DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks)
Compiled on Apr 14 2022 15:31:19
Current date and time: Wed Apr 16 15:14:26 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\16042025_CSP_CM\cis_Pool1_11042025_S1-A1_1_1186.d  --f G:\Shaswati_timsTOF\16042025_CSP_CM\CM_Pool1_11042025_S1-C1_1_1204.d  --f G:\Shaswati_timsTOF\16042025_CSP_CM\CMR1_11042025_S1-C5_1_1208.d  --f G:\Shaswati_timsTOF\16042025_CSP_CM\CMR2_11042025_S1-C6_1_1209.d  --f G:\Shaswati_timsTOF\16042025_CSP_CM\CMR3_11042025_S1-C7_1_1210.d  --f G:\Shaswati_timsTOF\16042025_CSP_CM\CMS1_11042025_S1-C2_1_1205.d  --f G:\Shaswati_timsTOF\16042025_CSP_CM\CMS2_11042025_S1-C3_1_1206.d  --f G:\Shaswati_timsTOF\16042025_CSP_CM\CMS3_11042025_S1-C4_1_1207.d  --f G:\Shaswati_timsTOF\16042025_CSP_CM\CSP_Pool1_11042025_S1-B1_1_1195.d  --f G:\Shaswati_timsTOF\16042025_CSP_CM\CSPR1_11042025_S1-B5_1_1199.d  --f G:\Shaswati_timsTOF\16042025_CSP_CM\CSPR2_11042025_S1-B6_1_1200.d  --f G:\Shaswati_timsTOF\16042025_CSP_CM\CSPR3_11042025_S1-B7_1_1201.d  --f G:\Shaswati_timsTOF\16042025_CSP_CM\CSPS1_11042025_S1-B2_1_1196.d  --f G:\Shaswati_timsTOF\16042025_CSP_CM\CSPS2_11042025_S1-B3_1_1197.d  --f G:\Shaswati_timsTOF\16042025_CSP_CM\CSPS3_11042025_S1-B4_1_1198.d  --lib  --threads 4 --verbose 1 --out G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report.tsv --qvalue 0.01 --matrices --out-lib G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report-lib.tsv --gen-spec-lib --predictor --fasta G:\Shaswati_timsTOF\16042025_CSP_CM\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 100 --max-pr-mz 1700 --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 100
Max precursor m/z set to 1700
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 

15 files will be processed
[0:00] Loading FASTA G:\Shaswati_timsTOF\16042025_CSP_CM\uniprotkb_proteome_UP000005640_AND_revi_2025_03_20.fasta
[3:57] Processing FASTA
[4:23] Assembling elution groups
[4:42] 9066558 precursors generated
[4:42] Gene names missing for some isoforms
[4:42] Library contains 20382 proteins, and 20188 genes
[4:42] [5:07] [143:43] [176:32] [177:39] [177:47] Saving the library to G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report-lib.predicted.speclib
[178:39] Initialising library

[178:46] First pass: generating a spectral library from DIA data
[178:46] File #1/15
[178:46] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\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.
[180:28] 6581489 library precursors are potentially detectable
[180:29] Processing...
[234:57] RT window set to 2.70914
[234:57] Ion mobility window set to 0.0340222
[234:57] Peak width: 6.556
[234:57] Scan window radius set to 14
[234:58] Recommended MS1 mass accuracy setting: 12.4776 ppm
[303:18] Optimised mass accuracy: 10.1426 ppm
[393:55] Removing low confidence identifications
[393:56] Searching PTM decoys
[394:56] Removing interfering precursors
[395:00] Training neural networks: 16931 targets, 16708 decoys
[395:05] Number of IDs at 0.01 FDR: 12665
[395:05] Calculating protein q-values
[395:06] Number of genes identified at 1% FDR: 2416 (precursor-level), 2290 (protein-level) (inference performed using proteotypic peptides only)
[395:06] Quantification
[395:07] Precursors with monitored PTMs at 1% FDR: 0 out of 16
[395:07] Unmodified precursors with monitored PTM sites at 1% FDR: 0 out of 9
[395:09] Quantification information saved to G:\Shaswati_timsTOF\16042025_CSP_CM\cis_Pool1_11042025_S1-A1_1_1186.d.quant.

