DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks)
Compiled on Apr 14 2022 15:31:19
Current date and time: Fri Apr 12 13:51:33 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_C3_rep1_re.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C3_rep2.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C3_rep3.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C4_rep1.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C4_rep2.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C4_rep3.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T3_rep1.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T3_rep2.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T3_rep3.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T4_rep1.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T4_rep2.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T4_rep3.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T5_rep1.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T5_rep2.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T5_rep3.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T6_rep1.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T6_rep2.raw  --f W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T6_rep3.raw  --lib  --threads 18 --verbose 1 --out W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_mouse\report.tsv --qvalue 0.01 --matrices --out-lib W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_mouse\lib.tsv --gen-spec-lib --predictor --fasta W:\personal\KI\FASTA_Files_Libraries\uniprotkb_proteome_UP000000589_mouse_2024_02_07_SP_TB_canonical_isoform.fasta --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

18 files will be processed
[0:00] Loading FASTA W:\personal\KI\FASTA_Files_Libraries\uniprotkb_proteome_UP000000589_mouse_2024_02_07_SP_TB_canonical_isoform.fasta
[0:06] Loading FASTA W:\personal\KI\FASTA_Files_Libraries\uniprotkb_proteome_UP000005640_human 2024_02_07_SP_TB_canonical_isoform.fasta
[0:22] Processing FASTA
[0:36] Assembling elution groups
[1:03] 8461072 precursors generated
[1:04] Gene names missing for some isoforms
[1:04] Library contains 136681 proteins, and 42452 genes
[1:05] [1:21] [153:42] [187:16] [187:27] [187:34] Saving the library to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_mouse\lib.predicted.speclib
[201:11] Initialising library

[201:17] First pass: generating a spectral library from DIA data
[201:17] File #1/18
[201:17] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C3_rep1_re.raw
[201:58] 2210915 library precursors are potentially detectable
[201:58] Processing...
[203:35] RT window set to 2.85061
[203:35] Peak width: 2.836
[203:35] Scan window radius set to 6
[203:35] Recommended MS1 mass accuracy setting: 4.65957 ppm
[204:46] Optimised mass accuracy: 4.56882 ppm
[205:19] Removing low confidence identifications
[205:19] Removing interfering precursors
[205:20] Training neural networks: 15144 targets, 9539 decoys
[205:21] Number of IDs at 0.01 FDR: 7227
[205:21] Translating peaks within elution groups
[205:22] Number of IDs at 0.01 FDR: 7278
[205:22] Calculating protein q-values
[205:23] Number of genes identified at 1% FDR: 1742 (precursor-level), 1552 (protein-level) (inference performed using proteotypic peptides only)
[205:23] Quantification
[205:25] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C3_rep1_re.raw.quant.

[205:26] File #2/18
[205:26] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C3_rep2.raw
[206:17] 2210915 library precursors are potentially detectable
[206:17] Processing...
[207:15] RT window set to 2.70908
[207:16] Recommended MS1 mass accuracy setting: 4.36852 ppm
[208:06] Removing low confidence identifications
[208:06] Removing interfering precursors
[208:07] Training neural networks: 33734 targets, 21882 decoys
[208:09] Number of IDs at 0.01 FDR: 15874
[208:09] Translating peaks within elution groups
[208:10] Number of IDs at 0.01 FDR: 15952
[208:10] Calculating protein q-values
[208:11] Number of genes identified at 1% FDR: 3073 (precursor-level), 2738 (protein-level) (inference performed using proteotypic peptides only)
[208:11] Quantification
[208:16] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C3_rep2.raw.quant.

[208:16] File #3/18
[208:16] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C3_rep3.raw
[209:07] 2210915 library precursors are potentially detectable
[209:07] Processing...
[210:05] RT window set to 2.80131
[210:05] Recommended MS1 mass accuracy setting: 3.98357 ppm
[210:56] Removing low confidence identifications
[210:57] Removing interfering precursors
[210:58] Training neural networks: 32134 targets, 20116 decoys
[211:00] Number of IDs at 0.01 FDR: 15019
[211:00] Translating peaks within elution groups
[211:01] Number of IDs at 0.01 FDR: 15106
[211:01] Calculating protein q-values
[211:01] Number of genes identified at 1% FDR: 3015 (precursor-level), 2575 (protein-level) (inference performed using proteotypic peptides only)
[211:02] Quantification
[211:09] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C3_rep3.raw.quant.

