DIA-NN 2.3.2 Academia  (Data-Independent Acquisition by Neural Networks)
Compiled on Jan 22 2026 10:50:24
Current date and time: Mon May  4 09:33:22 2026
CPU: GenuineIntel 13th Gen Intel(R) Core(TM) i9-13900K
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 
Logical CPU cores: 32
110Gb out of 127Gb RAM is free
diann.exe --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S01.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S02.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S03.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S04.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S05.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S06.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S07.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S08.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S09.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S10.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S11.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S12.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S13.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S14.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S15.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S16.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S17.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S18.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S19.raw  --f D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S20.raw  --lib C:\FASTAs\Spectral_Libraries\20260223_Homo_sapiens.predicted.speclib --threads 24 --verbose 1 --out D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report.parquet --qvalue 0.05 --matrices --out-lib D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report-lib.parquet --gen-spec-lib --xic --fasta camprotR_240512_cRAP_20190401_full_tags.fasta --cont-quant-exclude cRAP- --fasta C:\FASTAs\Spectral_Libraries\20260129_Uniprot_human_can+iso.fasta --met-excision --min-pep-len 7 --max-pep-len 30 --min-pr-mz 380 --max-pr-mz 980 --min-pr-charge 2 --max-pr-charge 5 --min-fr-mz 150 --max-fr-mz 2000 --cut K*,R* --missed-cleavages 2 --unimod4 --var-mods 3 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --var-mod UniMod:21,79.966331,STY --proteoforms --reanalyse --rt-profiling --pg-level 0 

Thread number set to 24
Output will be filtered at 0.05 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
A spectral library will be generated
XICs within 10 seconds from the apex will be extracted for each precursor and saved in .parquet format, a folder will be created next to the main report for the XICs storage
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
N-terminal methionine excision enabled
Min peptide length set to 7
Max peptide length set to 30
Min precursor m/z set to 380
Max precursor m/z set to 980
Min precursor charge set to 2
Max precursor charge set to 5
Min fragment m/z set to 150
Max fragment m/z set to 2000
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 2
Cysteine carbamidomethylation enabled as a fixed modification
Maximum number of variable modifications set to 3
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
Modification UniMod:1 with mass delta 42.0106 at *n will be considered as variable
Modification UniMod:21 with mass delta 79.9663 at STY will be considered as variable
Protein identification will rely on peptidoform confidence for matched peptides
MBR enabled; .quant files will only be saved to disk during the first pass
The spectral library (if generated) will retain the original spectra but will include empirically-aligned RTs
Implicit protein grouping: isoform IDs; this determines which peptides are considered 'proteotypic' and thus affects protein FDR calculation
DIA-NN will automatically optimise the mass accuracy for the first run of the experiment, use this mode for preliminary analyses only
The following variable modifications will be localised: UniMod:35 UniMod:1 UniMod:21 
WARNING: protein inference will only be performed for precursors identified with global q-value <= 0.05 or q-value <= 0.05.

20 files will be processed
[0:00] Loading spectral library C:\FASTAs\Spectral_Libraries\20260223_Homo_sapiens.predicted.speclib
[0:29] Library annotated with sequence database(s): camprotR_240512_cRAP_20190401_full_tags.fasta; C:\FASTAs\Spectral_Libraries\20260129_Uniprot_human_can+iso.fasta
[0:35] Spectral library loaded: 42654 protein isoforms, 70821 protein groups and 59890726 precursors in 35233104 elution groups.
[0:35] Loading protein annotations from FASTA camprotR_240512_cRAP_20190401_full_tags.fasta
[0:35] Loading protein annotations from FASTA C:\FASTAs\Spectral_Libraries\20260129_Uniprot_human_can+iso.fasta
[0:36] Annotating library proteins with information from the FASTA database
[0:36] Gene names missing for some isoforms
[0:36] Library contains 20535 proteins, and 20289 genes
[1:20] Initialising library

First pass: generating a spectral library from DIA data

[3:14] File #1/20
[3:14] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S01.raw
[3:20] Pre-processing...
[3:24] 1346 MS1 and 134915 MS2 scans in 673 (inferred) and 673 (encoded) cycles, 59872885 precursors in range
[3:30] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[24:55] RT window set to 1.43944
[24:55] Peak width: 5.096
[24:55] Scan window radius set to 11
[24:58] Recommended MS1 mass accuracy setting: 2.2 ppm
[84:47] Optimised mass accuracy: 7 ppm
[99:08] Main search
[123:41] Removing low confidence identifications
[124:00] Removing interfering precursors
[124:25] Training neural networks on 25888 target and 18001 decoy PSMs
[124:39] IDs at 0.01 FDR: 7427
[124:46] Number of IDs at 0.01 FDR: 8157
[124:46] Calculating protein q-values
[124:47] Number of protein isoforms identified at 1% FDR: 920 (precursor-level), 744 (protein-level) (inference performed using proteotypic peptides only)
[124:47] Quantification
[124:48] Precursors with scored PTMs at 1% FDR: 1922 out of 1922 considered
[124:48] Precursors with all scored PTM sites unoccupied at 1% FDR: 6235
[124:48] Precursors with PTMs localised (when required) with > 90% confidence: 1839 out of 1922
[124:50] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S01.raw.quant

[124:51] File #2/20
[124:51] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S02.raw
[124:58] Pre-processing...
[125:01] 1347 MS1 and 134989 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 59872885 precursors in range
[125:08] Calibrating with mass accuracies 22 (MS1), 25 (MS2)
[158:14] RT window set to 0.847378
[158:17] Recommended MS1 mass accuracy setting: 1.8 ppm
[169:27] Main search
[186:45] Removing low confidence identifications
[187:03] Removing interfering precursors
[187:28] Training neural networks on 20902 target and 14259 decoy PSMs
[187:40] IDs at 0.01 FDR: 6365
[187:46] Number of IDs at 0.01 FDR: 6989
[187:46] Calculating protein q-values
[187:48] Number of protein isoforms identified at 1% FDR: 679 (precursor-level), 548 (protein-level) (inference performed using proteotypic peptides only)
[187:48] Quantification
[187:49] Precursors with scored PTMs at 1% FDR: 1181 out of 1181 considered
[187:49] Precursors with all scored PTM sites unoccupied at 1% FDR: 5808
[187:49] Precursors with PTMs localised (when required) with > 90% confidence: 1130 out of 1181
[187:51] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S02.raw.quant

