DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks)
Compiled on Apr 14 2022 15:31:19
Current date and time: Mon Apr 14 18:52:35 2025
CPU: GenuineIntel Intel(R) Xeon(R) CPU E5-1607 v4 @ 3.10GHz
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 
Logical CPU cores: 4
diann.exe --f G:\Shaswati_timsTOF\14042025_tims\cis_Pool1_11042025_S1-A1_1_1186.d  --f G:\Shaswati_timsTOF\14042025_tims\cisR1_11042025_S1-A5_1_1190.d  --f G:\Shaswati_timsTOF\14042025_tims\cisR2_11042025_S1-A6_1_1191.d  --f G:\Shaswati_timsTOF\14042025_tims\cisR3_11042025_S1-A7_1_1192.d  --f G:\Shaswati_timsTOF\14042025_tims\cisS1_11042025_S1-A2_1_1187.d  --f G:\Shaswati_timsTOF\14042025_tims\cisS2_11042025_S1-A3_1_1188.d  --f G:\Shaswati_timsTOF\14042025_tims\cisS3_11042025_S1-A4_1_1189.d  --f G:\Shaswati_timsTOF\14042025_tims\CSP_Pool1_11042025_S1-B1_1_1195.d  --lib  --threads 4 --verbose 1 --out G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report.tsv --qvalue 0.01 --matrices --out-lib G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report-lib.tsv --gen-spec-lib --predictor --fasta G:\Shaswati_timsTOF\14042025_tims\uniprotkb_proteome_UP000005640_AND_revi_2025_03_20.fasta --fasta-search --min-fr-mz 300 --max-fr-mz 1500 --cut K*,R* --missed-cleavages 2 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 385 --max-pr-mz 1015 --min-pr-charge 2 --max-pr-charge 5 --unimod4 --var-mods 5 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --monitor-mod UniMod:1 --reanalyse --relaxed-prot-inf --smart-profiling --peak-center --no-ifs-removal 

Thread number set to 4
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
A spectral library will be generated
Deep learning will be used to generate a new in silico spectral library from peptides provided
Library-free search enabled
Min fragment m/z set to 300
Max fragment m/z set to 1500
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 2
Min peptide length set to 7
Max peptide length set to 30
Min precursor m/z set to 385
Max precursor m/z set to 1015
Min precursor charge set to 2
Max precursor charge set to 5
Cysteine carbamidomethylation enabled as a fixed modification
Maximum number of variable modifications set to 5
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
A spectral library will be created from the DIA runs and used to reanalyse them; .quant files will only be saved to disk during the first step
Highly heuristic protein grouping will be used, to reduce the number of protein groups obtained; this mode is recommended for benchmarking protein ID numbers; use with caution for anything else
When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones
Fixed-width center of each elution peak will be used for quantification
Interference removal from fragment elution curves disabled
DIA-NN will optimise the mass accuracy automatically using the first run in the experiment. This is useful primarily for quick initial analyses, when it is not yet known which mass accuracy setting works best for a particular acquisition scheme.
Exclusion of fragments shared between heavy and light peptides from quantification is not supported in FASTA digest mode - disabled; to enable, generate an in silico predicted spectral library and analyse with this library
The following variable modifications will be scored: UniMod:1 

8 files will be processed
[0:00] Loading FASTA G:\Shaswati_timsTOF\14042025_tims\uniprotkb_proteome_UP000005640_AND_revi_2025_03_20.fasta
[3:54] Processing FASTA
[4:17] Assembling elution groups
[4:30] 5824030 precursors generated
[4:30] Gene names missing for some isoforms
[4:30] Library contains 20382 proteins, and 20188 genes
[4:31] [4:47] [86:52] [114:45] [115:28] [115:33] Saving the library to G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report-lib.predicted.speclib
[116:15] Initialising library