[211:09] File #4/18
[211:09] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C4_rep1.raw
[212:02] 2210915 library precursors are potentially detectable
[212:03] Processing...
[213:01] RT window set to 2.732
[213:01] Recommended MS1 mass accuracy setting: 4.28821 ppm
[213:51] Removing low confidence identifications
[213:51] Removing interfering precursors
[213:53] Training neural networks: 31234 targets, 19462 decoys
[213:55] Number of IDs at 0.01 FDR: 14546
[213:55] Translating peaks within elution groups
[213:55] Number of IDs at 0.01 FDR: 14641
[213:55] Calculating protein q-values
[213:56] Number of genes identified at 1% FDR: 3050 (precursor-level), 2759 (protein-level) (inference performed using proteotypic peptides only)
[213:56] Quantification
[214:01] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C4_rep1.raw.quant.

[214:01] File #5/18
[214:01] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C4_rep2.raw
[215:08] 2210915 library precursors are potentially detectable
[215:08] Processing...
[215:53] RT window set to 2.77317
[215:53] Recommended MS1 mass accuracy setting: 4.81505 ppm
[216:50] Removing low confidence identifications
[216:50] Removing interfering precursors
[216:51] Training neural networks: 46250 targets, 29742 decoys
[216:54] Number of IDs at 0.01 FDR: 22350
[216:54] Translating peaks within elution groups
[216:55] Number of IDs at 0.01 FDR: 22491
[216:55] Calculating protein q-values
[216:56] Number of genes identified at 1% FDR: 4262 (precursor-level), 3662 (protein-level) (inference performed using proteotypic peptides only)
[216:56] Quantification
[217:03] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C4_rep2.raw.quant.

[217:03] File #6/18
[217:03] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C4_rep3.raw
[218:05] 2210915 library precursors are potentially detectable
[218:06] Processing...
[218:55] RT window set to 2.59761
[218:55] Recommended MS1 mass accuracy setting: 3.47252 ppm
[219:47] Removing low confidence identifications
[219:47] Removing interfering precursors
[219:48] Training neural networks: 41144 targets, 26617 decoys
[219:51] Number of IDs at 0.01 FDR: 20627
[219:51] Translating peaks within elution groups
[219:52] Number of IDs at 0.01 FDR: 20739
[219:52] Calculating protein q-values
[219:53] Number of genes identified at 1% FDR: 4031 (precursor-level), 3601 (protein-level) (inference performed using proteotypic peptides only)
[219:53] Quantification
[219:59] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C4_rep3.raw.quant.

[219:59] File #7/18
[219:59] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T3_rep1.raw
[221:05] 2210915 library precursors are potentially detectable
[221:05] Processing...
[221:56] RT window set to 2.57681
[221:56] Recommended MS1 mass accuracy setting: 3.34997 ppm
[222:49] Removing low confidence identifications
[222:49] Removing interfering precursors
[222:51] Training neural networks: 41974 targets, 26818 decoys
[222:53] Number of IDs at 0.01 FDR: 20908
[222:53] Translating peaks within elution groups
[222:54] Number of IDs at 0.01 FDR: 21042
[222:54] Calculating protein q-values
[222:55] Number of genes identified at 1% FDR: 3786 (precursor-level), 3370 (protein-level) (inference performed using proteotypic peptides only)
[222:55] Quantification
[223:01] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T3_rep1.raw.quant.

[223:02] File #8/18
[223:02] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T3_rep2.raw
[224:09] 2210915 library precursors are potentially detectable
[224:09] Processing...
[225:02] RT window set to 2.52957
[225:02] Recommended MS1 mass accuracy setting: 3.75862 ppm
[225:54] Removing low confidence identifications
[225:54] Removing interfering precursors
[225:55] Training neural networks: 42198 targets, 27140 decoys
[225:58] Number of IDs at 0.01 FDR: 20831
[225:58] Translating peaks within elution groups
[225:58] Number of IDs at 0.01 FDR: 20979
[225:58] Calculating protein q-values
[225:59] Number of genes identified at 1% FDR: 3593 (precursor-level), 3156 (protein-level) (inference performed using proteotypic peptides only)
[226:00] Quantification
[226:06] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T3_rep2.raw.quant.

[226:06] File #9/18
[226:06] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T3_rep3.raw
[227:19] 2210915 library precursors are potentially detectable
[227:20] Processing...
[228:12] RT window set to 2.6207
[228:13] Recommended MS1 mass accuracy setting: 2.94385 ppm
[229:10] Removing low confidence identifications
[229:10] Removing interfering precursors
[229:12] Training neural networks: 44733 targets, 28490 decoys
[229:14] Number of IDs at 0.01 FDR: 22091
[229:14] Translating peaks within elution groups
[229:15] Number of IDs at 0.01 FDR: 22245
[229:15] Calculating protein q-values
[229:16] Number of genes identified at 1% FDR: 3886 (precursor-level), 3374 (protein-level) (inference performed using proteotypic peptides only)
[229:16] Quantification
[229:23] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T3_rep3.raw.quant.