[187:51] File #3/20
[187:51] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S03.raw
[188:00] Pre-processing...
[188:04] 1347 MS1 and 135008 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 59872885 precursors in range
[188:10] Calibrating with mass accuracies 22 (MS1), 25 (MS2)
[216:07] RT window set to 0.84176
[216:10] Recommended MS1 mass accuracy setting: 1.9 ppm
[228:36] Main search
[248:25] Removing low confidence identifications
[248:43] Removing interfering precursors
[249:08] Training neural networks on 21922 target and 15058 decoy PSMs
[249:21] IDs at 0.01 FDR: 6873
[249:27] Number of IDs at 0.01 FDR: 7696
[249:27] Calculating protein q-values
[249:28] Number of protein isoforms identified at 1% FDR: 690 (precursor-level), 596 (protein-level) (inference performed using proteotypic peptides only)
[249:29] Quantification
[249:30] Precursors with scored PTMs at 1% FDR: 1465 out of 1465 considered
[249:30] Precursors with all scored PTM sites unoccupied at 1% FDR: 6231
[249:30] Precursors with PTMs localised (when required) with > 90% confidence: 1403 out of 1465
[249:32] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S03.raw.quant

[249:32] File #4/20
[249:32] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S04.raw
[249:40] Pre-processing...
[249:43] 1347 MS1 and 134992 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 59872885 precursors in range
[249:50] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[276:42] RT window set to 0.900293
[276:46] Recommended MS1 mass accuracy setting: 1.8 ppm
[289:08] Main search
[308:35] Removing low confidence identifications
[308:53] Removing interfering precursors
[309:18] Training neural networks on 23184 target and 15685 decoy PSMs
[309:31] IDs at 0.01 FDR: 6908
[309:37] Number of IDs at 0.01 FDR: 8108
[309:37] Calculating protein q-values
[309:39] Number of protein isoforms identified at 1% FDR: 699 (precursor-level), 597 (protein-level) (inference performed using proteotypic peptides only)
[309:39] Quantification
[309:40] Precursors with scored PTMs at 1% FDR: 1605 out of 1605 considered
[309:40] Precursors with all scored PTM sites unoccupied at 1% FDR: 6503
[309:40] Precursors with PTMs localised (when required) with > 90% confidence: 1556 out of 1605
[309:42] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S04.raw.quant

[309:42] File #5/20
[309:42] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S05.raw
[309:50] Pre-processing...
[309:53] 1347 MS1 and 135017 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 59872885 precursors in range
[310:00] Calibrating with mass accuracies 22 (MS1), 25 (MS2)
[332:32] RT window set to 0.818491
[332:34] Recommended MS1 mass accuracy setting: 2.2 ppm
[344:18] Main search
[363:27] Removing low confidence identifications
[363:46] Removing interfering precursors
[364:10] Training neural networks on 26972 target and 18369 decoy PSMs
[364:26] IDs at 0.01 FDR: 7728
[364:32] Number of IDs at 0.01 FDR: 8804
[364:32] Calculating protein q-values
[364:34] Number of protein isoforms identified at 1% FDR: 839 (precursor-level), 716 (protein-level) (inference performed using proteotypic peptides only)
[364:34] Quantification
[364:35] Precursors with scored PTMs at 1% FDR: 1629 out of 1629 considered
[364:35] Precursors with all scored PTM sites unoccupied at 1% FDR: 7175
[364:35] Precursors with PTMs localised (when required) with > 90% confidence: 1579 out of 1629
[364:37] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S05.raw.quant

[364:37] File #6/20
[364:37] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S06.raw
[364:44] Pre-processing...
[364:48] 1346 MS1 and 134931 MS2 scans in 673 (inferred) and 673 (encoded) cycles, 59872885 precursors in range
[364:54] Calibrating with mass accuracies 22 (MS1), 25 (MS2)
[387:09] RT window set to 0.893334
[387:11] Recommended MS1 mass accuracy setting: 1.9 ppm
[397:07] Main search
[417:32] Removing low confidence identifications
[417:53] Removing interfering precursors
[418:18] Training neural networks on 40042 target and 27295 decoy PSMs
[418:38] IDs at 0.01 FDR: 13075
[418:44] Number of IDs at 0.01 FDR: 14020
[418:44] Calculating protein q-values
[418:45] Number of protein isoforms identified at 1% FDR: 1243 (precursor-level), 1052 (protein-level) (inference performed using proteotypic peptides only)
[418:45] Quantification
[418:46] Precursors with scored PTMs at 1% FDR: 3095 out of 3095 considered
[418:46] Precursors with all scored PTM sites unoccupied at 1% FDR: 10925
[418:46] Precursors with PTMs localised (when required) with > 90% confidence: 3004 out of 3095
[418:48] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S06.raw.quant

[418:48] File #7/20
[418:48] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S07.raw
[418:55] Pre-processing...
[418:58] 1346 MS1 and 134892 MS2 scans in 673 (inferred) and 673 (encoded) cycles, 59872885 precursors in range
[419:05] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[440:25] RT window set to 0.818762
[440:27] Recommended MS1 mass accuracy setting: 1.8 ppm
[450:01] Main search
[467:25] Removing low confidence identifications
[467:45] Removing interfering precursors
[468:09] Training neural networks on 32906 target and 22474 decoy PSMs
[468:26] IDs at 0.01 FDR: 10834
[468:32] Number of IDs at 0.01 FDR: 12227
[468:32] Calculating protein q-values
[468:33] Number of protein isoforms identified at 1% FDR: 986 (precursor-level), 840 (protein-level) (inference performed using proteotypic peptides only)
[468:34] Quantification
[468:35] Precursors with scored PTMs at 1% FDR: 1811 out of 1811 considered
[468:35] Precursors with all scored PTM sites unoccupied at 1% FDR: 10416
[468:35] Precursors with PTMs localised (when required) with > 90% confidence: 1703 out of 1811
[468:37] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S07.raw.quant

[468:37] File #8/20
[468:37] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S08.raw
[468:43] Pre-processing...
[468:47] 1347 MS1 and 134893 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 59872885 precursors in range
[468:54] Calibrating with mass accuracies 22 (MS1), 25 (MS2)
[490:40] RT window set to 0.851742
[490:42] Recommended MS1 mass accuracy setting: 1.5 ppm
[501:42] Main search
[520:05] Removing low confidence identifications
[520:23] Removing interfering precursors
[520:48] Training neural networks on 24860 target and 17889 decoy PSMs
[521:03] IDs at 0.01 FDR: 6848
[521:09] Number of IDs at 0.01 FDR: 8122
[521:09] Calculating protein q-values
[521:10] Number of protein isoforms identified at 1% FDR: 701 (precursor-level), 543 (protein-level) (inference performed using proteotypic peptides only)
[521:10] Quantification
[521:11] Precursors with scored PTMs at 1% FDR: 1333 out of 1333 considered
[521:11] Precursors with all scored PTM sites unoccupied at 1% FDR: 6789
[521:11] Precursors with PTMs localised (when required) with > 90% confidence: 1271 out of 1333
[521:13] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S08.raw.quant

