DIA-NN 1.9.1 (Data-Independent Acquisition by Neural Networks)
Compiled on Jul 15 2024 15:40:36
Current date and time: Mon Oct 14 09:25:50 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_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_4factor_10e4_rep1.raw  --f W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_4factor_10e4_rep2.raw  --f W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_4factor_10e4_rep3.raw  --f W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_8factor_10e4_rep1.raw  --f W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_8factor_10e4_rep2.raw  --f W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_8factor_10e4_rep3.raw  --f W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_100eggs_rep1.raw  --f W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_100eggs_rep2.raw  --f W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_100eggs_rep3.raw  --lib  --threads 18 --verbose 1 --out W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\report.tsv --qvalue 0.01 --matrices --out-lib W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\lib.parquet --gen-spec-lib --predictor --fasta camprotR_240512_cRAP_20190401_full_tags.fasta --cont-quant-exclude cRAP- --fasta C:\Users\liqer\Box\Per_210963_Koshi Imami\Data\Database\uniprotkb_proteome_UP000000589_mouse_2024_02_07_SP_TB_canonical_isoform.fasta --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --met-excision --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --cut K*,R* --missed-cleavages 1 --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --reanalyse --relaxed-prot-inf --rt-profiling --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
Peptides corresponding to protein sequence IDs tagged with cRAP- will be excluded from normalisation as well as quantification of protein groups that do not include proteins bearing the tag
DIA-NN will carry out FASTA digest for in silico lib generation
Min fragment m/z set to 200
Max fragment m/z set to 1800
N-terminal methionine excision enabled
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
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
Cysteine carbamidomethylation enabled as a fixed modification
Maximum number of variable modifications set to 1
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
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
Heuristic protein grouping will be used, to reduce the number of protein groups obtained; this mode is recommended for benchmarking protein ID numbers, GO/pathway and system-scale analyses
The spectral library (if generated) will retain the original spectra but will include empirically-aligned RTs
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
Heuristic protein grouping will be used, to reduce the number of protein groups obtained; this mode is recommended for benchmarking protein ID numbers, GO/pathway and system-scale analyses
Precursor/protein x sample matrices will be filtered at 0.01 precursor & protein-level FDR
Protein x sample matrices will be filtered at 0.001 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.
WARNING: it is strongly recommended to first generate an in silico-predicted library in a separate pipeline step and then use it to process the raw data, now without activating FASTA digest
WARNING: peptidoform scoring enabled because variable modifications have been declared; to disable, use --no-peptidoforms
The following variable modifications will be scored: UniMod:35 

9 files will be processed
[0:00] Loading FASTA camprotR_240512_cRAP_20190401_full_tags.fasta
[0:00] Loading FASTA C:\Users\liqer\Box\Per_210963_Koshi Imami\Data\Database\uniprotkb_proteome_UP000000589_mouse_2024_02_07_SP_TB_canonical_isoform.fasta
[0:12] Processing FASTA
[0:22] Assembling elution groups
[0:32] 6344566 precursors generated
[0:32] Gene names missing for some isoforms
[0:32] Library contains 54728 proteins, and 22065 genes
[0:37] [0:51] [11:09] [12:09] [12:16] [12:17] Saving the library to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\lib.predicted.speclib
[31:46] Initialising library
[31:59] Loading spectral library W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\lib.predicted.speclib
[37:18] Library annotated with sequence database(s): camprotR_240512_cRAP_20190401_full_tags.fasta; C:\Users\liqer\Box\Per_210963_Koshi Imami\Data\Database\uniprotkb_proteome_UP000000589_mouse_2024_02_07_SP_TB_canonical_isoform.fasta
[37:20] Spectral library loaded: 63094 protein isoforms, 107324 protein groups and 6344566 precursors in 1974827 elution groups.
[37:20] Loading protein annotations from FASTA camprotR_240512_cRAP_20190401_full_tags.fasta
[37:20] Loading protein annotations from FASTA C:\Users\liqer\Box\Per_210963_Koshi Imami\Data\Database\uniprotkb_proteome_UP000000589_mouse_2024_02_07_SP_TB_canonical_isoform.fasta
[37:23] Annotating library proteins with information from the FASTA database
[37:23] Gene names missing for some isoforms
[37:23] Library contains 54728 proteins, and 22065 genes
[37:29] [37:42] [47:57] [48:57] [49:03] [49:04] Saving the library to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\lib.predicted.speclib
[68:43] Initialising library