[229:23] File #10/18
[229:23] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T4_rep1.raw
[230:33] 2210915 library precursors are potentially detectable
[230:34] Processing...
[231:25] RT window set to 2.58382
[231:26] Recommended MS1 mass accuracy setting: 2.99477 ppm
[232:22] Removing low confidence identifications
[232:22] Removing interfering precursors
[232:24] Training neural networks: 45677 targets, 29303 decoys
[232:26] Number of IDs at 0.01 FDR: 22903
[232:26] Translating peaks within elution groups
[232:27] Number of IDs at 0.01 FDR: 23046
[232:27] Calculating protein q-values
[232:28] Number of genes identified at 1% FDR: 4194 (precursor-level), 3698 (protein-level) (inference performed using proteotypic peptides only)
[232:28] Quantification
[232:35] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T4_rep1.raw.quant.

[232:35] File #11/18
[232:35] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T4_rep2.raw
[233:45] 2210915 library precursors are potentially detectable
[233:45] Processing...
[234:38] RT window set to 2.52981
[234:38] Recommended MS1 mass accuracy setting: 3.46359 ppm
[235:31] Removing low confidence identifications
[235:32] Removing interfering precursors
[235:33] Training neural networks: 43432 targets, 28003 decoys
[235:35] Number of IDs at 0.01 FDR: 21893
[235:36] Translating peaks within elution groups
[235:36] Number of IDs at 0.01 FDR: 22037
[235:36] Calculating protein q-values
[235:37] Number of genes identified at 1% FDR: 4072 (precursor-level), 3671 (protein-level) (inference performed using proteotypic peptides only)
[235:37] Quantification
[235:44] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T4_rep2.raw.quant.

[235:44] File #12/18
[235:44] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T4_rep3.raw
[236:54] 2210915 library precursors are potentially detectable
[236:54] Processing...
[237:46] RT window set to 2.64322
[237:46] Recommended MS1 mass accuracy setting: 3.03548 ppm
[238:42] Removing low confidence identifications
[238:42] Removing interfering precursors
[238:43] Training neural networks: 42412 targets, 27257 decoys
[238:46] Number of IDs at 0.01 FDR: 21135
[238:46] Translating peaks within elution groups
[238:47] Number of IDs at 0.01 FDR: 21275
[238:47] Calculating protein q-values
[238:48] Number of genes identified at 1% FDR: 3978 (precursor-level), 3501 (protein-level) (inference performed using proteotypic peptides only)
[238:48] Quantification
[238:54] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T4_rep3.raw.quant.

[238:55] File #13/18
[238:55] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T5_rep1.raw
[240:02] 2210915 library precursors are potentially detectable
[240:02] Processing...
[240:53] RT window set to 2.53406
[240:54] Recommended MS1 mass accuracy setting: 3.2966 ppm
[241:46] Removing low confidence identifications
[241:46] Removing interfering precursors
[241:47] Training neural networks: 40771 targets, 26058 decoys
[241:50] Number of IDs at 0.01 FDR: 19874
[241:50] Translating peaks within elution groups
[241:51] Number of IDs at 0.01 FDR: 19983
[241:51] Calculating protein q-values
[241:51] Number of genes identified at 1% FDR: 3635 (precursor-level), 3256 (protein-level) (inference performed using proteotypic peptides only)
[241:52] Quantification
[241:58] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T5_rep1.raw.quant.

[241:58] File #14/18
[241:58] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T5_rep2.raw
[243:08] 2210915 library precursors are potentially detectable
[243:08] Processing...
[244:00] RT window set to 2.59251
[244:00] Recommended MS1 mass accuracy setting: 3.44422 ppm
[244:55] Removing low confidence identifications
[244:55] Removing interfering precursors
[244:56] Training neural networks: 43928 targets, 28441 decoys
[244:58] Number of IDs at 0.01 FDR: 21861
[244:59] Translating peaks within elution groups
[244:59] Number of IDs at 0.01 FDR: 21976
[244:59] Calculating protein q-values
[245:00] Number of genes identified at 1% FDR: 3878 (precursor-level), 3470 (protein-level) (inference performed using proteotypic peptides only)
[245:00] Quantification
[245:07] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T5_rep2.raw.quant.