[116:19] First pass: generating a spectral library from DIA data
[116:19] File #1/8
[116:19] Loading run G:\Shaswati_timsTOF\14042025_tims\cis_Pool1_11042025_S1-A1_1_1186.d
For most diaPASEF datasets it is better to manually fix both the MS1 and MS2 mass accuracies to values in the range 10-15 ppm.
[117:49] 5824030 library precursors are potentially detectable
[117:49] Processing...
[170:15] RT window set to 2.45522
[170:15] Ion mobility window set to 0.0341488
[170:15] Peak width: 6.76
[170:15] Scan window radius set to 14
[170:16] Recommended MS1 mass accuracy setting: 12.3266 ppm
[247:02] Optimised mass accuracy: 12.4979 ppm
[331:21] Removing low confidence identifications
[331:21] Searching PTM decoys
[332:17] Removing interfering precursors
[332:21] Training neural networks: 34674 targets, 21965 decoys
[332:27] Number of IDs at 0.01 FDR: 17871
[332:28] Calculating protein q-values
[332:28] Number of genes identified at 1% FDR: 3302 (precursor-level), 2989 (protein-level) (inference performed using proteotypic peptides only)
[332:29] Quantification
[332:29] Precursors with monitored PTMs at 1% FDR: 0 out of 17
[332:29] Unmodified precursors with monitored PTM sites at 1% FDR: 0 out of 9
[332:31] Quantification information saved to G:\Shaswati_timsTOF\14042025_tims\cis_Pool1_11042025_S1-A1_1_1186.d.quant.

[332:34] File #2/8
[332:34] Loading run G:\Shaswati_timsTOF\14042025_tims\cisR1_11042025_S1-A5_1_1190.d
[334:54] 5824030 library precursors are potentially detectable
[334:54] Processing...
[377:21] RT window set to 2.62923
[377:21] Ion mobility window set to 0.0370694
[377:22] Recommended MS1 mass accuracy setting: 12.5553 ppm
[501:46] Removing low confidence identifications
[501:47] Searching PTM decoys
[503:20] Removing interfering precursors
[503:26] Training neural networks: 57619 targets, 38016 decoys
[503:36] Number of IDs at 0.01 FDR: 26968
[503:37] Calculating protein q-values
[503:38] Number of genes identified at 1% FDR: 4815 (precursor-level), 4380 (protein-level) (inference performed using proteotypic peptides only)
[503:38] Quantification
[503:39] Precursors with monitored PTMs at 1% FDR: 0 out of 34
[503:39] Unmodified precursors with monitored PTM sites at 1% FDR: 0 out of 13
[503:42] Quantification information saved to G:\Shaswati_timsTOF\14042025_tims\cisR1_11042025_S1-A5_1_1190.d.quant.

[503:45] File #3/8
[503:45] Loading run G:\Shaswati_timsTOF\14042025_tims\cisR2_11042025_S1-A6_1_1191.d
[506:06] 5824030 library precursors are potentially detectable
[506:06] Processing...
[547:33] RT window set to 2.46826
[547:33] Ion mobility window set to 0.0365554
[547:33] Recommended MS1 mass accuracy setting: 12.6144 ppm
[664:50] Removing low confidence identifications
[664:51] Searching PTM decoys
[666:18] Removing interfering precursors
[666:24] Training neural networks: 56964 targets, 37703 decoys
[666:34] Number of IDs at 0.01 FDR: 27080
[666:35] Calculating protein q-values
[666:36] Number of genes identified at 1% FDR: 4827 (precursor-level), 4370 (protein-level) (inference performed using proteotypic peptides only)
[666:36] Quantification
[666:37] Precursors with monitored PTMs at 1% FDR: 0 out of 32
[666:37] Unmodified precursors with monitored PTM sites at 1% FDR: 0 out of 16
[666:40] Quantification information saved to G:\Shaswati_timsTOF\14042025_tims\cisR2_11042025_S1-A6_1_1191.d.quant.

[666:43] File #4/8
[666:43] Loading run G:\Shaswati_timsTOF\14042025_tims\cisR3_11042025_S1-A7_1_1192.d
[668:45] 5824030 library precursors are potentially detectable
[668:45] Processing...
[716:26] RT window set to 2.59232
[716:26] Ion mobility window set to 0.0358789
[716:27] Recommended MS1 mass accuracy setting: 12.3974 ppm
[831:32] Removing low confidence identifications
[831:33] Searching PTM decoys
[832:58] Removing interfering precursors
[833:02] Training neural networks: 48571 targets, 31272 decoys
[833:11] Number of IDs at 0.01 FDR: 24088
[833:12] Calculating protein q-values
[833:13] Number of genes identified at 1% FDR: 4560 (precursor-level), 4110 (protein-level) (inference performed using proteotypic peptides only)
[833:13] Quantification
[833:14] Precursors with monitored PTMs at 1% FDR: 0 out of 34
[833:14] Unmodified precursors with monitored PTM sites at 1% FDR: 0 out of 15
[833:16] Quantification information saved to G:\Shaswati_timsTOF\14042025_tims\cisR3_11042025_S1-A7_1_1192.d.quant.