[521:14] File #9/20
[521:14] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S09.raw
[521:20] Pre-processing...
[521:24] 1347 MS1 and 134964 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 59872885 precursors in range
[521:30] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[543:05] RT window set to 0.859501
[543:08] Recommended MS1 mass accuracy setting: 1.6 ppm
[554:16] Main search
[572:07] Removing low confidence identifications
[572:26] Removing interfering precursors
[572:50] Training neural networks on 32418 target and 23096 decoy PSMs
[573:07] IDs at 0.01 FDR: 9840
[573:13] Number of IDs at 0.01 FDR: 10959
[573:13] Calculating protein q-values
[573:14] Number of protein isoforms identified at 1% FDR: 960 (precursor-level), 750 (protein-level) (inference performed using proteotypic peptides only)
[573:15] Quantification
[573:16] Precursors with scored PTMs at 1% FDR: 2043 out of 2043 considered
[573:16] Precursors with all scored PTM sites unoccupied at 1% FDR: 8916
[573:16] Precursors with PTMs localised (when required) with > 90% confidence: 1962 out of 2043
[573:18] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S09.raw.quant

[573:18] File #10/20
[573:18] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S10.raw
[573:24] Pre-processing...
[573:28] 1346 MS1 and 135053 MS2 scans in 673 (inferred) and 673 (encoded) cycles, 59872885 precursors in range
[573:34] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[598:10] RT window set to 0.801677
[598:12] Recommended MS1 mass accuracy setting: 2 ppm
[608:23] Main search
[624:15] Removing low confidence identifications
[624:33] Removing interfering precursors
[624:57] Training neural networks on 21222 target and 13401 decoy PSMs
[625:09] IDs at 0.01 FDR: 7217
[625:15] Number of IDs at 0.01 FDR: 8298
[625:15] Calculating protein q-values
[625:16] Number of protein isoforms identified at 1% FDR: 804 (precursor-level), 634 (protein-level) (inference performed using proteotypic peptides only)
[625:17] Quantification
[625:18] Precursors with scored PTMs at 1% FDR: 1740 out of 1740 considered
[625:18] Precursors with all scored PTM sites unoccupied at 1% FDR: 6558
[625:18] Precursors with PTMs localised (when required) with > 90% confidence: 1683 out of 1740
[625:20] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S10.raw.quant

[625:20] File #11/20
[625:20] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S11.raw
[625:26] Pre-processing...
[625:30] 1347 MS1 and 134848 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 59872885 precursors in range
[625:36] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[655:01] RT window set to 1.08295
[655:04] Recommended MS1 mass accuracy setting: 1.6 ppm
[667:11] Main search
[687:03] Removing low confidence identifications
[687:20] Removing interfering precursors
[687:44] Training neural networks on 12372 target and 8697 decoy PSMs
[687:55] IDs at 0.01 FDR: 3991
[688:01] Number of IDs at 0.01 FDR: 4418
[688:01] Calculating protein q-values
[688:02] Number of protein isoforms identified at 1% FDR: 531 (precursor-level), 469 (protein-level) (inference performed using proteotypic peptides only)
[688:02] Quantification
[688:03] Precursors with scored PTMs at 1% FDR: 797 out of 797 considered
[688:03] Precursors with all scored PTM sites unoccupied at 1% FDR: 3621
[688:03] Precursors with PTMs localised (when required) with > 90% confidence: 725 out of 797
[688:05] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S11.raw.quant

[688:05] File #12/20
[688:05] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S12.raw
[688:12] Pre-processing...
[688:16] 1347 MS1 and 134891 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 59872885 precursors in range
[688:23] Calibrating with mass accuracies 23 (MS1), 25 (MS2)
[709:44] RT window set to 0.790091
[709:46] Recommended MS1 mass accuracy setting: 1.8 ppm
[720:16] Main search
[737:18] Removing low confidence identifications
[737:35] Removing interfering precursors
[738:00] Training neural networks on 23660 target and 16319 decoy PSMs
[738:13] IDs at 0.01 FDR: 7645
[738:19] Number of IDs at 0.01 FDR: 8546
[738:19] Calculating protein q-values
[738:20] Number of protein isoforms identified at 1% FDR: 763 (precursor-level), 603 (protein-level) (inference performed using proteotypic peptides only)
[738:21] Quantification
[738:22] Precursors with scored PTMs at 1% FDR: 1707 out of 1707 considered
[738:22] Precursors with all scored PTM sites unoccupied at 1% FDR: 6839
[738:22] Precursors with PTMs localised (when required) with > 90% confidence: 1613 out of 1707
[738:24] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S12.raw.quant

[738:24] File #13/20
[738:24] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S13.raw
[738:32] Pre-processing...
[738:35] 1348 MS1 and 134941 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 59872885 precursors in range
[738:42] Calibrating with mass accuracies 22 (MS1), 25 (MS2)
[765:23] RT window set to 0.749682
[765:26] Recommended MS1 mass accuracy setting: 1.9 ppm
[774:48] Main search
[791:55] Removing low confidence identifications
[792:12] Removing interfering precursors
[792:36] Training neural networks on 19299 target and 13449 decoy PSMs
[792:48] IDs at 0.01 FDR: 5822
[792:54] Number of IDs at 0.01 FDR: 6529
[792:54] Calculating protein q-values
[792:55] Number of protein isoforms identified at 1% FDR: 633 (precursor-level), 544 (protein-level) (inference performed using proteotypic peptides only)
[792:56] Quantification
[792:57] Precursors with scored PTMs at 1% FDR: 1230 out of 1230 considered
[792:57] Precursors with all scored PTM sites unoccupied at 1% FDR: 5299
[792:57] Precursors with PTMs localised (when required) with > 90% confidence: 1153 out of 1230
[792:59] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S13.raw.quant

[792:59] File #14/20
[792:59] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S14.raw
[793:06] Pre-processing...
[793:10] 1348 MS1 and 134882 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 59872885 precursors in range
[793:16] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[814:08] RT window set to 0.803776
[814:10] Recommended MS1 mass accuracy setting: 1.5 ppm
[824:43] Main search
[841:06] Removing low confidence identifications
[841:24] Removing interfering precursors
[841:48] Training neural networks on 27460 target and 19667 decoy PSMs
[842:03] IDs at 0.01 FDR: 7508
[842:09] Number of IDs at 0.01 FDR: 8708
[842:09] Calculating protein q-values
[842:10] Number of protein isoforms identified at 1% FDR: 762 (precursor-level), 653 (protein-level) (inference performed using proteotypic peptides only)
[842:11] Quantification
[842:12] Precursors with scored PTMs at 1% FDR: 928 out of 928 considered
[842:12] Precursors with all scored PTM sites unoccupied at 1% FDR: 7780
[842:12] Precursors with PTMs localised (when required) with > 90% confidence: 859 out of 928
[842:14] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S14.raw.quant