[395:15] File #2/15
[395:15] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CM_Pool1_11042025_S1-C1_1_1204.d
[396:54] 6581489 library precursors are potentially detectable
[396:55] Processing...
[451:21] RT window set to 2.67355
[451:21] Ion mobility window set to 0.0349583
[451:21] Recommended MS1 mass accuracy setting: 12.1194 ppm
[542:35] Removing low confidence identifications
[542:36] Searching PTM decoys
[543:38] Removing interfering precursors
[543:42] Training neural networks: 45706 targets, 28428 decoys
[543:51] Number of IDs at 0.01 FDR: 20898
[543:51] Calculating protein q-values
[543:52] Number of genes identified at 1% FDR: 3707 (precursor-level), 3312 (protein-level) (inference performed using proteotypic peptides only)
[543:52] Quantification
[543:53] Precursors with monitored PTMs at 1% FDR: 0 out of 19
[543:53] Unmodified precursors with monitored PTM sites at 1% FDR: 0 out of 12
[543:55] Quantification information saved to G:\Shaswati_timsTOF\16042025_CSP_CM\CM_Pool1_11042025_S1-C1_1_1204.d.quant.

[544:00] File #3/15
[544:00] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMR1_11042025_S1-C5_1_1208.d
[546:05] 6581489 library precursors are potentially detectable
[546:06] Processing...
[603:59] RT window set to 2.66353
[603:59] Ion mobility window set to 0.0358285
[604:00] Recommended MS1 mass accuracy setting: 12.0352 ppm
[716:18] Removing low confidence identifications
[716:19] Searching PTM decoys
[717:36] Removing interfering precursors
[717:41] Training neural networks: 48367 targets, 29213 decoys
[717:49] Number of IDs at 0.01 FDR: 22737
[717:50] Calculating protein q-values
[717:51] Number of genes identified at 1% FDR: 3796 (precursor-level), 3382 (protein-level) (inference performed using proteotypic peptides only)
[717:51] Quantification
[717:52] Precursors with monitored PTMs at 1% FDR: 0 out of 25
[717:52] Unmodified precursors with monitored PTM sites at 1% FDR: 0 out of 14
[717:59] Quantification information saved to G:\Shaswati_timsTOF\16042025_CSP_CM\CMR1_11042025_S1-C5_1_1208.d.quant.

[718:04] File #4/15
[718:04] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMR2_11042025_S1-C6_1_1209.d
[720:06] 6581489 library precursors are potentially detectable
[720:07] Processing...
[776:08] RT window set to 2.59605
[776:08] Ion mobility window set to 0.0369647
[776:09] Recommended MS1 mass accuracy setting: 12.3556 ppm
[882:33] Removing low confidence identifications
[882:33] Searching PTM decoys
[883:46] Removing interfering precursors
[883:51] Training neural networks: 40896 targets, 24468 decoys
[883:58] Number of IDs at 0.01 FDR: 20673
[883:59] Calculating protein q-values
[884:00] Number of genes identified at 1% FDR: 3510 (precursor-level), 3140 (protein-level) (inference performed using proteotypic peptides only)
[884:00] Quantification
[884:01] Precursors with monitored PTMs at 1% FDR: 0 out of 27
[884:01] Unmodified precursors with monitored PTM sites at 1% FDR: 0 out of 12
[884:03] Quantification information saved to G:\Shaswati_timsTOF\16042025_CSP_CM\CMR2_11042025_S1-C6_1_1209.d.quant.

[884:08] File #5/15
[884:08] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMR3_11042025_S1-C7_1_1210.d
[886:05] 6581489 library precursors are potentially detectable
[886:06] Processing...
[942:27] RT window set to 2.6141
[942:27] Ion mobility window set to 0.0362005
[942:28] Recommended MS1 mass accuracy setting: 11.8413 ppm
[1047:03] Removing low confidence identifications
[1047:04] Searching PTM decoys
[1048:16] Removing interfering precursors
[1048:21] Training neural networks: 47067 targets, 29262 decoys
[1048:30] Number of IDs at 0.01 FDR: 22463
[1048:31] Calculating protein q-values
[1048:31] Number of genes identified at 1% FDR: 3712 (precursor-level), 3335 (protein-level) (inference performed using proteotypic peptides only)
[1048:32] Quantification
[1048:33] Precursors with monitored PTMs at 1% FDR: 0 out of 25
[1048:33] Unmodified precursors with monitored PTM sites at 1% FDR: 0 out of 15
[1048:35] Quantification information saved to G:\Shaswati_timsTOF\16042025_CSP_CM\CMR3_11042025_S1-C7_1_1210.d.quant.