[833:19] File #5/8
[833:19] Loading run G:\Shaswati_timsTOF\14042025_tims\cisS1_11042025_S1-A2_1_1187.d
[834:59] 5824030 library precursors are potentially detectable
[835:00] Processing...
[881:23] RT window set to 2.51486
[881:23] Ion mobility window set to 0.0325038
[881:24] Recommended MS1 mass accuracy setting: 11.8689 ppm
[975:13] Removing low confidence identifications
[975:14] Searching PTM decoys
[976:18] Removing interfering precursors
[976:22] Training neural networks: 45228 targets, 31028 decoys
[976:31] Number of IDs at 0.01 FDR: 22040
[976:31] Calculating protein q-values
[976:32] Number of genes identified at 1% FDR: 4258 (precursor-level), 3897 (protein-level) (inference performed using proteotypic peptides only)
[976:32] Quantification
[976:33] Precursors with monitored PTMs at 1% FDR: 0 out of 20
[976:33] Unmodified precursors with monitored PTM sites at 1% FDR: 0 out of 12
[976:35] Quantification information saved to G:\Shaswati_timsTOF\14042025_tims\cisS1_11042025_S1-A2_1_1187.d.quant.

[976:38] File #6/8
[976:38] Loading run G:\Shaswati_timsTOF\14042025_tims\cisS2_11042025_S1-A3_1_1188.d
[978:09] 5824030 library precursors are potentially detectable
[978:10] Processing...
[1023:57] RT window set to 2.50709
[1023:57] Ion mobility window set to 0.0323576
[1023:58] Recommended MS1 mass accuracy setting: 11.9846 ppm
[1113:11] Removing low confidence identifications
[1113:12] Searching PTM decoys
[1114:13] Removing interfering precursors
[1114:17] Training neural networks: 37752 targets, 22521 decoys
[1114:24] Number of IDs at 0.01 FDR: 18709
[1114:24] Calculating protein q-values
[1114:25] Number of genes identified at 1% FDR: 3815 (precursor-level), 3606 (protein-level) (inference performed using proteotypic peptides only)
[1114:25] Quantification
[1114:26] Precursors with monitored PTMs at 1% FDR: 0 out of 16
[1114:26] Unmodified precursors with monitored PTM sites at 1% FDR: 0 out of 10
[1114:28] Quantification information saved to G:\Shaswati_timsTOF\14042025_tims\cisS2_11042025_S1-A3_1_1188.d.quant.

[1114:31] File #7/8
[1114:31] Loading run G:\Shaswati_timsTOF\14042025_tims\cisS3_11042025_S1-A4_1_1189.d
[1116:01] 5824030 library precursors are potentially detectable
[1116:02] Processing...
[1171:07] RT window set to 2.48903
[1171:07] Ion mobility window set to 0.0352818
[1171:07] Recommended MS1 mass accuracy setting: 12.4345 ppm
[1262:18] Removing low confidence identifications
[1262:18] Searching PTM decoys
[1263:20] Removing interfering precursors
[1263:24] Training neural networks: 38857 targets, 24276 decoys
[1263:31] Number of IDs at 0.01 FDR: 19516
[1263:31] Calculating protein q-values
[1263:32] Number of genes identified at 1% FDR: 3934 (precursor-level), 3612 (protein-level) (inference performed using proteotypic peptides only)
[1263:32] Quantification
[1263:33] Precursors with monitored PTMs at 1% FDR: 0 out of 14
[1263:33] Unmodified precursors with monitored PTM sites at 1% FDR: 0 out of 13
[1263:35] Quantification information saved to G:\Shaswati_timsTOF\14042025_tims\cisS3_11042025_S1-A4_1_1189.d.quant.