[245:07] File #15/18
[245:07] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T5_rep3.raw
[246:15] 2210915 library precursors are potentially detectable
[246:15] Processing...
[247:06] RT window set to 2.75787
[247:06] Recommended MS1 mass accuracy setting: 3.2701 ppm
[248:03] Removing low confidence identifications
[248:03] Removing interfering precursors
[248:04] Training neural networks: 44012 targets, 28447 decoys
[248:07] Number of IDs at 0.01 FDR: 21655
[248:07] Translating peaks within elution groups
[248:08] Number of IDs at 0.01 FDR: 21781
[248:08] Calculating protein q-values
[248:09] Number of genes identified at 1% FDR: 3885 (precursor-level), 3432 (protein-level) (inference performed using proteotypic peptides only)
[248:09] Quantification
[248:15] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T5_rep3.raw.quant.

[248:16] File #16/18
[248:16] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T6_rep1.raw
[249:36] 2210915 library precursors are potentially detectable
[249:36] Processing...
[250:16] RT window set to 2.71745
[250:16] Recommended MS1 mass accuracy setting: 2.98872 ppm
[251:16] Removing low confidence identifications
[251:17] Removing interfering precursors
[251:18] Training neural networks: 55117 targets, 35856 decoys
[251:21] Number of IDs at 0.01 FDR: 27903
[251:21] Translating peaks within elution groups
[251:22] Number of IDs at 0.01 FDR: 28169
[251:22] Calculating protein q-values
[251:23] Number of genes identified at 1% FDR: 4886 (precursor-level), 4335 (protein-level) (inference performed using proteotypic peptides only)
[251:23] Quantification
[251:31] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T6_rep1.raw.quant.

[251:32] File #17/18
[251:32] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T6_rep2.raw
[252:52] 2210915 library precursors are potentially detectable
[252:53] Processing...
[253:40] RT window set to 2.61221
[253:41] Recommended MS1 mass accuracy setting: 3.02267 ppm
[254:39] Removing low confidence identifications
[254:39] Removing interfering precursors
[254:41] Training neural networks: 51642 targets, 33387 decoys
[254:44] Number of IDs at 0.01 FDR: 26444
[254:44] Translating peaks within elution groups
[254:45] Number of IDs at 0.01 FDR: 26680
[254:45] Calculating protein q-values
[254:46] Number of genes identified at 1% FDR: 4707 (precursor-level), 4143 (protein-level) (inference performed using proteotypic peptides only)
[254:46] Quantification
[254:54] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T6_rep2.raw.quant.

[254:55] File #18/18
[254:55] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T6_rep3.raw
[256:08] 2210915 library precursors are potentially detectable
[256:09] Processing...
[257:02] RT window set to 2.56442
[257:02] Recommended MS1 mass accuracy setting: 3.45583 ppm
[257:59] Removing low confidence identifications
[257:59] Removing interfering precursors
[258:00] Training neural networks: 45331 targets, 29167 decoys
[258:03] Number of IDs at 0.01 FDR: 22227
[258:03] Translating peaks within elution groups
[258:04] Number of IDs at 0.01 FDR: 22384
[258:04] Calculating protein q-values
[258:04] Number of genes identified at 1% FDR: 4113 (precursor-level), 3654 (protein-level) (inference performed using proteotypic peptides only)
[258:05] Quantification
[258:13] Quantification information saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T6_rep3.raw.quant.