[1048:40] File #6/15
[1048:40] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMS1_11042025_S1-C2_1_1205.d
[1050:14] 6581489 library precursors are potentially detectable
[1050:15] Processing...
[1103:32] RT window set to 2.7314
[1103:32] Ion mobility window set to 0.0367723
[1103:32] Recommended MS1 mass accuracy setting: 11.6399 ppm
[1196:25] Removing low confidence identifications
[1196:26] Searching PTM decoys
[1197:29] Removing interfering precursors
[1197:33] Training neural networks: 37892 targets, 23872 decoys
[1197:40] Number of IDs at 0.01 FDR: 19525
[1197:41] Calculating protein q-values
[1197:42] Number of genes identified at 1% FDR: 3447 (precursor-level), 3089 (protein-level) (inference performed using proteotypic peptides only)
[1197:42] Quantification
[1197:43] Precursors with monitored PTMs at 1% FDR: 0 out of 25
[1197:43] Unmodified precursors with monitored PTM sites at 1% FDR: 0 out of 17
[1197:45] Quantification information saved to G:\Shaswati_timsTOF\16042025_CSP_CM\CMS1_11042025_S1-C2_1_1205.d.quant.

[1197:49] File #7/15
[1197:49] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMS2_11042025_S1-C3_1_1206.d
[1199:34] 6581489 library precursors are potentially detectable
[1199:35] Processing...
[1255:36] RT window set to 2.69991
[1255:36] Ion mobility window set to 0.0355536
[1255:37] Recommended MS1 mass accuracy setting: 12.1332 ppm
[1353:46] Removing low confidence identifications
[1353:47] Searching PTM decoys
[1354:54] Removing interfering precursors
[1354:59] Training neural networks: 47673 targets, 30282 decoys
[1355:08] Number of IDs at 0.01 FDR: 23808
[1355:08] Calculating protein q-values
[1355:09] Number of genes identified at 1% FDR: 3956 (precursor-level), 3545 (protein-level) (inference performed using proteotypic peptides only)
[1355:09] Quantification
[1355:10] Precursors with monitored PTMs at 1% FDR: 0 out of 35
[1355:10] Unmodified precursors with monitored PTM sites at 1% FDR: 0 out of 17
[1355:17] Quantification information saved to G:\Shaswati_timsTOF\16042025_CSP_CM\CMS2_11042025_S1-C3_1_1206.d.quant.

[1355:22] File #8/15
[1355:22] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMS3_11042025_S1-C4_1_1207.d
[1357:05] 6581489 library precursors are potentially detectable
[1357:06] Processing...
[1412:36] RT window set to 2.71238
[1412:36] Ion mobility window set to 0.0347697
[1412:37] Recommended MS1 mass accuracy setting: 12.4834 ppm
[1513:39] Removing low confidence identifications
[1513:39] Searching PTM decoys
[1514:48] Removing interfering precursors
[1514:52] Training neural networks: 38695 targets, 23641 decoys
[1515:00] Number of IDs at 0.01 FDR: 19732
[1515:00] Calculating protein q-values
[1515:01] Number of genes identified at 1% FDR: 3446 (precursor-level), 3148 (protein-level) (inference performed using proteotypic peptides only)
[1515:01] Quantification
[1515:02] Precursors with monitored PTMs at 1% FDR: 0 out of 32
[1515:02] Unmodified precursors with monitored PTM sites at 1% FDR: 0 out of 14
[1515:05] Quantification information saved to G:\Shaswati_timsTOF\16042025_CSP_CM\CMS3_11042025_S1-C4_1_1207.d.quant.