[842:14] File #15/20
[842:14] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S15.raw
[842:22] Pre-processing...
[842:26] 1348 MS1 and 134942 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 59872885 precursors in range
[842:32] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[864:08] RT window set to 0.822993
[864:10] Recommended MS1 mass accuracy setting: 2 ppm
[875:20] Main search
[893:11] Removing low confidence identifications
[893:30] Removing interfering precursors
[893:54] Training neural networks on 30117 target and 21386 decoy PSMs
[894:10] IDs at 0.01 FDR: 8082
[894:16] Number of IDs at 0.01 FDR: 9252
[894:16] Calculating protein q-values
[894:17] Number of protein isoforms identified at 1% FDR: 778 (precursor-level), 614 (protein-level) (inference performed using proteotypic peptides only)
[894:18] Quantification
[894:18] Precursors with scored PTMs at 1% FDR: 843 out of 843 considered
[894:18] Precursors with all scored PTM sites unoccupied at 1% FDR: 8409
[894:18] Precursors with PTMs localised (when required) with > 90% confidence: 769 out of 843
[894:21] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S15.raw.quant

[894:21] File #16/20
[894:21] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S16.raw
[894:27] Pre-processing...
[894:30] 1346 MS1 and 134850 MS2 scans in 673 (inferred) and 673 (encoded) cycles, 59872885 precursors in range
[894:37] Calibrating with mass accuracies 22 (MS1), 25 (MS2)
[915:25] RT window set to 0.856534
[915:27] Recommended MS1 mass accuracy setting: 1.8 ppm
[926:21] Main search
[943:44] Removing low confidence identifications
[944:02] Removing interfering precursors
[944:27] Training neural networks on 30343 target and 21213 decoy PSMs
[944:43] IDs at 0.01 FDR: 8642
[944:49] Number of IDs at 0.01 FDR: 9750
[944:49] Calculating protein q-values
[944:50] Number of protein isoforms identified at 1% FDR: 890 (precursor-level), 710 (protein-level) (inference performed using proteotypic peptides only)
[944:50] Quantification
[944:51] Precursors with scored PTMs at 1% FDR: 2088 out of 2088 considered
[944:51] Precursors with all scored PTM sites unoccupied at 1% FDR: 7662
[944:51] Precursors with PTMs localised (when required) with > 90% confidence: 1993 out of 2088
[944:53] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S16.raw.quant

[944:53] File #17/20
[944:53] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S17.raw
[944:59] Pre-processing...
[945:03] 1346 MS1 and 134881 MS2 scans in 673 (inferred) and 673 (encoded) cycles, 59872885 precursors in range
[945:09] Calibrating with mass accuracies 23 (MS1), 25 (MS2)
[965:55] RT window set to 0.77299
[965:57] Recommended MS1 mass accuracy setting: 1.7 ppm
[972:47] Main search
[988:59] Removing low confidence identifications
[989:20] Removing interfering precursors
[989:44] Training neural networks on 50144 target and 36142 decoy PSMs
[990:08] IDs at 0.01 FDR: 15037
[990:14] Number of IDs at 0.01 FDR: 16493
[990:14] Calculating protein q-values
[990:15] Number of protein isoforms identified at 1% FDR: 1198 (precursor-level), 1036 (protein-level) (inference performed using proteotypic peptides only)
[990:16] Quantification
[990:17] Precursors with scored PTMs at 1% FDR: 1307 out of 1307 considered
[990:17] Precursors with all scored PTM sites unoccupied at 1% FDR: 15186
[990:17] Precursors with PTMs localised (when required) with > 90% confidence: 1182 out of 1307
[990:19] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S17.raw.quant

[990:19] File #18/20
[990:19] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S18.raw
[990:25] Pre-processing...
[990:29] 1347 MS1 and 134887 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 59872885 precursors in range
[990:35] Calibrating with mass accuracies 22 (MS1), 25 (MS2)
[1011:17] RT window set to 0.793544
[1011:19] Recommended MS1 mass accuracy setting: 1.7 ppm
[1021:35] Main search
[1038:12] Removing low confidence identifications
[1038:30] Removing interfering precursors
[1038:54] Training neural networks on 26126 target and 17883 decoy PSMs
[1039:09] IDs at 0.01 FDR: 9206
[1039:15] Number of IDs at 0.01 FDR: 10134
[1039:15] Calculating protein q-values
[1039:16] Number of protein isoforms identified at 1% FDR: 864 (precursor-level), 710 (protein-level) (inference performed using proteotypic peptides only)
[1039:16] Quantification
[1039:17] Precursors with scored PTMs at 1% FDR: 1097 out of 1097 considered
[1039:17] Precursors with all scored PTM sites unoccupied at 1% FDR: 9037
[1039:17] Precursors with PTMs localised (when required) with > 90% confidence: 1011 out of 1097
[1039:19] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S18.raw.quant

[1039:20] File #19/20
[1039:20] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S19.raw
[1039:25] Pre-processing...
[1039:29] 1346 MS1 and 134937 MS2 scans in 673 (inferred) and 673 (encoded) cycles, 59872885 precursors in range
[1039:35] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[1059:50] RT window set to 0.804913
[1059:52] Recommended MS1 mass accuracy setting: 1.7 ppm
[1069:37] Main search
[1085:14] Removing low confidence identifications
[1085:32] Removing interfering precursors
[1085:56] Training neural networks on 25987 target and 18187 decoy PSMs
[1086:11] IDs at 0.01 FDR: 8037
[1086:17] Number of IDs at 0.01 FDR: 8869
[1086:17] Calculating protein q-values
[1086:18] Number of protein isoforms identified at 1% FDR: 814 (precursor-level), 633 (protein-level) (inference performed using proteotypic peptides only)
[1086:18] Quantification
[1086:19] Precursors with scored PTMs at 1% FDR: 827 out of 827 considered
[1086:19] Precursors with all scored PTM sites unoccupied at 1% FDR: 8042
[1086:19] Precursors with PTMs localised (when required) with > 90% confidence: 763 out of 827
[1086:21] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S19.raw.quant

[1086:21] File #20/20
[1086:21] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S20.raw
[1086:31] Pre-processing...
[1086:34] 1346 MS1 and 135088 MS2 scans in 673 (inferred) and 673 (encoded) cycles, 59872885 precursors in range
[1086:41] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[1120:22] RT window set to 0.96537
[1120:25] Recommended MS1 mass accuracy setting: 1.9 ppm
[1133:58] Main search
[1156:20] Removing low confidence identifications
[1156:38] Removing interfering precursors
[1157:02] Training neural networks on 21370 target and 15548 decoy PSMs
[1157:15] IDs at 0.01 FDR: 6027
[1157:21] Number of IDs at 0.01 FDR: 6809
[1157:21] Calculating protein q-values
[1157:22] Number of protein isoforms identified at 1% FDR: 588 (precursor-level), 448 (protein-level) (inference performed using proteotypic peptides only)
[1157:23] Quantification
[1157:23] Precursors with scored PTMs at 1% FDR: 633 out of 633 considered
[1157:23] Precursors with all scored PTM sites unoccupied at 1% FDR: 6176
[1157:23] Precursors with PTMs localised (when required) with > 90% confidence: 577 out of 633
[1157:26] Quantification information saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S20.raw.quant