[258:14] Cross-run analysis
[258:14] Reading quantification information: 18 files
[258:43] Quantifying peptides
[258:48] Assembling protein groups
[258:58] Quantifying proteins
[258:59] Calculating q-values for protein and gene groups
[259:01] Calculating global q-values for protein and gene groups
[259:01] Writing report
[265:01] Report saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_mouse\report-first-pass.tsv.
[265:01] Saving precursor levels matrix
[265:05] 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_mouse\report-first-pass.pr_matrix.tsv.
[265:05] Saving protein group levels matrix
[265:06] 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_mouse\report-first-pass.pg_matrix.tsv.
[265:06] Saving gene group levels matrix
[265:07] 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_mouse\report-first-pass.gg_matrix.tsv.
[265:07] Saving unique genes levels matrix
[265:07] 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_mouse\report-first-pass.unique_genes_matrix.tsv.
[265:07] Stats report saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_mouse\report-first-pass.stats.tsv
[265:07] Generating spectral library:
[265:07] 31605 precursors passing the FDR threshold are to be extracted
[265:07] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C3_rep1_re.raw
[265:48] 2210915 library precursors are potentially detectable
[265:49] 30 spectra added to the library
[265:49] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C3_rep2.raw
[266:40] 2210915 library precursors are potentially detectable
[266:41] 168 spectra added to the library
[266:41] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C3_rep3.raw
[267:31] 2210915 library precursors are potentially detectable
[267:32] 358 spectra added to the library
[267:32] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C4_rep1.raw
[268:25] 2210915 library precursors are potentially detectable
[268:26] 648 spectra added to the library
[268:26] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C4_rep2.raw
[269:32] 2210915 library precursors are potentially detectable
[269:33] 631 spectra added to the library
[269:33] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C4_rep3.raw
[270:36] 2210915 library precursors are potentially detectable
[270:36] 1139 spectra added to the library
[270:36] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T3_rep1.raw
[271:42] 2210915 library precursors are potentially detectable
[271:43] 700 spectra added to the library
[271:43] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T3_rep2.raw
[272:50] 2210915 library precursors are potentially detectable
[272:51] 1289 spectra added to the library
[272:51] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T3_rep3.raw
[274:03] 2210915 library precursors are potentially detectable
[274:04] 855 spectra added to the library
[274:04] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T4_rep1.raw
[275:14] 2210915 library precursors are potentially detectable
[275:15] 2477 spectra added to the library
[275:15] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T4_rep2.raw
[276:24] 2210915 library precursors are potentially detectable
[276:25] 715 spectra added to the library
[276:25] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T4_rep3.raw
[277:34] 2210915 library precursors are potentially detectable
[277:35] 354 spectra added to the library
[277:35] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T5_rep1.raw
[278:42] 2210915 library precursors are potentially detectable
[278:42] 83 spectra added to the library
[278:43] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T5_rep2.raw
[279:52] 2210915 library precursors are potentially detectable
[279:53] 785 spectra added to the library
[279:53] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T5_rep3.raw
[281:01] 2210915 library precursors are potentially detectable
[281:01] 1472 spectra added to the library
[281:01] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T6_rep1.raw
[282:22] 2210915 library precursors are potentially detectable
[282:23] 2666 spectra added to the library
[282:23] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T6_rep2.raw
[283:43] 2210915 library precursors are potentially detectable
[283:44] 9426 spectra added to the library
[283:44] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T6_rep3.raw
[284:58] 2210915 library precursors are potentially detectable
[284:59] 896 spectra added to the library
[284:59] Saving spectral library to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_mouse\lib.tsv
[285:43] 31605 precursors saved
[285:43] Loading the generated library and saving it in the .speclib format
[285:43] Loading spectral library W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_mouse\lib.tsv
[285:54] Spectral library loaded: 52347 protein isoforms, 19041 protein groups and 31605 precursors in 31017 elution groups.
[285:54] Loading protein annotations from FASTA W:\personal\KI\FASTA_Files_Libraries\uniprotkb_proteome_UP000000589_mouse_2024_02_07_SP_TB_canonical_isoform.fasta
[285:57] Loading protein annotations from FASTA W:\personal\KI\FASTA_Files_Libraries\uniprotkb_proteome_UP000005640_human 2024_02_07_SP_TB_canonical_isoform.fasta
[286:02] Gene names missing for some isoforms
[286:02] Library contains 40745 proteins, and 13507 genes
[286:02] Saving the library to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_mouse\lib.tsv.speclib

[286:15] Second pass: using the newly created spectral library to reanalyse the data
[286:15] File #1/18
[286:15] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C3_rep1_re.raw
[286:50] 31605 library precursors are potentially detectable
[286:50] Processing...
[286:51] RT window set to 1.01118
[286:51] Recommended MS1 mass accuracy setting: 5.25366 ppm
[286:52] Removing low confidence identifications
[286:52] Removing interfering precursors
[286:52] Training neural networks: 10161 targets, 2806 decoys
[286:52] Number of IDs at 0.01 FDR: 9239
[286:52] Translating peaks within elution groups
[286:52] Number of IDs at 0.01 FDR: 9276
[286:52] Calculating protein q-values
[286:52] Number of genes identified at 1% FDR: 2213 (precursor-level), 1984 (protein-level) (inference performed using proteotypic peptides only)
[286:52] Quantification

[286:53] File #2/18
[286:53] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C3_rep2.raw
[287:37] 31605 library precursors are potentially detectable
[287:37] Processing...
[287:38] RT window set to 1.21704
[287:38] Recommended MS1 mass accuracy setting: 4.27853 ppm
[287:38] Removing low confidence identifications
[287:38] Removing interfering precursors
[287:39] Training neural networks: 21728 targets, 6977 decoys
[287:40] Number of IDs at 0.01 FDR: 20062
[287:40] Translating peaks within elution groups
[287:40] Number of IDs at 0.01 FDR: 20121
[287:40] Calculating protein q-values
[287:40] Number of genes identified at 1% FDR: 3757 (precursor-level), 3317 (protein-level) (inference performed using proteotypic peptides only)
[287:40] Quantification