First pass: generating a spectral library from DIA data

[68:54] File #1/9
[68:54] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_4factor_10e4_rep1.raw
[70:36] 1656837 library precursors are potentially detectable
[70:37] Processing...
[70:49] RT window set to 2.04631
[70:49] Peak width: 2.992
[70:49] Scan window radius set to 6
[70:49] Recommended MS1 mass accuracy setting: 2.63362 ppm
[71:03] Optimised mass accuracy: 21.105 ppm
[71:41] Removing low confidence identifications
[71:56] Precursors at 1% peptidoform FDR: 26729
[71:57] Removing interfering precursors
[72:00] Training neural networks: 59935 targets, 34281 decoys
[72:04] Number of IDs at 0.01 FDR: 38123
[72:04] Translating peaks within elution groups
[72:04] Number of IDs at 0.01 FDR: 38183
[72:09] Precursors at 1% peptidoform FDR: 28919
[72:10] Calculating protein q-values
[72:10] Number of genes identified at 1% FDR: 9530 (precursor-level), 9360 (protein-level) (inference performed using proteotypic peptides only)
[72:11] Quantification
[72:11] Precursors with monitored PTMs at 1% FDR: 4266 out of 11786 considered
[72:11] Unmodified precursors with monitored PTM sites at 1% FDR: 22
[72:11] Precursors with PTMs localised (when required) with > 90% confidence: 4265 out of 4266
[72:26] Quantification information saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_4factor_10e4_rep1.raw.quant

[72:26] File #2/9
[72:26] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_4factor_10e4_rep2.raw
[74:07] 1656837 library precursors are potentially detectable
[74:08] Processing...
[74:21] RT window set to 2.47609
[74:21] Recommended MS1 mass accuracy setting: 2.70938 ppm
[75:09] Removing low confidence identifications
[75:28] Precursors at 1% peptidoform FDR: 27330
[75:29] Removing interfering precursors
[75:32] Training neural networks: 62030 targets, 35393 decoys
[75:36] Number of IDs at 0.01 FDR: 38337
[75:36] Translating peaks within elution groups
[75:37] Number of IDs at 0.01 FDR: 38401
[75:42] Precursors at 1% peptidoform FDR: 28247
[75:43] Calculating protein q-values
[75:43] Number of genes identified at 1% FDR: 9675 (precursor-level), 9482 (protein-level) (inference performed using proteotypic peptides only)
[75:43] Quantification
[75:44] Precursors with monitored PTMs at 1% FDR: 4155 out of 12360 considered
[75:44] Unmodified precursors with monitored PTM sites at 1% FDR: 51
[75:44] Precursors with PTMs localised (when required) with > 90% confidence: 4153 out of 4155
[75:58] Quantification information saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_4factor_10e4_rep2.raw.quant

[75:58] File #3/9
[75:58] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_4factor_10e4_rep3.raw
[77:34] 1656837 library precursors are potentially detectable
[77:35] Processing...
[77:48] RT window set to 2.2222
[77:48] Recommended MS1 mass accuracy setting: 2.52727 ppm
[78:32] Removing low confidence identifications
[78:49] Precursors at 1% peptidoform FDR: 27605
[78:50] Removing interfering precursors
[78:53] Training neural networks: 63177 targets, 35909 decoys
[78:57] Number of IDs at 0.01 FDR: 39379
[78:57] Translating peaks within elution groups
[78:57] Number of IDs at 0.01 FDR: 39453
[79:03] Precursors at 1% peptidoform FDR: 28468
[79:03] Calculating protein q-values
[79:04] Number of genes identified at 1% FDR: 9775 (precursor-level), 9546 (protein-level) (inference performed using proteotypic peptides only)
[79:04] Quantification
[79:04] Precursors with monitored PTMs at 1% FDR: 4185 out of 12681 considered
[79:04] Unmodified precursors with monitored PTM sites at 1% FDR: 56
[79:04] Precursors with PTMs localised (when required) with > 90% confidence: 4183 out of 4185
[79:19] Quantification information saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_4factor_10e4_rep3.raw.quant