[1515:09] File #9/15
[1515:09] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSP_Pool1_11042025_S1-B1_1_1195.d
[1516:58] 6581489 library precursors are potentially detectable
[1516:59] Processing...
[1573:45] RT window set to 2.78914
[1573:45] Ion mobility window set to 0.0354879
[1573:46] Recommended MS1 mass accuracy setting: 12.053 ppm
[1673:38] Removing low confidence identifications
[1673:38] Searching PTM decoys
[1674:44] Removing interfering precursors
[1674:49] Training neural networks: 43475 targets, 27414 decoys
[1674:57] Number of IDs at 0.01 FDR: 20929
[1674:58] Calculating protein q-values
[1674:58] Number of genes identified at 1% FDR: 3646 (precursor-level), 3295 (protein-level) (inference performed using proteotypic peptides only)
[1674:59] Quantification
[1675:00] Precursors with monitored PTMs at 1% FDR: 0 out of 15
[1675:00] Unmodified precursors with monitored PTM sites at 1% FDR: 0 out of 9
[1675:07] Quantification information saved to G:\Shaswati_timsTOF\16042025_CSP_CM\CSP_Pool1_11042025_S1-B1_1_1195.d.quant.

[1675:11] File #10/15
[1675:11] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPR1_11042025_S1-B5_1_1199.d
[1676:49] 6581489 library precursors are potentially detectable
[1676:49] Processing...
[1751:33] RT window set to 2.46299
[1751:33] Ion mobility window set to 0.0332693
[1751:34] Recommended MS1 mass accuracy setting: 12.6791 ppm
[1833:18] Removing low confidence identifications
[1833:19] Searching PTM decoys
[1834:12] Removing interfering precursors
[1834:16] Training neural networks: 33422 targets, 20605 decoys
[1834:22] Number of IDs at 0.01 FDR: 15151
[1834:22] Calculating protein q-values
[1834:23] Number of genes identified at 1% FDR: 3109 (precursor-level), 2796 (protein-level) (inference performed using proteotypic peptides only)
[1834:24] Quantification
[1834:26] Quantification information saved to G:\Shaswati_timsTOF\16042025_CSP_CM\CSPR1_11042025_S1-B5_1_1199.d.quant.

[1834:30] File #11/15
[1834:30] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPR2_11042025_S1-B6_1_1200.d
[1836:07] 6581489 library precursors are potentially detectable
[1836:08] Processing...
[1912:54] RT window set to 2.39918
[1912:54] Ion mobility window set to 0.0319768
[1912:55] Recommended MS1 mass accuracy setting: 11.917 ppm
[1990:54] Removing low confidence identifications
[1990:54] Searching PTM decoys
[1991:46] Removing interfering precursors
[1991:49] Training neural networks: 34616 targets, 21965 decoys
[1991:56] Number of IDs at 0.01 FDR: 15681
[1991:57] Calculating protein q-values
[1991:57] Number of genes identified at 1% FDR: 3209 (precursor-level), 2872 (protein-level) (inference performed using proteotypic peptides only)
[1991:58] Quantification
[1992:05] Quantification information saved to G:\Shaswati_timsTOF\16042025_CSP_CM\CSPR2_11042025_S1-B6_1_1200.d.quant.

[1992:10] File #12/15
[1992:10] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPR3_11042025_S1-B7_1_1201.d
[1993:49] 6581489 library precursors are potentially detectable
[1993:49] Processing...
[2070:17] RT window set to 2.44429
[2070:17] Ion mobility window set to 0.0336309
[2070:18] Recommended MS1 mass accuracy setting: 11.962 ppm
[2152:45] Removing low confidence identifications
[2152:45] Searching PTM decoys
[2153:39] Removing interfering precursors
[2153:43] Training neural networks: 33395 targets, 21742 decoys
[2153:49] Number of IDs at 0.01 FDR: 15829
[2153:50] Calculating protein q-values
[2153:50] Number of genes identified at 1% FDR: 3264 (precursor-level), 2904 (protein-level) (inference performed using proteotypic peptides only)
[2153:51] Quantification
[2153:53] Quantification information saved to G:\Shaswati_timsTOF\16042025_CSP_CM\CSPR3_11042025_S1-B7_1_1201.d.quant.

[2153:58] File #13/15
[2153:58] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPS1_11042025_S1-B2_1_1196.d
[2155:40] 6581489 library precursors are potentially detectable
[2155:41] Processing...
[2234:05] RT window set to 2.65608
[2234:05] Ion mobility window set to 0.0371642
[2234:06] Recommended MS1 mass accuracy setting: 12.376 ppm
[2325:12] Removing low confidence identifications
[2325:12] Searching PTM decoys
[2326:11] Removing interfering precursors
[2326:15] Training neural networks: 32889 targets, 21396 decoys
[2326:21] Number of IDs at 0.01 FDR: 14852
[2326:21] Calculating protein q-values
[2326:22] Number of genes identified at 1% FDR: 2605 (precursor-level), 2328 (protein-level) (inference performed using proteotypic peptides only)
[2326:22] Quantification
[2326:25] Quantification information saved to G:\Shaswati_timsTOF\16042025_CSP_CM\CSPS1_11042025_S1-B2_1_1196.d.quant.