[1263:38] File #8/8
[1263:38] Loading run G:\Shaswati_timsTOF\14042025_tims\CSP_Pool1_11042025_S1-B1_1_1195.d
[1265:14] 5824030 library precursors are potentially detectable
[1265:15] Processing...
[1310:53] RT window set to 2.69531
[1310:53] Ion mobility window set to 0.0371208
[1310:54] Recommended MS1 mass accuracy setting: 12.6703 ppm
[1409:02] Removing low confidence identifications
[1409:03] Searching PTM decoys
[1410:09] Removing interfering precursors
[1410:14] Training neural networks: 47062 targets, 29525 decoys
[1410:22] Number of IDs at 0.01 FDR: 22334
[1410:23] Calculating protein q-values
[1410:23] Number of genes identified at 1% FDR: 3860 (precursor-level), 3492 (protein-level) (inference performed using proteotypic peptides only)
[1410:23] Quantification
[1410:24] Precursors with monitored PTMs at 1% FDR: 0 out of 24
[1410:24] Unmodified precursors with monitored PTM sites at 1% FDR: 0 out of 15
[1410:27] Quantification information saved to G:\Shaswati_timsTOF\14042025_tims\CSP_Pool1_11042025_S1-B1_1_1195.d.quant.

[1410:29] Cross-run analysis
[1410:29] Reading quantification information: 8 files
[1410:30] Quantifying peptides
[1410:33] Assembling protein groups
[1410:37] Quantifying proteins
[1410:38] Calculating q-values for protein and gene groups
[1410:39] Calculating global q-values for protein and gene groups
[1410:39] Writing report
[1410:54] Report saved to G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report-first-pass.tsv.
[1410:54] Saving precursor levels matrix
[1410:55] Precursor levels matrix (1% precursor and protein group FDR) saved to G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report-first-pass.pr_matrix.tsv.
[1410:55] Saving protein group levels matrix
[1410:55] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report-first-pass.pg_matrix.tsv.
[1410:55] Saving gene group levels matrix
[1410:55] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report-first-pass.gg_matrix.tsv.
[1410:55] Saving unique genes levels matrix
[1410:55] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report-first-pass.unique_genes_matrix.tsv.
[1410:55] Stats report saved to G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report-first-pass.stats.tsv
[1410:55] Generating spectral library:
[1410:55] 38903 precursors passing the FDR threshold are to be extracted
[1410:55] Loading run G:\Shaswati_timsTOF\14042025_tims\cis_Pool1_11042025_S1-A1_1_1186.d
[1412:24] 5824030 library precursors are potentially detectable
[1412:25] 1942 spectra added to the library
[1412:28] Loading run G:\Shaswati_timsTOF\14042025_tims\cisR1_11042025_S1-A5_1_1190.d
[1414:46] 5824030 library precursors are potentially detectable
[1414:48] 5019 spectra added to the library
[1414:52] Loading run G:\Shaswati_timsTOF\14042025_tims\cisR2_11042025_S1-A6_1_1191.d
[1417:12] 5824030 library precursors are potentially detectable
[1417:14] 4714 spectra added to the library
[1417:17] Loading run G:\Shaswati_timsTOF\14042025_tims\cisR3_11042025_S1-A7_1_1192.d
[1419:18] 5824030 library precursors are potentially detectable
[1419:20] 4549 spectra added to the library
[1419:24] Loading run G:\Shaswati_timsTOF\14042025_tims\cisS1_11042025_S1-A2_1_1187.d
[1421:04] 5824030 library precursors are potentially detectable
[1421:06] 2907 spectra added to the library
[1421:09] Loading run G:\Shaswati_timsTOF\14042025_tims\cisS2_11042025_S1-A3_1_1188.d
[1422:40] 5824030 library precursors are potentially detectable
[1422:41] 2028 spectra added to the library
[1422:45] Loading run G:\Shaswati_timsTOF\14042025_tims\cisS3_11042025_S1-A4_1_1189.d
[1424:15] 5824030 library precursors are potentially detectable
[1424:16] 129 spectra added to the library
[1424:19] Loading run G:\Shaswati_timsTOF\14042025_tims\CSP_Pool1_11042025_S1-B1_1_1195.d
[1425:56] 5824030 library precursors are potentially detectable
[1425:58] 7635 spectra added to the library
[1426:01] Saving spectral library to G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report-lib.tsv
[1426:10] 38903 precursors saved
[1426:10] Loading the generated library and saving it in the .speclib format
[1426:10] Loading spectral library G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report-lib.tsv
[1426:13] Spectral library loaded: 6981 protein isoforms, 7310 protein groups and 38903 precursors in 36722 elution groups.
[1426:13] Loading protein annotations from FASTA G:\Shaswati_timsTOF\14042025_tims\uniprotkb_proteome_UP000005640_AND_revi_2025_03_20.fasta
[1426:14] Gene names missing for some isoforms
[1426:14] Library contains 6981 proteins, and 6970 genes
[1426:14] Saving the library to G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report-lib.tsv.speclib