[79:19] File #4/9
[79:19] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_8factor_10e4_rep1.raw
[80:34] 1656837 library precursors are potentially detectable
[80:35] Processing...
[80:47] RT window set to 1.81434
[80:47] Recommended MS1 mass accuracy setting: 2.75531 ppm
[81:18] Removing low confidence identifications
[81:30] Precursors at 1% peptidoform FDR: 24134
[81:31] Removing interfering precursors
[81:34] Training neural networks: 56014 targets, 32780 decoys
[81:38] Number of IDs at 0.01 FDR: 35553
[81:38] Translating peaks within elution groups
[81:39] Number of IDs at 0.01 FDR: 35612
[81:44] Precursors at 1% peptidoform FDR: 27263
[81:45] Calculating protein q-values
[81:45] Number of genes identified at 1% FDR: 9139 (precursor-level), 8968 (protein-level) (inference performed using proteotypic peptides only)
[81:46] Quantification
[81:46] Precursors with monitored PTMs at 1% FDR: 4218 out of 11168 considered
[81:46] Unmodified precursors with monitored PTM sites at 1% FDR: 4
[81:46] Precursors with PTMs localised (when required) with > 90% confidence: 4218 out of 4218
[81:59] Quantification information saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_8factor_10e4_rep1.raw.quant

[81:59] File #5/9
[81:59] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_8factor_10e4_rep2.raw
[83:40] 1656837 library precursors are potentially detectable
[83:41] Processing...
[83:56] RT window set to 2.56909
[83:56] Recommended MS1 mass accuracy setting: 2.67131 ppm
[84:50] Removing low confidence identifications
[85:10] Precursors at 1% peptidoform FDR: 25042
[85:11] Removing interfering precursors
[85:14] Training neural networks: 59258 targets, 33174 decoys
[85:18] Number of IDs at 0.01 FDR: 36047
[85:18] Translating peaks within elution groups
[85:18] Number of IDs at 0.01 FDR: 36107
[85:23] Precursors at 1% peptidoform FDR: 25753
[85:24] Calculating protein q-values
[85:25] Number of genes identified at 1% FDR: 9639 (precursor-level), 9465 (protein-level) (inference performed using proteotypic peptides only)
[85:25] Quantification
[85:25] Precursors with monitored PTMs at 1% FDR: 3685 out of 11830 considered
[85:25] Unmodified precursors with monitored PTM sites at 1% FDR: 38
[85:25] Precursors with PTMs localised (when required) with > 90% confidence: 3685 out of 3685
[85:39] Quantification information saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_8factor_10e4_rep2.raw.quant

[85:39] File #6/9
[85:39] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_8factor_10e4_rep3.raw
[87:21] 1656837 library precursors are potentially detectable
[87:23] Processing...
[87:36] RT window set to 2.64448
[87:36] Recommended MS1 mass accuracy setting: 2.74169 ppm
[88:29] Removing low confidence identifications
[88:50] Precursors at 1% peptidoform FDR: 27659
[88:51] Removing interfering precursors
[88:54] Training neural networks: 62071 targets, 36004 decoys
[88:59] Number of IDs at 0.01 FDR: 38689
[88:59] Translating peaks within elution groups
[88:59] Number of IDs at 0.01 FDR: 38750
[89:05] Precursors at 1% peptidoform FDR: 27941
[89:05] Calculating protein q-values
[89:06] Number of genes identified at 1% FDR: 9830 (precursor-level), 9641 (protein-level) (inference performed using proteotypic peptides only)
[89:06] Quantification
[89:07] Precursors with monitored PTMs at 1% FDR: 3872 out of 13506 considered
[89:07] Unmodified precursors with monitored PTM sites at 1% FDR: 924
[89:07] Precursors with PTMs localised (when required) with > 90% confidence: 3860 out of 3872
[89:21] Quantification information saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_8factor_10e4_rep3.raw.quant