[2326:30] File #14/15
[2326:30] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPS2_11042025_S1-B3_1_1197.d
[2328:02] 6581489 library precursors are potentially detectable
[2328:02] Processing...
[2415:50] RT window set to 2.37185
[2415:50] Ion mobility window set to 0.0319618
[2415:51] Recommended MS1 mass accuracy setting: 11.9919 ppm
[2488:45] Removing low confidence identifications
[2488:46] Searching PTM decoys
[2489:31] Removing interfering precursors
[2489:34] Training neural networks: 26409 targets, 16057 decoys
[2489:40] Number of IDs at 0.01 FDR: 12182
[2489:40] Calculating protein q-values
[2489:41] Number of genes identified at 1% FDR: 2246 (precursor-level), 1922 (protein-level) (inference performed using proteotypic peptides only)
[2489:41] Quantification
[2489:44] Quantification information saved to G:\Shaswati_timsTOF\16042025_CSP_CM\CSPS2_11042025_S1-B3_1_1197.d.quant.

[2489:48] File #15/15
[2489:48] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPS3_11042025_S1-B4_1_1198.d
[2491:15] 6581489 library precursors are potentially detectable
[2491:16] Processing...
[2579:11] RT window set to 2.37351
[2579:11] Ion mobility window set to 0.031448
[2579:12] Recommended MS1 mass accuracy setting: 11.8427 ppm
[2649:17] Removing low confidence identifications
[2649:18] Searching PTM decoys
[2650:02] Removing interfering precursors
[2650:05] Training neural networks: 21857 targets, 12869 decoys
[2650:09] Number of IDs at 0.01 FDR: 10146
[2650:10] Calculating protein q-values
[2650:11] Number of genes identified at 1% FDR: 1919 (precursor-level), 1682 (protein-level) (inference performed using proteotypic peptides only)
[2650:11] Quantification
[2650:13] Quantification information saved to G:\Shaswati_timsTOF\16042025_CSP_CM\CSPS3_11042025_S1-B4_1_1198.d.quant.