[1157:26] Cross-run analysis
[1157:26] Reading quantification information: 20 files
[1158:38] Quantifying peptides
[1159:05] Assembling protein groups
[1159:08] Quantifying proteins
[1159:09] Calculating q-values for protein and gene groups
[1159:42] Calculating global q-values for protein and gene groups
[1159:43] Protein groups with global q-value <= 0.01: 2427
[1159:44] Compressed report saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[1159:44] Site report saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report-first-pass.site_report.parquet
[1159:44] Saving precursor levels matrix
[1159:44] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report-first-pass.pr_matrix.tsv.
[1159:44] Manifest saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report-first-pass.manifest.txt
[1159:44] Stats report saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report-first-pass.stats.tsv
[1159:47] Generating spectral library:
[1159:48] 31595 target and 1576 decoy precursors saved
[1159:48] Spectral library saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report-lib.parquet

[1159:52] Loading spectral library D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report-lib.parquet
[1159:52] Spectral library loaded: 7920 protein isoforms, 4623 protein groups and 33171 precursors in 30865 elution groups.
[1159:52] Loading protein annotations from FASTA camprotR_240512_cRAP_20190401_full_tags.fasta
[1159:52] Loading protein annotations from FASTA C:\FASTAs\Spectral_Libraries\20260129_Uniprot_human_can+iso.fasta
[1159:53] Annotating library proteins with information from the FASTA database
[1159:53] Gene names missing for some isoforms
[1159:53] Library contains 4482 proteins, and 4466 genes
[1159:53] Initialising library
[1159:54] Saving the library to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report-lib.parquet.skyline.speclib


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

[1159:54] File #1/20
[1159:54] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S01.raw
[1160:00] Pre-processing...
[1160:00] 1346 MS1 and 134915 MS2 scans in 673 (inferred) and 673 (encoded) cycles, 31595 precursors in range
[1160:00] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[1160:01] RT window set to 0.585518
[1160:01] Recommended MS1 mass accuracy setting: 2.7 ppm
[1160:02] Main search
[1160:03] Removing low confidence identifications
[1160:03] Removing interfering precursors
[1160:03] Training neural networks on 21081 target and 10542 decoy PSMs
[1160:10] IDs at 0.01 FDR: 10092
[1160:10] Number of IDs at 0.01 FDR: 10514
[1160:10] Calculating protein q-values
[1160:10] Number of protein isoforms identified at 1% FDR: 1022 (precursor-level), 1132 (protein-level) (inference performed using proteotypic peptides only)
[1160:10] Quantification
[1160:10] Precursors with scored PTMs at 1% FDR: 2423 out of 2423 considered
[1160:10] Precursors with all scored PTM sites unoccupied at 1% FDR: 8091
[1160:10] Precursors with PTMs localised (when required) with > 90% confidence: 2309 out of 2423
[1160:11] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S01.xic.parquet

[1160:11] File #2/20
[1160:11] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S02.raw
[1160:18] Pre-processing...
[1160:19] 1347 MS1 and 134989 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 31595 precursors in range
[1160:19] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[1160:20] RT window set to 0.234187
[1160:20] Recommended MS1 mass accuracy setting: 2.6 ppm
[1160:21] Main search
[1160:21] Removing low confidence identifications
[1160:22] Removing interfering precursors
[1160:22] Training neural networks on 21445 target and 10538 decoy PSMs
[1160:29] IDs at 0.01 FDR: 8684
[1160:29] Number of IDs at 0.01 FDR: 9637
[1160:29] Calculating protein q-values
[1160:29] Number of protein isoforms identified at 1% FDR: 807 (precursor-level), 884 (protein-level) (inference performed using proteotypic peptides only)
[1160:29] Quantification
[1160:29] Precursors with scored PTMs at 1% FDR: 1746 out of 1746 considered
[1160:29] Precursors with all scored PTM sites unoccupied at 1% FDR: 7891
[1160:29] Precursors with PTMs localised (when required) with > 90% confidence: 1649 out of 1746
[1160:30] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S02.xic.parquet

[1160:30] File #3/20
[1160:30] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S03.raw
[1160:39] Pre-processing...
[1160:39] 1347 MS1 and 135008 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 31595 precursors in range
[1160:39] Calibrating with mass accuracies 22 (MS1), 25 (MS2)
[1160:41] RT window set to 0.235383
[1160:41] Recommended MS1 mass accuracy setting: 2.7 ppm
[1160:41] Main search
[1160:42] Removing low confidence identifications
[1160:43] Removing interfering precursors
[1160:43] Training neural networks on 21819 target and 10826 decoy PSMs
[1160:49] IDs at 0.01 FDR: 9430
[1160:49] Number of IDs at 0.01 FDR: 10749
[1160:49] Calculating protein q-values
[1160:49] Number of protein isoforms identified at 1% FDR: 818 (precursor-level), 952 (protein-level) (inference performed using proteotypic peptides only)
[1160:49] Quantification
[1160:50] Precursors with scored PTMs at 1% FDR: 2086 out of 2086 considered
[1160:50] Precursors with all scored PTM sites unoccupied at 1% FDR: 8663
[1160:50] Precursors with PTMs localised (when required) with > 90% confidence: 1967 out of 2086
[1160:51] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S03.xic.parquet

[1160:51] File #4/20
[1160:51] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S04.raw
[1160:58] Pre-processing...
[1160:59] 1347 MS1 and 134992 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 31595 precursors in range
[1160:59] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[1161:00] RT window set to 0.233602
[1161:00] Recommended MS1 mass accuracy setting: 2.5 ppm
[1161:00] Main search
[1161:01] Removing low confidence identifications
[1161:02] Removing interfering precursors
[1161:02] Training neural networks on 21071 target and 10333 decoy PSMs
[1161:08] IDs at 0.01 FDR: 9112
[1161:08] Number of IDs at 0.01 FDR: 9969
[1161:08] Calculating protein q-values
[1161:08] Number of protein isoforms identified at 1% FDR: 808 (precursor-level), 821 (protein-level) (inference performed using proteotypic peptides only)
[1161:08] Quantification
[1161:09] Precursors with scored PTMs at 1% FDR: 1974 out of 1974 considered
[1161:09] Precursors with all scored PTM sites unoccupied at 1% FDR: 7995
[1161:09] Precursors with PTMs localised (when required) with > 90% confidence: 1904 out of 1974
[1161:09] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S04.xic.parquet