[89:21] File #7/9
[89:21] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_100eggs_rep1.raw
[90:23] 1656837 library precursors are potentially detectable
[90:24] Processing...
[90:41] RT window set to 2.32944
[90:42] Recommended MS1 mass accuracy setting: 2.88552 ppm
[91:14] Removing low confidence identifications
[91:24] Precursors at 1% peptidoform FDR: 15663
[91:25] Removing interfering precursors
[91:28] Training neural networks: 35156 targets, 20520 decoys
[91:31] Number of IDs at 0.01 FDR: 22473
[91:31] Translating peaks within elution groups
[91:31] Number of IDs at 0.01 FDR: 22511
[91:35] Precursors at 1% peptidoform FDR: 16885
[91:36] Calculating protein q-values
[91:36] Number of genes identified at 1% FDR: 6806 (precursor-level), 6659 (protein-level) (inference performed using proteotypic peptides only)
[91:36] Quantification
[91:37] Precursors with monitored PTMs at 1% FDR: 2542 out of 6910 considered
[91:37] Unmodified precursors with monitored PTM sites at 1% FDR: 11
[91:37] Precursors with PTMs localised (when required) with > 90% confidence: 2542 out of 2542
[91:45] Quantification information saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_100eggs_rep1.raw.quant

[91:45] File #8/9
[91:45] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_100eggs_rep2.raw
[92:46] 1656837 library precursors are potentially detectable
[92:47] Processing...
[93:02] RT window set to 2.27442
[93:02] Recommended MS1 mass accuracy setting: 2.52986 ppm
[93:35] Removing low confidence identifications
[93:45] Precursors at 1% peptidoform FDR: 18305
[93:46] Removing interfering precursors
[93:49] Training neural networks: 40705 targets, 23706 decoys
[93:52] Number of IDs at 0.01 FDR: 26327
[93:52] Translating peaks within elution groups
[93:52] Number of IDs at 0.01 FDR: 26354
[93:56] Precursors at 1% peptidoform FDR: 19612
[93:57] Calculating protein q-values
[93:58] Number of genes identified at 1% FDR: 7447 (precursor-level), 7172 (protein-level) (inference performed using proteotypic peptides only)
[93:58] Quantification
[93:58] Precursors with monitored PTMs at 1% FDR: 3036 out of 8115 considered
[93:58] Unmodified precursors with monitored PTM sites at 1% FDR: 7
[93:58] Precursors with PTMs localised (when required) with > 90% confidence: 3034 out of 3036
[98:39] Quantification information saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_100eggs_rep2.raw.quant

[98:39] File #9/9
[98:39] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_100eggs_rep3.raw
[100:38] 1656837 library precursors are potentially detectable
[100:39] Processing...
[100:55] RT window set to 2.02429
[100:55] Recommended MS1 mass accuracy setting: 3.14631 ppm
[101:28] Removing low confidence identifications
[101:39] Precursors at 1% peptidoform FDR: 19250
[101:40] Removing interfering precursors
[101:43] Training neural networks: 44508 targets, 25761 decoys
[101:47] Number of IDs at 0.01 FDR: 28028
[101:47] Translating peaks within elution groups
[101:47] Number of IDs at 0.01 FDR: 28060
[101:51] Precursors at 1% peptidoform FDR: 20959
[101:52] Calculating protein q-values
[101:53] Number of genes identified at 1% FDR: 7808 (precursor-level), 7601 (protein-level) (inference performed using proteotypic peptides only)
[101:53] Quantification
[101:53] Precursors with monitored PTMs at 1% FDR: 3198 out of 8920 considered
[101:53] Unmodified precursors with monitored PTM sites at 1% FDR: 10
[101:53] Precursors with PTMs localised (when required) with > 90% confidence: 3198 out of 3198
[107:05] Quantification information saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_100eggs_rep3.raw.quant

[107:05] Cross-run analysis
[107:05] Reading quantification information: 9 files
[108:15] Quantifying peptides
[108:32] Assembling protein groups
[108:36] Quantifying proteins
[108:36] Calculating q-values for protein and gene groups
[108:39] Calculating global q-values for protein and gene groups
[108:40] Protein groups with global q-value <= 0.01: 16642
[109:14] Compressed report saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\report-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[109:17] Writing report
[131:00] Report saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\report-first-pass.tsv.
[131:00] Saving precursor levels matrix
[131:06] Precursor levels matrix (1% precursor and protein group FDR) saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\report-first-pass.pr_matrix.tsv.
[131:06] Manifest saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\report-first-pass.manifest.txt
[131:06] Stats report saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\report-first-pass.stats.tsv
[131:06] Generating spectral library:
[131:11] 74335 target and 471 decoy precursors saved
[131:11] Spectral library saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\lib.parquet