[2650:17] Cross-run analysis
[2650:17] Reading quantification information: 15 files
[2650:19] Quantifying peptides
[2650:24] Assembling protein groups
[2650:29] Quantifying proteins
[2650:31] Calculating q-values for protein and gene groups
[2650:32] Calculating global q-values for protein and gene groups
[2650:32] Writing report
[2650:55] Report saved to G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report-first-pass.tsv.
[2650:55] Saving precursor levels matrix
[2650:56] Precursor levels matrix (1% precursor and protein group FDR) saved to G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report-first-pass.pr_matrix.tsv.
[2650:56] Saving protein group levels matrix
[2650:56] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report-first-pass.pg_matrix.tsv.
[2650:56] Saving gene group levels matrix
[2650:56] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report-first-pass.gg_matrix.tsv.
[2650:56] Saving unique genes levels matrix
[2650:56] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report-first-pass.unique_genes_matrix.tsv.
[2650:56] Stats report saved to G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report-first-pass.stats.tsv
[2650:56] Generating spectral library:
[2650:56] 35934 precursors passing the FDR threshold are to be extracted
[2650:56] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\cis_Pool1_11042025_S1-A1_1_1186.d
[2652:33] 6581489 library precursors are potentially detectable
[2652:34] 244 spectra added to the library
[2652:38] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CM_Pool1_11042025_S1-C1_1_1204.d
[2654:11] 6581489 library precursors are potentially detectable
[2654:13] 1142 spectra added to the library
[2654:17] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMR1_11042025_S1-C5_1_1208.d
[2656:14] 6581489 library precursors are potentially detectable
[2656:16] 2228 spectra added to the library
[2656:21] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMR2_11042025_S1-C6_1_1209.d
[2658:16] 6581489 library precursors are potentially detectable
[2658:18] 2898 spectra added to the library
[2658:23] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMR3_11042025_S1-C7_1_1210.d
[2660:13] 6581489 library precursors are potentially detectable
[2660:16] 6663 spectra added to the library
[2660:21] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMS1_11042025_S1-C2_1_1205.d
[2661:49] 6581489 library precursors are potentially detectable
[2661:50] 1149 spectra added to the library
[2661:55] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMS2_11042025_S1-C3_1_1206.d
[2663:34] 6581489 library precursors are potentially detectable
[2663:35] 1883 spectra added to the library
[2663:40] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMS3_11042025_S1-C4_1_1207.d
[2665:18] 6581489 library precursors are potentially detectable
[2665:19] 721 spectra added to the library
[2665:24] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSP_Pool1_11042025_S1-B1_1_1195.d
[2667:06] 6581489 library precursors are potentially detectable
[2667:07] 3440 spectra added to the library
[2667:12] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPR1_11042025_S1-B5_1_1199.d
[2668:44] 6581489 library precursors are potentially detectable
[2668:45] 503 spectra added to the library
[2668:50] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPR2_11042025_S1-B6_1_1200.d
[2670:21] 6581489 library precursors are potentially detectable
[2670:22] 1185 spectra added to the library
[2670:27] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPR3_11042025_S1-B7_1_1201.d
[2672:00] 6581489 library precursors are potentially detectable
[2672:01] 2051 spectra added to the library
[2672:06] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPS1_11042025_S1-B2_1_1196.d
[2673:41] 6581489 library precursors are potentially detectable
[2673:42] 550 spectra added to the library
[2673:47] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPS2_11042025_S1-B3_1_1197.d
[2675:11] 6581489 library precursors are potentially detectable
[2675:12] 229 spectra added to the library
[2675:17] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPS3_11042025_S1-B4_1_1198.d
[2676:38] 6581489 library precursors are potentially detectable
[2676:39] 260 spectra added to the library
[2676:44] Saving spectral library to G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report-lib.tsv
[2676:52] 35934 precursors saved
[2676:52] Loading the generated library and saving it in the .speclib format
[2676:52] Loading spectral library G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report-lib.tsv
[2676:54] Spectral library loaded: 6495 protein isoforms, 6643 protein groups and 35934 precursors in 34015 elution groups.
[2676:54] Loading protein annotations from FASTA G:\Shaswati_timsTOF\16042025_CSP_CM\uniprotkb_proteome_UP000005640_AND_revi_2025_03_20.fasta
[2676:55] Gene names missing for some isoforms
[2676:55] Library contains 6495 proteins, and 6488 genes
[2676:55] Saving the library to G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report-lib.tsv.speclib

[2677:05] Second pass: using the newly created spectral library to reanalyse the data
[2677:05] File #1/15
[2677:05] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\cis_Pool1_11042025_S1-A1_1_1186.d
[2678:33] 35934 library precursors are potentially detectable
[2678:34] Processing...
[2679:00] RT window set to 0.957683
[2679:00] Ion mobility window set to 0.0101165
[2679:00] Recommended MS1 mass accuracy setting: 12.2178 ppm
[2679:16] Removing low confidence identifications
[2679:16] Searching PTM decoys
[2679:16] Removing interfering precursors
[2679:18] Training neural networks: 35108 targets, 28754 decoys
[2679:24] Number of IDs at 0.01 FDR: 31940
[2679:25] Calculating protein q-values
[2679:25] Number of genes identified at 1% FDR: 4855 (precursor-level), 4119 (protein-level) (inference performed using proteotypic peptides only)
[2679:25] Quantification

[2679:32] File #2/15
[2679:32] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CM_Pool1_11042025_S1-C1_1_1204.d
[2680:59] 35934 library precursors are potentially detectable
[2680:59] Processing...
[2681:26] RT window set to 0.979171
[2681:26] Ion mobility window set to 0.0101927
[2681:26] Recommended MS1 mass accuracy setting: 12.7171 ppm
[2681:42] Removing low confidence identifications
[2681:42] Searching PTM decoys
[2681:42] Removing interfering precursors
[2681:44] Training neural networks: 35316 targets, 29300 decoys
[2681:51] Number of IDs at 0.01 FDR: 32535
[2681:51] Calculating protein q-values
[2681:51] Number of genes identified at 1% FDR: 4909 (precursor-level), 4130 (protein-level) (inference performed using proteotypic peptides only)
[2681:52] Quantification