[287:40] File #3/18
[287:40] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C3_rep3.raw
[288:24] 31605 library precursors are potentially detectable
[288:24] Processing...
[288:26] RT window set to 1.02866
[288:26] Recommended MS1 mass accuracy setting: 3.89114 ppm
[288:26] Removing low confidence identifications
[288:26] Removing interfering precursors
[288:27] Training neural networks: 20419 targets, 6386 decoys
[288:27] Number of IDs at 0.01 FDR: 18877
[288:28] Translating peaks within elution groups
[288:28] Number of IDs at 0.01 FDR: 18946
[288:28] Calculating protein q-values
[288:28] Number of genes identified at 1% FDR: 3645 (precursor-level), 3236 (protein-level) (inference performed using proteotypic peptides only)
[288:28] Quantification

[288:28] File #4/18
[288:28] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C4_rep1.raw
[289:14] 31605 library precursors are potentially detectable
[289:14] Processing...
[289:15] RT window set to 1.09246
[289:15] Recommended MS1 mass accuracy setting: 3.81043 ppm
[289:16] Removing low confidence identifications
[289:16] Removing interfering precursors
[289:16] Training neural networks: 20515 targets, 7409 decoys
[289:17] Number of IDs at 0.01 FDR: 18480
[289:17] Translating peaks within elution groups
[289:17] Number of IDs at 0.01 FDR: 18550
[289:17] Calculating protein q-values
[289:17] Number of genes identified at 1% FDR: 3695 (precursor-level), 3338 (protein-level) (inference performed using proteotypic peptides only)
[289:17] Quantification

[289:18] File #5/18
[289:18] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C4_rep2.raw
[290:17] 31605 library precursors are potentially detectable
[290:17] Processing...
[290:18] RT window set to 1.19879
[290:18] Recommended MS1 mass accuracy setting: 4.52142 ppm
[290:19] Removing low confidence identifications
[290:19] Removing interfering precursors
[290:19] Training neural networks: 27390 targets, 10319 decoys
[290:20] Number of IDs at 0.01 FDR: 26373
[290:20] Translating peaks within elution groups
[290:20] Number of IDs at 0.01 FDR: 26466
[290:20] Calculating protein q-values
[290:21] Number of genes identified at 1% FDR: 4830 (precursor-level), 4266 (protein-level) (inference performed using proteotypic peptides only)
[290:21] Quantification

[290:21] File #6/18
[290:21] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_C4_rep3.raw
[291:16] 31605 library precursors are potentially detectable
[291:16] Processing...
[291:17] RT window set to 1.26235
[291:17] Recommended MS1 mass accuracy setting: 3.33773 ppm
[291:18] Removing low confidence identifications
[291:18] Removing interfering precursors
[291:18] Training neural networks: 25913 targets, 9218 decoys
[291:19] Number of IDs at 0.01 FDR: 24795
[291:19] Translating peaks within elution groups
[291:19] Number of IDs at 0.01 FDR: 24872
[291:19] Calculating protein q-values
[291:19] Number of genes identified at 1% FDR: 4629 (precursor-level), 4116 (protein-level) (inference performed using proteotypic peptides only)
[291:19] Quantification

[291:20] File #7/18
[291:20] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T3_rep1.raw
[292:19] 31605 library precursors are potentially detectable
[292:19] Processing...
[292:20] RT window set to 1.24746
[292:20] Recommended MS1 mass accuracy setting: 3.77655 ppm
[292:20] Removing low confidence identifications
[292:20] Removing interfering precursors
[292:21] Training neural networks: 26493 targets, 9707 decoys
[292:22] Number of IDs at 0.01 FDR: 25423
[292:22] Translating peaks within elution groups
[292:22] Number of IDs at 0.01 FDR: 25515
[292:22] Calculating protein q-values
[292:22] Number of genes identified at 1% FDR: 4434 (precursor-level), 3800 (protein-level) (inference performed using proteotypic peptides only)
[292:22] Quantification

[292:22] File #8/18
[292:22] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T3_rep2.raw
[293:22] 31605 library precursors are potentially detectable
[293:22] Processing...
[293:23] RT window set to 1.25341
[293:23] Recommended MS1 mass accuracy setting: 3.80255 ppm
[293:23] Removing low confidence identifications
[293:23] Removing interfering precursors
[293:24] Training neural networks: 26662 targets, 9452 decoys
[293:25] Number of IDs at 0.01 FDR: 25476
[293:25] Translating peaks within elution groups
[293:25] Number of IDs at 0.01 FDR: 25574
[293:25] Calculating protein q-values
[293:25] Number of genes identified at 1% FDR: 4340 (precursor-level), 3768 (protein-level) (inference performed using proteotypic peptides only)
[293:25] Quantification