[131:13] Loading spectral library W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\lib.parquet
[131:16] Spectral library loaded: 20941 protein isoforms, 16933 protein groups and 74806 precursors in 74466 elution groups.
[131:16] Loading protein annotations from FASTA camprotR_240512_cRAP_20190401_full_tags.fasta
[131:16] Loading protein annotations from FASTA C:\Users\liqer\Box\Per_210963_Koshi Imami\Data\Database\uniprotkb_proteome_UP000000589_mouse_2024_02_07_SP_TB_canonical_isoform.fasta
[131:20] Annotating library proteins with information from the FASTA database
[131:20] Gene names missing for some isoforms
[131:20] Library contains 17675 proteins, and 15167 genes
[131:20] Initialising library
[131:20] Saving the library to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\lib.parquet.skyline.speclib


Second pass: using the newly created spectral library to reanalyse the data

[131:28] File #1/9
[131:28] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_4factor_10e4_rep1.raw
[132:58] 74335 library precursors are potentially detectable
[132:58] Processing...
[132:59] RT window set to 1.10484
[132:59] Recommended MS1 mass accuracy setting: 2.47972 ppm
[133:01] Removing low confidence identifications
[133:02] Precursors at 1% peptidoform FDR: 28826
[133:02] Removing interfering precursors
[133:02] Training neural networks: 58953 targets, 31089 decoys
[133:05] Number of IDs at 0.01 FDR: 37176
[133:05] Translating peaks within elution groups
[133:05] Number of IDs at 0.01 FDR: 37201
[133:08] Precursors at 1% peptidoform FDR: 29820
[133:08] Calculating protein q-values
[133:08] Number of genes identified at 1% FDR: 9283 (precursor-level), 8550 (protein-level) (inference performed using proteotypic peptides only)
[133:08] Quantification
[133:08] Precursors with monitored PTMs at 1% FDR: 4648 out of 10453 considered
[133:08] Unmodified precursors with monitored PTM sites at 1% FDR: 39
[133:08] Precursors with PTMs localised (when required) with > 90% confidence: 4646 out of 4648

[133:08] File #2/9
[133:08] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_4factor_10e4_rep2.raw
[134:42] 74335 library precursors are potentially detectable
[134:42] Processing...
[134:43] RT window set to 1.10825
[134:43] Recommended MS1 mass accuracy setting: 2.58454 ppm
[134:45] Removing low confidence identifications
[134:46] Precursors at 1% peptidoform FDR: 28342
[134:46] Removing interfering precursors
[134:47] Training neural networks: 58213 targets, 30715 decoys
[134:49] Number of IDs at 0.01 FDR: 35854
[134:49] Translating peaks within elution groups
[134:49] Number of IDs at 0.01 FDR: 35882
[134:52] Precursors at 1% peptidoform FDR: 29248
[134:52] Calculating protein q-values
[134:52] Number of genes identified at 1% FDR: 8968 (precursor-level), 8350 (protein-level) (inference performed using proteotypic peptides only)
[134:52] Quantification
[134:52] Precursors with monitored PTMs at 1% FDR: 4541 out of 9620 considered
[134:52] Unmodified precursors with monitored PTM sites at 1% FDR: 67
[134:52] Precursors with PTMs localised (when required) with > 90% confidence: 4540 out of 4541

[134:53] File #3/9
[134:53] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_4factor_10e4_rep3.raw
[136:22] 74335 library precursors are potentially detectable
[136:22] Processing...
[136:22] RT window set to 1.1073
[136:22] Recommended MS1 mass accuracy setting: 2.41804 ppm
[136:25] Removing low confidence identifications
[136:25] Precursors at 1% peptidoform FDR: 28329
[136:26] Removing interfering precursors
[136:26] Training neural networks: 58846 targets, 31090 decoys
[136:29] Number of IDs at 0.01 FDR: 37508
[136:29] Translating peaks within elution groups
[136:29] Number of IDs at 0.01 FDR: 37537
[136:32] Precursors at 1% peptidoform FDR: 29572
[136:32] Calculating protein q-values
[136:32] Number of genes identified at 1% FDR: 9382 (precursor-level), 8609 (protein-level) (inference performed using proteotypic peptides only)
[136:32] Quantification
[136:32] Precursors with monitored PTMs at 1% FDR: 4621 out of 10910 considered
[136:32] Unmodified precursors with monitored PTM sites at 1% FDR: 70
[136:32] Precursors with PTMs localised (when required) with > 90% confidence: 4619 out of 4621