[1161:09] File #5/20
[1161:09] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S05.raw
[1161:17] Pre-processing...
[1161:17] 1347 MS1 and 135017 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 31595 precursors in range
[1161:17] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[1161:19] RT window set to 0.293298
[1161:19] Recommended MS1 mass accuracy setting: 2.7 ppm
[1161:19] Main search
[1161:20] Removing low confidence identifications
[1161:21] Removing interfering precursors
[1161:21] Training neural networks on 21885 target and 11039 decoy PSMs
[1161:27] IDs at 0.01 FDR: 9826
[1161:27] Number of IDs at 0.01 FDR: 10898
[1161:27] Calculating protein q-values
[1161:27] Number of protein isoforms identified at 1% FDR: 941 (precursor-level), 978 (protein-level) (inference performed using proteotypic peptides only)
[1161:27] Quantification
[1161:28] Precursors with scored PTMs at 1% FDR: 2114 out of 2114 considered
[1161:28] Precursors with all scored PTM sites unoccupied at 1% FDR: 8784
[1161:28] Precursors with PTMs localised (when required) with > 90% confidence: 2030 out of 2114
[1161:29] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S05.xic.parquet

[1161:29] File #6/20
[1161:29] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S06.raw
[1161:35] Pre-processing...
[1161:35] 1346 MS1 and 134931 MS2 scans in 673 (inferred) and 673 (encoded) cycles, 31595 precursors in range
[1161:35] Calibrating with mass accuracies 22 (MS1), 25 (MS2)
[1161:36] RT window set to 0.354253
[1161:36] Recommended MS1 mass accuracy setting: 2.5 ppm
[1161:36] Main search
[1161:37] Removing low confidence identifications
[1161:38] Removing interfering precursors
[1161:38] Training neural networks on 23736 target and 11675 decoy PSMs
[1161:45] IDs at 0.01 FDR: 14738
[1161:45] Number of IDs at 0.01 FDR: 15245
[1161:45] Calculating protein q-values
[1161:45] Number of protein isoforms identified at 1% FDR: 1258 (precursor-level), 1184 (protein-level) (inference performed using proteotypic peptides only)
[1161:45] Quantification
[1161:46] Precursors with scored PTMs at 1% FDR: 3253 out of 3253 considered
[1161:46] Precursors with all scored PTM sites unoccupied at 1% FDR: 11992
[1161:46] Precursors with PTMs localised (when required) with > 90% confidence: 3141 out of 3253
[1161:47] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S06.xic.parquet

[1161:47] File #7/20
[1161:47] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S07.raw
[1161:52] Pre-processing...
[1161:53] 1346 MS1 and 134892 MS2 scans in 673 (inferred) and 673 (encoded) cycles, 31595 precursors in range
[1161:53] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[1161:54] RT window set to 0.242204
[1161:54] Recommended MS1 mass accuracy setting: 2.4 ppm
[1161:54] Main search
[1161:54] Removing low confidence identifications
[1161:55] Removing interfering precursors
[1161:55] Training neural networks on 23570 target and 11834 decoy PSMs
[1162:03] IDs at 0.01 FDR: 13649
[1162:03] Number of IDs at 0.01 FDR: 14787
[1162:03] Calculating protein q-values
[1162:03] Number of protein isoforms identified at 1% FDR: 1097 (precursor-level), 1149 (protein-level) (inference performed using proteotypic peptides only)
[1162:03] Quantification
[1162:04] Precursors with scored PTMs at 1% FDR: 2380 out of 2380 considered
[1162:04] Precursors with all scored PTM sites unoccupied at 1% FDR: 12407
[1162:04] Precursors with PTMs localised (when required) with > 90% confidence: 2253 out of 2380
[1162:05] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S07.xic.parquet

[1162:05] File #8/20
[1162:05] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S08.raw
[1162:10] Pre-processing...
[1162:11] 1347 MS1 and 134893 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 31595 precursors in range
[1162:11] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[1162:12] RT window set to 0.236959
[1162:12] Recommended MS1 mass accuracy setting: 2.2 ppm
[1162:13] Main search
[1162:13] Removing low confidence identifications
[1162:14] Removing interfering precursors
[1162:14] Training neural networks on 21580 target and 10868 decoy PSMs
[1162:21] IDs at 0.01 FDR: 9036
[1162:21] Number of IDs at 0.01 FDR: 9900
[1162:21] Calculating protein q-values
[1162:21] Number of protein isoforms identified at 1% FDR: 781 (precursor-level), 981 (protein-level) (inference performed using proteotypic peptides only)
[1162:21] Quantification
[1162:21] Precursors with scored PTMs at 1% FDR: 1737 out of 1737 considered
[1162:21] Precursors with all scored PTM sites unoccupied at 1% FDR: 8163
[1162:21] Precursors with PTMs localised (when required) with > 90% confidence: 1636 out of 1737
[1162:22] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S08.xic.parquet

[1162:22] File #9/20
[1162:22] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S09.raw
[1162:28] Pre-processing...
[1162:29] 1347 MS1 and 134964 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 31595 precursors in range
[1162:29] Calibrating with mass accuracies 22 (MS1), 25 (MS2)
[1162:30] RT window set to 0.268311
[1162:30] Recommended MS1 mass accuracy setting: 2.7 ppm
[1162:30] Main search
[1162:31] Removing low confidence identifications
[1162:32] Removing interfering precursors
[1162:32] Training neural networks on 22883 target and 11724 decoy PSMs
[1162:39] IDs at 0.01 FDR: 12854
[1162:39] Number of IDs at 0.01 FDR: 13121
[1162:39] Calculating protein q-values
[1162:39] Number of protein isoforms identified at 1% FDR: 1048 (precursor-level), 1106 (protein-level) (inference performed using proteotypic peptides only)
[1162:39] Quantification
[1162:40] Precursors with scored PTMs at 1% FDR: 2450 out of 2450 considered
[1162:40] Precursors with all scored PTM sites unoccupied at 1% FDR: 10671
[1162:40] Precursors with PTMs localised (when required) with > 90% confidence: 2355 out of 2450
[1162:41] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S09.xic.parquet

[1162:41] File #10/20
[1162:41] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S10.raw
[1162:46] Pre-processing...
[1162:46] 1346 MS1 and 135053 MS2 scans in 673 (inferred) and 673 (encoded) cycles, 31595 precursors in range
[1162:46] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[1162:47] RT window set to 0.237851
[1162:47] Recommended MS1 mass accuracy setting: 2.7 ppm
[1162:48] Main search
[1162:48] Removing low confidence identifications
[1162:49] Removing interfering precursors
[1162:49] Training neural networks on 21474 target and 10634 decoy PSMs
[1162:56] IDs at 0.01 FDR: 9403
[1162:56] Number of IDs at 0.01 FDR: 10295
[1162:56] Calculating protein q-values
[1162:56] Number of protein isoforms identified at 1% FDR: 894 (precursor-level), 1085 (protein-level) (inference performed using proteotypic peptides only)
[1162:56] Quantification
[1162:57] Precursors with scored PTMs at 1% FDR: 2156 out of 2156 considered
[1162:57] Precursors with all scored PTM sites unoccupied at 1% FDR: 8139
[1162:57] Precursors with PTMs localised (when required) with > 90% confidence: 2085 out of 2156
[1162:57] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S10.xic.parquet