[293:26] File #9/18
[293:26] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T3_rep3.raw
[294:32] 31605 library precursors are potentially detectable
[294:32] Processing...
[294:32] RT window set to 1.26653
[294:32] Recommended MS1 mass accuracy setting: 3.35487 ppm
[294:33] Removing low confidence identifications
[294:33] Removing interfering precursors
[294:33] Training neural networks: 27927 targets, 11642 decoys
[294:34] Number of IDs at 0.01 FDR: 26736
[294:35] Translating peaks within elution groups
[294:35] Number of IDs at 0.01 FDR: 26822
[294:35] Calculating protein q-values
[294:35] Number of genes identified at 1% FDR: 4565 (precursor-level), 3975 (protein-level) (inference performed using proteotypic peptides only)
[294:35] Quantification

[294:35] File #10/18
[294:35] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T4_rep1.raw
[295:39] 31605 library precursors are potentially detectable
[295:39] Processing...
[295:39] RT window set to 1.25094
[295:39] Recommended MS1 mass accuracy setting: 3.18959 ppm
[295:40] Removing low confidence identifications
[295:40] Removing interfering precursors
[295:41] Training neural networks: 28133 targets, 10867 decoys
[295:42] Number of IDs at 0.01 FDR: 27315
[295:42] Translating peaks within elution groups
[295:42] Number of IDs at 0.01 FDR: 27408
[295:42] Calculating protein q-values
[295:42] Number of genes identified at 1% FDR: 4809 (precursor-level), 4145 (protein-level) (inference performed using proteotypic peptides only)
[295:42] Quantification

[295:42] File #11/18
[295:42] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T4_rep2.raw
[296:45] 31605 library precursors are potentially detectable
[296:45] Processing...
[296:45] RT window set to 1.26496
[296:45] Recommended MS1 mass accuracy setting: 3.83517 ppm
[296:46] Removing low confidence identifications
[296:46] Removing interfering precursors
[296:47] Training neural networks: 27405 targets, 10534 decoys
[296:48] Number of IDs at 0.01 FDR: 26393
[296:48] Translating peaks within elution groups
[296:48] Number of IDs at 0.01 FDR: 26506
[296:48] Calculating protein q-values
[296:48] Number of genes identified at 1% FDR: 4749 (precursor-level), 4080 (protein-level) (inference performed using proteotypic peptides only)
[296:48] Quantification

[296:48] File #12/18
[296:48] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T4_rep3.raw
[297:51] 31605 library precursors are potentially detectable
[297:51] Processing...
[297:52] RT window set to 1.28774
[297:52] Recommended MS1 mass accuracy setting: 3.52909 ppm
[297:52] Removing low confidence identifications
[297:52] Removing interfering precursors
[297:53] Training neural networks: 27007 targets, 10718 decoys
[297:54] Number of IDs at 0.01 FDR: 26036
[297:54] Translating peaks within elution groups
[297:54] Number of IDs at 0.01 FDR: 26129
[297:54] Calculating protein q-values
[297:54] Number of genes identified at 1% FDR: 4695 (precursor-level), 4097 (protein-level) (inference performed using proteotypic peptides only)
[297:54] Quantification

[297:55] File #13/18
[297:55] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T5_rep1.raw
[298:55] 31605 library precursors are potentially detectable
[298:55] Processing...
[298:56] RT window set to 1.28065
[298:56] Recommended MS1 mass accuracy setting: 3.39596 ppm
[298:56] Removing low confidence identifications
[298:56] Removing interfering precursors
[298:57] Training neural networks: 25800 targets, 9641 decoys
[298:58] Number of IDs at 0.01 FDR: 24703
[298:58] Translating peaks within elution groups
[298:58] Number of IDs at 0.01 FDR: 24792
[298:58] Calculating protein q-values
[298:58] Number of genes identified at 1% FDR: 4387 (precursor-level), 3788 (protein-level) (inference performed using proteotypic peptides only)
[298:58] Quantification