[136:32] File #4/9
[136:32] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_8factor_10e4_rep1.raw
[137:35] 74335 library precursors are potentially detectable
[137:35] Processing...
[137:36] RT window set to 1.08808
[137:36] Recommended MS1 mass accuracy setting: 2.97095 ppm
[137:37] Removing low confidence identifications
[137:38] Precursors at 1% peptidoform FDR: 27409
[137:38] Removing interfering precursors
[137:38] Training neural networks: 52849 targets, 28292 decoys
[137:41] Number of IDs at 0.01 FDR: 34116
[137:41] Translating peaks within elution groups
[137:41] Number of IDs at 0.01 FDR: 34156
[137:44] Precursors at 1% peptidoform FDR: 28270
[137:44] Calculating protein q-values
[137:44] Number of genes identified at 1% FDR: 8501 (precursor-level), 7745 (protein-level) (inference performed using proteotypic peptides only)
[137:44] Quantification
[137:44] Precursors with monitored PTMs at 1% FDR: 4590 out of 9036 considered
[137:44] Unmodified precursors with monitored PTM sites at 1% FDR: 14
[137:44] Precursors with PTMs localised (when required) with > 90% confidence: 4588 out of 4590

[137:44] File #5/9
[137:44] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_8factor_10e4_rep2.raw
[139:18] 74335 library precursors are potentially detectable
[139:18] Processing...
[139:19] RT window set to 1.10375
[139:19] Recommended MS1 mass accuracy setting: 2.46389 ppm
[139:21] Removing low confidence identifications
[139:22] Precursors at 1% peptidoform FDR: 26209
[139:22] Removing interfering precursors
[139:23] Training neural networks: 57331 targets, 30271 decoys
[139:25] Number of IDs at 0.01 FDR: 34224
[139:25] Translating peaks within elution groups
[139:25] Number of IDs at 0.01 FDR: 34264
[139:28] Precursors at 1% peptidoform FDR: 27333
[139:28] Calculating protein q-values
[139:28] Number of genes identified at 1% FDR: 9191 (precursor-level), 8505 (protein-level) (inference performed using proteotypic peptides only)
[139:28] Quantification
[139:29] Precursors with monitored PTMs at 1% FDR: 4268 out of 9797 considered
[139:29] Unmodified precursors with monitored PTM sites at 1% FDR: 45
[139:29] Precursors with PTMs localised (when required) with > 90% confidence: 4267 out of 4268

[139:29] File #6/9
[139:29] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_8factor_10e4_rep3.raw
[141:05] 74335 library precursors are potentially detectable
[141:05] Processing...
[141:06] RT window set to 1.11191
[141:06] Recommended MS1 mass accuracy setting: 2.38802 ppm
[141:08] Removing low confidence identifications
[141:09] Precursors at 1% peptidoform FDR: 28215
[141:09] Removing interfering precursors
[141:10] Training neural networks: 57197 targets, 30422 decoys
[141:12] Number of IDs at 0.01 FDR: 35265
[141:12] Translating peaks within elution groups
[141:12] Number of IDs at 0.01 FDR: 35304
[141:15] Precursors at 1% peptidoform FDR: 29121
[141:15] Calculating protein q-values
[141:15] Number of genes identified at 1% FDR: 8866 (precursor-level), 8141 (protein-level) (inference performed using proteotypic peptides only)
[141:15] Quantification
[141:15] Precursors with monitored PTMs at 1% FDR: 4409 out of 9569 considered
[141:15] Unmodified precursors with monitored PTM sites at 1% FDR: 658
[141:15] Precursors with PTMs localised (when required) with > 90% confidence: 4402 out of 4409

[141:16] File #7/9
[141:16] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_100eggs_rep1.raw
[142:08] 74335 library precursors are potentially detectable
[142:08] Processing...
[142:09] RT window set to 1.06449
[142:09] Recommended MS1 mass accuracy setting: 3.07228 ppm
[142:10] Removing low confidence identifications
[142:11] Precursors at 1% peptidoform FDR: 17308
[142:11] Removing interfering precursors
[142:11] Training neural networks: 37546 targets, 20661 decoys
[142:13] Number of IDs at 0.01 FDR: 21716
[142:13] Translating peaks within elution groups
[142:13] Number of IDs at 0.01 FDR: 21756
[142:15] Precursors at 1% peptidoform FDR: 18419
[142:15] Calculating protein q-values
[142:15] Number of genes identified at 1% FDR: 6419 (precursor-level), 5574 (protein-level) (inference performed using proteotypic peptides only)
[142:15] Quantification
[142:15] Precursors with monitored PTMs at 1% FDR: 3041 out of 5665 considered
[142:15] Unmodified precursors with monitored PTM sites at 1% FDR: 11
[142:15] Precursors with PTMs localised (when required) with > 90% confidence: 3041 out of 3041