[1162:58] File #11/20
[1162:58] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S11.raw
[1163:03] Pre-processing...
[1163:04] 1347 MS1 and 134848 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 31595 precursors in range
[1163:04] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[1163:06] RT window set to 0.366859
[1163:06] Recommended MS1 mass accuracy setting: 2.3 ppm
[1163:06] Main search
[1163:07] Removing low confidence identifications
[1163:07] Removing interfering precursors
[1163:07] Training neural networks on 17653 target and 8655 decoy PSMs
[1163:13] IDs at 0.01 FDR: 5104
[1163:13] Number of IDs at 0.01 FDR: 6039
[1163:13] Calculating protein q-values
[1163:13] Number of protein isoforms identified at 1% FDR: 650 (precursor-level), 764 (protein-level) (inference performed using proteotypic peptides only)
[1163:13] Quantification
[1163:14] Precursors with scored PTMs at 1% FDR: 1058 out of 1058 considered
[1163:14] Precursors with all scored PTM sites unoccupied at 1% FDR: 4981
[1163:14] Precursors with PTMs localised (when required) with > 90% confidence: 958 out of 1058
[1163:14] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S11.xic.parquet

[1163:14] File #12/20
[1163:14] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S12.raw
[1163:20] Pre-processing...
[1163:21] 1347 MS1 and 134891 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 31595 precursors in range
[1163:21] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[1163:22] RT window set to 0.284437
[1163:22] Recommended MS1 mass accuracy setting: 2.3 ppm
[1163:22] Main search
[1163:23] Removing low confidence identifications
[1163:24] Removing interfering precursors
[1163:24] Training neural networks on 22067 target and 11365 decoy PSMs
[1163:31] IDs at 0.01 FDR: 10566
[1163:31] Number of IDs at 0.01 FDR: 11043
[1163:31] Calculating protein q-values
[1163:31] Number of protein isoforms identified at 1% FDR: 940 (precursor-level), 951 (protein-level) (inference performed using proteotypic peptides only)
[1163:31] Quantification
[1163:32] Precursors with scored PTMs at 1% FDR: 2297 out of 2297 considered
[1163:32] Precursors with all scored PTM sites unoccupied at 1% FDR: 8746
[1163:32] Precursors with PTMs localised (when required) with > 90% confidence: 2166 out of 2297
[1163:33] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S12.xic.parquet

[1163:33] File #13/20
[1163:33] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S13.raw
[1163:39] Pre-processing...
[1163:40] 1348 MS1 and 134941 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 31595 precursors in range
[1163:40] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[1163:42] RT window set to 0.234757
[1163:42] Recommended MS1 mass accuracy setting: 2.3 ppm
[1163:42] Main search
[1163:43] Removing low confidence identifications
[1163:43] Removing interfering precursors
[1163:43] Training neural networks on 20808 target and 10577 decoy PSMs
[1163:50] IDs at 0.01 FDR: 7326
[1163:50] Number of IDs at 0.01 FDR: 7942
[1163:50] Calculating protein q-values
[1163:50] Number of protein isoforms identified at 1% FDR: 703 (precursor-level), 811 (protein-level) (inference performed using proteotypic peptides only)
[1163:50] Quantification
[1163:51] Precursors with scored PTMs at 1% FDR: 1524 out of 1524 considered
[1163:51] Precursors with all scored PTM sites unoccupied at 1% FDR: 6418
[1163:51] Precursors with PTMs localised (when required) with > 90% confidence: 1426 out of 1524
[1163:51] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S13.xic.parquet

[1163:52] File #14/20
[1163:52] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S14.raw
[1163:57] Pre-processing...
[1163:58] 1348 MS1 and 134882 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 31595 precursors in range
[1163:58] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[1163:59] RT window set to 0.237225
[1163:59] Recommended MS1 mass accuracy setting: 2.5 ppm
[1164:00] Main search
[1164:00] Removing low confidence identifications
[1164:01] Removing interfering precursors
[1164:01] Training neural networks on 22005 target and 11006 decoy PSMs
[1164:08] IDs at 0.01 FDR: 9766
[1164:08] Number of IDs at 0.01 FDR: 10903
[1164:08] Calculating protein q-values
[1164:08] Number of protein isoforms identified at 1% FDR: 857 (precursor-level), 968 (protein-level) (inference performed using proteotypic peptides only)
[1164:08] Quantification
[1164:09] Precursors with scored PTMs at 1% FDR: 1263 out of 1263 considered
[1164:09] Precursors with all scored PTM sites unoccupied at 1% FDR: 9640
[1164:09] Precursors with PTMs localised (when required) with > 90% confidence: 1166 out of 1263
[1164:10] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S14.xic.parquet

[1164:10] File #15/20
[1164:10] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S15.raw
[1164:17] Pre-processing...
[1164:17] 1348 MS1 and 134942 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 31595 precursors in range
[1164:17] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[1164:18] RT window set to 0.239966
[1164:18] Recommended MS1 mass accuracy setting: 2.5 ppm
[1164:19] Main search
[1164:19] Removing low confidence identifications
[1164:20] Removing interfering precursors
[1164:20] Training neural networks on 22312 target and 11241 decoy PSMs
[1164:27] IDs at 0.01 FDR: 10447
[1164:27] Number of IDs at 0.01 FDR: 11338
[1164:27] Calculating protein q-values
[1164:27] Number of protein isoforms identified at 1% FDR: 878 (precursor-level), 945 (protein-level) (inference performed using proteotypic peptides only)
[1164:27] Quantification
[1164:28] Precursors with scored PTMs at 1% FDR: 1133 out of 1133 considered
[1164:28] Precursors with all scored PTM sites unoccupied at 1% FDR: 10205
[1164:28] Precursors with PTMs localised (when required) with > 90% confidence: 1035 out of 1133
[1164:29] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S15.xic.parquet

[1164:29] File #16/20
[1164:29] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S16.raw
[1164:34] Pre-processing...
[1164:35] 1346 MS1 and 134850 MS2 scans in 673 (inferred) and 673 (encoded) cycles, 31595 precursors in range
[1164:35] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[1164:36] RT window set to 0.279496
[1164:36] Recommended MS1 mass accuracy setting: 2.4 ppm
[1164:36] Main search
[1164:37] Removing low confidence identifications
[1164:38] Removing interfering precursors
[1164:38] Training neural networks on 22403 target and 11318 decoy PSMs
[1164:45] IDs at 0.01 FDR: 11366
[1164:45] Number of IDs at 0.01 FDR: 11972
[1164:45] Calculating protein q-values
[1164:45] Number of protein isoforms identified at 1% FDR: 1015 (precursor-level), 1170 (protein-level) (inference performed using proteotypic peptides only)
[1164:45] Quantification
[1164:46] Precursors with scored PTMs at 1% FDR: 2531 out of 2531 considered
[1164:46] Precursors with all scored PTM sites unoccupied at 1% FDR: 9441
[1164:46] Precursors with PTMs localised (when required) with > 90% confidence: 2406 out of 2531
[1164:47] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S16.xic.parquet