[1426:20] Second pass: using the newly created spectral library to reanalyse the data
[1426:20] File #1/8
[1426:20] Loading run G:\Shaswati_timsTOF\14042025_tims\cis_Pool1_11042025_S1-A1_1_1186.d
[1427:49] 38903 library precursors are potentially detectable
[1427:49] Processing...
[1428:14] RT window set to 0.918606
[1428:14] Ion mobility window set to 0.01
[1428:14] Recommended MS1 mass accuracy setting: 12.5861 ppm
[1428:31] Removing low confidence identifications
[1428:31] Searching PTM decoys
[1428:31] Removing interfering precursors
[1428:33] Training neural networks: 37056 targets, 31566 decoys
[1428:39] Number of IDs at 0.01 FDR: 30734
[1428:40] Calculating protein q-values
[1428:40] Number of genes identified at 1% FDR: 5077 (precursor-level), 4353 (protein-level) (inference performed using proteotypic peptides only)
[1428:40] Quantification

[1428:45] File #2/8
[1428:45] Loading run G:\Shaswati_timsTOF\14042025_tims\cisR1_11042025_S1-A5_1_1190.d
[1431:03] 38903 library precursors are potentially detectable
[1431:03] Processing...
[1431:32] RT window set to 0.924748
[1431:32] Ion mobility window set to 0.0103776
[1431:32] Recommended MS1 mass accuracy setting: 12.5424 ppm
[1431:52] Removing low confidence identifications
[1431:52] Searching PTM decoys
[1431:52] Removing interfering precursors
[1431:55] Training neural networks: 37952 targets, 35945 decoys
[1432:02] Number of IDs at 0.01 FDR: 30942
[1432:03] Calculating protein q-values
[1432:03] Number of genes identified at 1% FDR: 5246 (precursor-level), 4598 (protein-level) (inference performed using proteotypic peptides only)
[1432:03] Quantification

[1432:09] File #3/8
[1432:09] Loading run G:\Shaswati_timsTOF\14042025_tims\cisR2_11042025_S1-A6_1_1191.d
[1434:28] 38903 library precursors are potentially detectable
[1434:28] Processing...
[1434:47] RT window set to 0.92639
[1434:47] Ion mobility window set to 0.0107164
[1434:47] Recommended MS1 mass accuracy setting: 12.4666 ppm
[1435:07] Removing low confidence identifications
[1435:07] Searching PTM decoys
[1435:07] Removing interfering precursors
[1435:09] Training neural networks: 37851 targets, 36147 decoys
[1435:17] Number of IDs at 0.01 FDR: 30910
[1435:17] Calculating protein q-values
[1435:17] Number of genes identified at 1% FDR: 5219 (precursor-level), 4508 (protein-level) (inference performed using proteotypic peptides only)
[1435:17] Quantification

[1435:23] File #4/8
[1435:23] Loading run G:\Shaswati_timsTOF\14042025_tims\cisR3_11042025_S1-A7_1_1192.d
[1437:24] 38903 library precursors are potentially detectable
[1437:24] Processing...
[1437:52] RT window set to 0.922381
[1437:52] Ion mobility window set to 0.0103516
[1437:52] Recommended MS1 mass accuracy setting: 12.1994 ppm
[1438:11] Removing low confidence identifications
[1438:11] Searching PTM decoys
[1438:11] Removing interfering precursors
[1438:14] Training neural networks: 37859 targets, 35235 decoys
[1438:21] Number of IDs at 0.01 FDR: 30711
[1438:21] Calculating protein q-values
[1438:21] Number of genes identified at 1% FDR: 5216 (precursor-level), 4595 (protein-level) (inference performed using proteotypic peptides only)
[1438:22] Quantification