[142:15] File #8/9
[142:15] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_100eggs_rep2.raw
[143:09] 74335 library precursors are potentially detectable
[143:09] Processing...
[143:10] RT window set to 1.0807
[143:10] Recommended MS1 mass accuracy setting: 2.95447 ppm
[143:12] Removing low confidence identifications
[143:12] Precursors at 1% peptidoform FDR: 19397
[143:12] Removing interfering precursors
[143:13] Training neural networks: 42357 targets, 23045 decoys
[143:15] Number of IDs at 0.01 FDR: 25340
[143:15] Translating peaks within elution groups
[143:15] Number of IDs at 0.01 FDR: 25384
[143:17] Precursors at 1% peptidoform FDR: 20969
[143:17] Calculating protein q-values
[143:17] Number of genes identified at 1% FDR: 7057 (precursor-level), 6188 (protein-level) (inference performed using proteotypic peptides only)
[143:17] Quantification
[143:17] Precursors with monitored PTMs at 1% FDR: 3508 out of 6972 considered
[143:17] Unmodified precursors with monitored PTM sites at 1% FDR: 11
[143:17] Precursors with PTMs localised (when required) with > 90% confidence: 3507 out of 3508

[143:17] File #9/9
[143:17] Loading run W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\20241011_KI_MM_128_IshiuchiLab_100eggs_rep3.raw
[144:16] 74335 library precursors are potentially detectable
[144:16] Processing...
[144:16] RT window set to 1.08822
[144:16] Recommended MS1 mass accuracy setting: 2.90867 ppm
[144:18] Removing low confidence identifications
[144:18] Precursors at 1% peptidoform FDR: 20839
[144:18] Removing interfering precursors
[144:19] Training neural networks: 45532 targets, 24612 decoys
[144:21] Number of IDs at 0.01 FDR: 26900
[144:21] Translating peaks within elution groups
[144:21] Number of IDs at 0.01 FDR: 26942
[144:23] Precursors at 1% peptidoform FDR: 22137
[144:23] Calculating protein q-values
[144:23] Number of genes identified at 1% FDR: 7345 (precursor-level), 6531 (protein-level) (inference performed using proteotypic peptides only)
[144:23] Quantification
[144:23] Precursors with monitored PTMs at 1% FDR: 3688 out of 7498 considered
[144:23] Unmodified precursors with monitored PTM sites at 1% FDR: 16
[144:23] Precursors with PTMs localised (when required) with > 90% confidence: 3688 out of 3688

[144:23] Cross-run analysis
[144:23] Reading quantification information: 9 files
[144:25] Quantifying peptides
[146:13] Quantification parameters: 0.212229, 0.00239056, 0.000689655, 0.0111782, 0.0125894, 0.0119507, 0.118207, 0.0378466, 0.022877, 0.0140366, 0.0430634, 0.0224648, 0.387253, 0.0503926, 0.057898, 0.0132687
[146:21] Quantifying proteins
[146:21] Calculating q-values for protein and gene groups
[146:21] Calculating global q-values for protein and gene groups
[146:21] Protein groups with global q-value <= 0.01: 11523
[146:28] Compressed report saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\report.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[146:28] Writing report
[147:40] Report saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\report.tsv.
[147:40] Saving precursor levels matrix
[147:45] Precursor levels matrix (1% precursor and protein group FDR) saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\report.pr_matrix.tsv.
[147:45] Saving protein group levels matrix
[147:45] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\report.pg_matrix.tsv.
[147:45] Saving gene group levels matrix
[147:46] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\report.gg_matrix.tsv.
[147:46] Saving unique genes levels matrix
[147:46] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\report.unique_genes_matrix.tsv.
[147:51] Manifest saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\report.manifest.txt
[147:51] Stats report saved to W:\mass_data\Eclipse\2024_10\20241011_128_IshiuchiLab_egg\diann\report.stats.tsv