[1164:47] File #17/20
[1164:47] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S17.raw
[1164:52] Pre-processing...
[1164:52] 1346 MS1 and 134881 MS2 scans in 673 (inferred) and 673 (encoded) cycles, 31595 precursors in range
[1164:52] Calibrating with mass accuracies 22 (MS1), 25 (MS2)
[1164:53] RT window set to 0.242515
[1164:53] Recommended MS1 mass accuracy setting: 2.5 ppm
[1164:54] Main search
[1164:54] Removing low confidence identifications
[1164:55] Removing interfering precursors
[1164:55] Training neural networks on 24293 target and 12132 decoy PSMs
[1165:03] IDs at 0.01 FDR: 16793
[1165:03] Number of IDs at 0.01 FDR: 17124
[1165:03] Calculating protein q-values
[1165:03] Number of protein isoforms identified at 1% FDR: 1175 (precursor-level), 1221 (protein-level) (inference performed using proteotypic peptides only)
[1165:03] Quantification
[1165:04] Precursors with scored PTMs at 1% FDR: 1584 out of 1584 considered
[1165:04] Precursors with all scored PTM sites unoccupied at 1% FDR: 15540
[1165:04] Precursors with PTMs localised (when required) with > 90% confidence: 1446 out of 1584
[1165:05] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S17.xic.parquet

[1165:05] File #18/20
[1165:05] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S18.raw
[1165:10] Pre-processing...
[1165:11] 1347 MS1 and 134887 MS2 scans in 674 (inferred) and 674 (encoded) cycles, 31595 precursors in range
[1165:11] Calibrating with mass accuracies 22 (MS1), 25 (MS2)
[1165:12] RT window set to 0.285495
[1165:12] Recommended MS1 mass accuracy setting: 2.4 ppm
[1165:12] Main search
[1165:13] Removing low confidence identifications
[1165:14] Removing interfering precursors
[1165:14] Training neural networks on 22945 target and 11629 decoy PSMs
[1165:21] IDs at 0.01 FDR: 12120
[1165:21] Number of IDs at 0.01 FDR: 13002
[1165:21] Calculating protein q-values
[1165:21] Number of protein isoforms identified at 1% FDR: 965 (precursor-level), 1130 (protein-level) (inference performed using proteotypic peptides only)
[1165:21] Quantification
[1165:22] Precursors with scored PTMs at 1% FDR: 1526 out of 1526 considered
[1165:22] Precursors with all scored PTM sites unoccupied at 1% FDR: 11476
[1165:22] Precursors with PTMs localised (when required) with > 90% confidence: 1392 out of 1526
[1165:23] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S18.xic.parquet

[1165:23] File #19/20
[1165:23] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S19.raw
[1165:28] Pre-processing...
[1165:28] 1346 MS1 and 134937 MS2 scans in 673 (inferred) and 673 (encoded) cycles, 31595 precursors in range
[1165:28] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[1165:30] RT window set to 0.237189
[1165:30] Recommended MS1 mass accuracy setting: 2.5 ppm
[1165:30] Main search
[1165:31] Removing low confidence identifications
[1165:31] Removing interfering precursors
[1165:31] Training neural networks on 22229 target and 11103 decoy PSMs
[1165:39] IDs at 0.01 FDR: 10320
[1165:39] Number of IDs at 0.01 FDR: 11217
[1165:39] Calculating protein q-values
[1165:39] Number of protein isoforms identified at 1% FDR: 890 (precursor-level), 1014 (protein-level) (inference performed using proteotypic peptides only)
[1165:39] Quantification
[1165:39] Precursors with scored PTMs at 1% FDR: 1117 out of 1117 considered
[1165:39] Precursors with all scored PTM sites unoccupied at 1% FDR: 10100
[1165:39] Precursors with PTMs localised (when required) with > 90% confidence: 1038 out of 1117
[1165:40] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S19.xic.parquet

[1165:40] File #20/20
[1165:40] Loading run D:\FW\Dundee\Daniel_Ungureanu\RAD52\Raw\20250228_FL_Daniel_JR_S20.raw
[1165:49] Pre-processing...
[1165:49] 1346 MS1 and 135088 MS2 scans in 673 (inferred) and 673 (encoded) cycles, 31595 precursors in range
[1165:49] Calibrating with mass accuracies 21 (MS1), 25 (MS2)
[1165:51] RT window set to 0.260387
[1165:51] Recommended MS1 mass accuracy setting: 2.6 ppm
[1165:51] Main search
[1165:52] Removing low confidence identifications
[1165:53] Removing interfering precursors
[1165:53] Training neural networks on 20538 target and 10562 decoy PSMs
[1165:59] IDs at 0.01 FDR: 7608
[1165:59] Number of IDs at 0.01 FDR: 8631
[1165:59] Calculating protein q-values
[1165:59] Number of protein isoforms identified at 1% FDR: 657 (precursor-level), 739 (protein-level) (inference performed using proteotypic peptides only)
[1165:59] Quantification
[1166:00] Precursors with scored PTMs at 1% FDR: 853 out of 853 considered
[1166:00] Precursors with all scored PTM sites unoccupied at 1% FDR: 7778
[1166:00] Precursors with PTMs localised (when required) with > 90% confidence: 783 out of 853
[1166:01] XICs saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN/report_xic/20250228_FL_Daniel_JR_S20.xic.parquet

[1166:01] Cross-run analysis
[1166:01] Reading quantification information: 20 files
[1166:01] Quantifying peptides
[1166:15] Quantification parameters: 0.429818, 0.00243866, 0.00169189, 0.0123037, 0.0123486, 0.0130493, 0.121725, 0.259016, 0.208381, 0.012383, 0.0251071, 0.0136169, 0.521708, 0.0521778, 0.0784703, 0.252843
[1166:17] Quantifying proteins
[1166:17] Calculating q-values for protein and gene groups
[1166:17] Calculating global q-values for protein and gene groups
[1166:17] Protein groups with global q-value <= 0.01: 2281
[1166:19] Compressed report saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[1166:19] Site report saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report.site_report.parquet
[1166:19] Saving precursor levels matrix
[1166:19] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report.pr_matrix.tsv.
[1166:19] Saving protein group levels matrix
[1166:19] Protein groups matrix saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report.pg_matrix.tsv.
[1166:19] Saving gene group levels matrix
[1166:19] Gene groups matrix saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report.gg_matrix.tsv.
[1166:19] Saving unique genes levels matrix
[1166:19] Unique genes matrix saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report.unique_genes_matrix.tsv.
[1166:19] Manifest saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report.manifest.txt
[1166:19] Stats report saved to D:\FW\Dundee\Daniel_Ungureanu\RAD52\DIA-NN\report.stats.tsv