[2681:59] File #3/15
[2681:59] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMR1_11042025_S1-C5_1_1208.d
[2683:50] 35934 library precursors are potentially detectable
[2683:50] Processing...
[2684:18] RT window set to 0.982258
[2684:18] Ion mobility window set to 0.0104818
[2684:18] Recommended MS1 mass accuracy setting: 12.2237 ppm
[2684:36] Removing low confidence identifications
[2684:36] Searching PTM decoys
[2684:36] Removing interfering precursors
[2684:38] Training neural networks: 35359 targets, 31287 decoys
[2684:45] Number of IDs at 0.01 FDR: 32222
[2684:45] Calculating protein q-values
[2684:45] Number of genes identified at 1% FDR: 4852 (precursor-level), 4223 (protein-level) (inference performed using proteotypic peptides only)
[2684:45] Quantification

[2684:53] File #4/15
[2684:53] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMR2_11042025_S1-C6_1_1209.d
[2686:42] 35934 library precursors are potentially detectable
[2686:42] Processing...
[2687:10] RT window set to 0.97209
[2687:10] Ion mobility window set to 0.0105052
[2687:10] Recommended MS1 mass accuracy setting: 11.6737 ppm
[2687:28] Removing low confidence identifications
[2687:28] Searching PTM decoys
[2687:28] Removing interfering precursors
[2687:31] Training neural networks: 35319 targets, 31156 decoys
[2687:37] Number of IDs at 0.01 FDR: 32184
[2687:38] Calculating protein q-values
[2687:38] Number of genes identified at 1% FDR: 4857 (precursor-level), 4052 (protein-level) (inference performed using proteotypic peptides only)
[2687:38] Quantification

[2687:45] File #5/15
[2687:45] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMR3_11042025_S1-C7_1_1210.d
[2689:30] 35934 library precursors are potentially detectable
[2689:30] Processing...
[2689:58] RT window set to 0.965451
[2689:58] Ion mobility window set to 0.0104321
[2689:58] Recommended MS1 mass accuracy setting: 12.5307 ppm
[2690:16] Removing low confidence identifications
[2690:16] Searching PTM decoys
[2690:16] Removing interfering precursors
[2690:18] Training neural networks: 35320 targets, 30795 decoys
[2690:24] Number of IDs at 0.01 FDR: 32125
[2690:25] Calculating protein q-values
[2690:25] Number of genes identified at 1% FDR: 4849 (precursor-level), 4154 (protein-level) (inference performed using proteotypic peptides only)
[2690:25] Quantification

[2690:32] File #6/15
[2690:32] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMS1_11042025_S1-C2_1_1205.d
[2691:56] 35934 library precursors are potentially detectable
[2691:56] Processing...
[2692:23] RT window set to 0.97893
[2692:23] Ion mobility window set to 0.0104347
[2692:23] Recommended MS1 mass accuracy setting: 12.4791 ppm
[2692:39] Removing low confidence identifications
[2692:39] Searching PTM decoys
[2692:39] Removing interfering precursors
[2692:42] Training neural networks: 35117 targets, 29324 decoys
[2692:48] Number of IDs at 0.01 FDR: 31623
[2692:48] Calculating protein q-values
[2692:49] Number of genes identified at 1% FDR: 4818 (precursor-level), 4025 (protein-level) (inference performed using proteotypic peptides only)
[2692:49] Quantification

[2692:55] File #7/15
[2692:55] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMS2_11042025_S1-C3_1_1206.d
[2694:30] 35934 library precursors are potentially detectable
[2694:30] Processing...
[2694:57] RT window set to 0.955204
[2694:57] Ion mobility window set to 0.0101979
[2694:57] Recommended MS1 mass accuracy setting: 12.7906 ppm
[2695:14] Removing low confidence identifications
[2695:14] Searching PTM decoys
[2695:14] Removing interfering precursors
[2695:16] Training neural networks: 35204 targets, 30224 decoys
[2695:23] Number of IDs at 0.01 FDR: 32049
[2695:23] Calculating protein q-values
[2695:24] Number of genes identified at 1% FDR: 4840 (precursor-level), 4076 (protein-level) (inference performed using proteotypic peptides only)
[2695:24] Quantification