[1438:27] File #5/8
[1438:27] Loading run G:\Shaswati_timsTOF\14042025_tims\cisS1_11042025_S1-A2_1_1187.d
[1440:06] 38903 library precursors are potentially detectable
[1440:06] Processing...
[1440:33] RT window set to 0.92946
[1440:33] Ion mobility window set to 0.010276
[1440:33] Recommended MS1 mass accuracy setting: 11.8801 ppm
[1440:51] Removing low confidence identifications
[1440:51] Searching PTM decoys
[1440:51] Removing interfering precursors
[1440:53] Training neural networks: 37219 targets, 33498 decoys
[1441:00] Number of IDs at 0.01 FDR: 29484
[1441:01] Calculating protein q-values
[1441:01] Number of genes identified at 1% FDR: 5147 (precursor-level), 4392 (protein-level) (inference performed using proteotypic peptides only)
[1441:01] Quantification

[1441:06] File #6/8
[1441:06] Loading run G:\Shaswati_timsTOF\14042025_tims\cisS2_11042025_S1-A3_1_1188.d
[1442:38] 38903 library precursors are potentially detectable
[1442:38] Processing...
[1443:04] RT window set to 0.921142
[1443:04] Ion mobility window set to 0.0100938
[1443:04] Recommended MS1 mass accuracy setting: 12.5809 ppm
[1443:21] Removing low confidence identifications
[1443:21] Searching PTM decoys
[1443:21] Removing interfering precursors
[1443:23] Training neural networks: 37227 targets, 32873 decoys
[1443:30] Number of IDs at 0.01 FDR: 29178
[1443:30] Calculating protein q-values
[1443:30] Number of genes identified at 1% FDR: 5108 (precursor-level), 4342 (protein-level) (inference performed using proteotypic peptides only)
[1443:30] Quantification

[1443:35] File #7/8
[1443:35] Loading run G:\Shaswati_timsTOF\14042025_tims\cisS3_11042025_S1-A4_1_1189.d
[1445:05] 38903 library precursors are potentially detectable
[1445:05] Processing...
[1445:31] RT window set to 0.91529
[1445:31] Ion mobility window set to 0.01
[1445:31] Recommended MS1 mass accuracy setting: 12.9087 ppm
[1445:48] Removing low confidence identifications
[1445:48] Searching PTM decoys
[1445:48] Removing interfering precursors
[1445:50] Training neural networks: 36797 targets, 32527 decoys
[1445:57] Number of IDs at 0.01 FDR: 28782
[1445:58] Calculating protein q-values
[1445:58] Number of genes identified at 1% FDR: 5069 (precursor-level), 4507 (protein-level) (inference performed using proteotypic peptides only)
[1445:58] Quantification

[1446:02] File #8/8
[1446:02] Loading run G:\Shaswati_timsTOF\14042025_tims\CSP_Pool1_11042025_S1-B1_1_1195.d
[1447:38] 38903 library precursors are potentially detectable
[1447:38] Processing...
[1448:05] RT window set to 0.912024
[1448:05] Ion mobility window set to 0.01
[1448:05] Recommended MS1 mass accuracy setting: 12.5987 ppm
[1448:22] Removing low confidence identifications
[1448:22] Searching PTM decoys
[1448:22] Removing interfering precursors
[1448:24] Training neural networks: 37493 targets, 32337 decoys
[1448:31] Number of IDs at 0.01 FDR: 32034
[1448:32] Calculating protein q-values
[1448:32] Number of genes identified at 1% FDR: 5205 (precursor-level), 4436 (protein-level) (inference performed using proteotypic peptides only)
[1448:32] Quantification

[1448:37] Cross-run analysis
[1448:37] Reading quantification information: 8 files
[1448:37] Quantifying peptides
[1448:41] Quantifying proteins
[1448:42] Calculating q-values for protein and gene groups
[1448:42] Calculating global q-values for protein and gene groups
[1448:42] Writing report
[1449:02] Report saved to G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report.tsv.
[1449:02] Saving precursor levels matrix
[1449:02] Precursor levels matrix (1% precursor and protein group FDR) saved to G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report.pr_matrix.tsv.
[1449:02] Saving protein group levels matrix
[1449:02] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report.pg_matrix.tsv.
[1449:02] Saving gene group levels matrix
[1449:02] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report.gg_matrix.tsv.
[1449:02] Saving unique genes levels matrix
[1449:03] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report.unique_genes_matrix.tsv.
[1449:03] Stats report saved to G:\Shaswati_timsTOF\14042025_tims\OUTPUT\report.stats.tsv

Finished