] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T2_rep3.raw
[148:11] 41131 library precursors are potentially detectable
[148:11] Processing...
[148:12] RT window set to 1.3188
[148:12] Recommended MS1 mass accuracy setting: 3.69334 ppm
[148:13] Removing low confidence identifications
[148:13] Removing interfering precursors
[148:13] Training neural networks: 38948 targets, 21257 decoys
[148:15] Number of IDs at 0.01 FDR: 37543
[148:15] Translating peaks within elution groups
[148:16] Number of IDs at 0.01 FDR: 37751
[148:16] Calculating protein q-values
[148:16] Number of genes identified at 1% FDR: 7436 (precursor-level), 6845 (protein-level) (inference performed using proteotypic peptides only)
[148:16] Quantification

[148:16] Cross-run analysis
[148:16] Reading quantification information: 12 files
[148:17] Quantifying peptides
[148:21] Quantifying proteins
[148:21] Calculating q-values for protein and gene groups
[148:22] Calculating global q-values for protein and gene groups
[148:22] Writing report
[156:44] Report saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\report.pr_matrix.tsv.
[156:44] Saving precursor levels matrix
[156:48] Precursor levels matrix (1% precursor and protein group FDR) saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\report.pr_matrix.pr_matrix.tsv.
[156:48] Saving protein group levels matrix
[156:49] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\report.pr_matrix.pg_matrix.tsv.
[156:49] Saving gene group levels matrix
[156:50] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\report.pr_matrix.gg_matrix.tsv.
[156:50] Saving unique genes levels matrix
[156:50] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\report.pr_matrix.unique_genes_matrix.tsv.
[156:50] Stats report saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_only\report.pr_matrix.stats.tsv

Finished