[298:58] File #14/18
[298:58] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T5_rep2.raw
[300:01] 31605 library precursors are potentially detectable
[300:01] Processing...
[300:02] RT window set to 1.26165
[300:02] Recommended MS1 mass accuracy setting: 3.57507 ppm
[300:02] Removing low confidence identifications
[300:02] Removing interfering precursors
[300:03] Training neural networks: 27536 targets, 10599 decoys
[300:04] Number of IDs at 0.01 FDR: 26567
[300:04] Translating peaks within elution groups
[300:04] Number of IDs at 0.01 FDR: 26650
[300:04] Calculating protein q-values
[300:04] Number of genes identified at 1% FDR: 4627 (precursor-level), 4059 (protein-level) (inference performed using proteotypic peptides only)
[300:04] Quantification

[300:05] File #15/18
[300:05] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T5_rep3.raw
[301:05] 31605 library precursors are potentially detectable
[301:05] Processing...
[301:06] RT window set to 1.26324
[301:06] Recommended MS1 mass accuracy setting: 3.30098 ppm
[301:07] Removing low confidence identifications
[301:07] Removing interfering precursors
[301:07] Training neural networks: 27129 targets, 10111 decoys
[301:08] Number of IDs at 0.01 FDR: 26158
[301:08] Translating peaks within elution groups
[301:09] Number of IDs at 0.01 FDR: 26244
[301:09] Calculating protein q-values
[301:09] Number of genes identified at 1% FDR: 4588 (precursor-level), 3926 (protein-level) (inference performed using proteotypic peptides only)
[301:09] Quantification

[301:09] File #16/18
[301:09] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T6_rep1.raw
[302:22] 31605 library precursors are potentially detectable
[302:23] Processing...
[302:23] RT window set to 1.30319
[302:23] Recommended MS1 mass accuracy setting: 3.19062 ppm
[302:24] Removing low confidence identifications
[302:24] Removing interfering precursors
[302:25] Training neural networks: 30061 targets, 13400 decoys
[302:26] Number of IDs at 0.01 FDR: 29552
[302:26] Translating peaks within elution groups
[302:26] Number of IDs at 0.01 FDR: 29694
[302:26] Calculating protein q-values
[302:26] Number of genes identified at 1% FDR: 5153 (precursor-level), 4347 (protein-level) (inference performed using proteotypic peptides only)
[302:26] Quantification

[302:26] File #17/18
[302:26] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T6_rep2.raw
[303:40] 31605 library precursors are potentially detectable
[303:40] Processing...
[303:41] RT window set to 1.30684
[303:41] Recommended MS1 mass accuracy setting: 3.14293 ppm
[303:42] Removing low confidence identifications
[303:42] Removing interfering precursors
[303:42] Training neural networks: 29811 targets, 13319 decoys
[303:43] Number of IDs at 0.01 FDR: 29122
[303:44] Translating peaks within elution groups
[303:44] Number of IDs at 0.01 FDR: 29259
[303:44] Calculating protein q-values
[303:44] Number of genes identified at 1% FDR: 5051 (precursor-level), 4284 (protein-level) (inference performed using proteotypic peptides only)
[303:44] Quantification

[303:44] File #18/18
[303:44] Loading run W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\20240221_KI_MM_81_Wenyi_T6_rep3.raw
[304:51] 31605 library precursors are potentially detectable
[304:51] Processing...
[304:52] RT window set to 1.32264
[304:52] Recommended MS1 mass accuracy setting: 3.27553 ppm
[304:53] Removing low confidence identifications
[304:53] Removing interfering precursors
[304:53] Training neural networks: 28171 targets, 12521 decoys
[304:54] Number of IDs at 0.01 FDR: 27012
[304:55] Translating peaks within elution groups
[304:55] Number of IDs at 0.01 FDR: 27122
[304:55] Calculating protein q-values
[304:55] Number of genes identified at 1% FDR: 4848 (precursor-level), 4079 (protein-level) (inference performed using proteotypic peptides only)
[304:55] Quantification

[304:55] Cross-run analysis
[304:55] Reading quantification information: 18 files
[304:56] Quantifying peptides
[305:01] Quantifying proteins
[305:02] Calculating q-values for protein and gene groups
[305:03] Calculating global q-values for protein and gene groups
[305:03] Writing report
[307:26] Report saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_mouse\report.tsv.
[307:26] Saving precursor levels matrix
[307:32] 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_mouse\report.pr_matrix.tsv.
[307:32] Saving protein group levels matrix
[307:34] 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_mouse\report.pg_matrix.tsv.
[307:34] Saving gene group levels matrix
[307:35] 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_mouse\report.gg_matrix.tsv.
[307:35] Saving unique genes levels matrix
[307:35] 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_mouse\report.unique_genes_matrix.tsv.
[307:35] Stats report saved to W:\mass_data\Eclipse\2024_02\20240221_81_Wenyi_EV\81_Wenyi_EV_DIANN\human_mouse\report.stats.tsv

Finished