[2695:30] File #8/15
[2695:30] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CMS3_11042025_S1-C4_1_1207.d
[2697:03] 35934 library precursors are potentially detectable
[2697:03] Processing...
[2697:30] RT window set to 0.972083
[2697:30] Ion mobility window set to 0.0104349
[2697:30] Recommended MS1 mass accuracy setting: 12.5929 ppm
[2697:47] Removing low confidence identifications
[2697:47] Searching PTM decoys
[2697:47] Removing interfering precursors
[2697:49] Training neural networks: 35215 targets, 30250 decoys
[2697:56] Number of IDs at 0.01 FDR: 31981
[2697:57] Calculating protein q-values
[2697:57] Number of genes identified at 1% FDR: 4858 (precursor-level), 4164 (protein-level) (inference performed using proteotypic peptides only)
[2697:57] Quantification

[2698:03] File #9/15
[2698:03] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSP_Pool1_11042025_S1-B1_1_1195.d
[2699:40] 35934 library precursors are potentially detectable
[2699:40] Processing...
[2700:08] RT window set to 0.955577
[2700:08] Ion mobility window set to 0.0102187
[2700:08] Recommended MS1 mass accuracy setting: 12.6386 ppm
[2700:24] Removing low confidence identifications
[2700:24] Searching PTM decoys
[2700:24] Removing interfering precursors
[2700:26] Training neural networks: 35323 targets, 29655 decoys
[2700:33] Number of IDs at 0.01 FDR: 32848
[2700:33] Calculating protein q-values
[2700:33] Number of genes identified at 1% FDR: 4932 (precursor-level), 3979 (protein-level) (inference performed using proteotypic peptides only)
[2700:33] Quantification

[2700:40] File #10/15
[2700:40] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPR1_11042025_S1-B5_1_1199.d
[2702:07] 35934 library precursors are potentially detectable
[2702:07] Processing...
[2702:33] RT window set to 0.906524
[2702:33] Ion mobility window set to 0.01
[2702:33] Recommended MS1 mass accuracy setting: 13.2954 ppm
[2702:47] Removing low confidence identifications
[2702:47] Searching PTM decoys
[2702:47] Removing interfering precursors
[2702:49] Training neural networks: 33062 targets, 27398 decoys
[2702:55] Number of IDs at 0.01 FDR: 24867
[2702:56] Calculating protein q-values
[2702:56] Number of genes identified at 1% FDR: 4325 (precursor-level), 3622 (protein-level) (inference performed using proteotypic peptides only)
[2702:56] Quantification

[2703:02] File #11/15
[2703:02] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPR2_11042025_S1-B6_1_1200.d
[2704:28] 35934 library precursors are potentially detectable
[2704:28] Processing...
[2704:55] RT window set to 0.894073
[2704:55] Ion mobility window set to 0.01
[2704:55] Recommended MS1 mass accuracy setting: 12.6862 ppm
[2705:09] Removing low confidence identifications
[2705:09] Searching PTM decoys
[2705:09] Removing interfering precursors
[2705:11] Training neural networks: 32997 targets, 27147 decoys
[2705:17] Number of IDs at 0.01 FDR: 25019
[2705:17] Calculating protein q-values
[2705:17] Number of genes identified at 1% FDR: 4302 (precursor-level), 3556 (protein-level) (inference performed using proteotypic peptides only)
[2705:17] Quantification

[2705:24] File #12/15
[2705:24] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPR3_11042025_S1-B7_1_1201.d
[2706:52] 35934 library precursors are potentially detectable
[2706:52] Processing...
[2707:18] RT window set to 0.885063
[2707:18] Ion mobility window set to 0.01
[2707:18] Recommended MS1 mass accuracy setting: 11.6633 ppm
[2707:32] Removing low confidence identifications
[2707:32] Searching PTM decoys
[2707:32] Removing interfering precursors
[2707:34] Training neural networks: 33005 targets, 27325 decoys
[2707:40] Number of IDs at 0.01 FDR: 25022
[2707:41] Calculating protein q-values
[2707:41] Number of genes identified at 1% FDR: 4339 (precursor-level), 3665 (protein-level) (inference performed using proteotypic peptides only)
[2707:41] Quantification

[2707:48] File #13/15
[2707:48] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPS1_11042025_S1-B2_1_1196.d
[2709:18] 35934 library precursors are potentially detectable
[2709:18] Processing...
[2709:45] RT window set to 0.939219
[2709:45] Ion mobility window set to 0.0102135
[2709:45] Recommended MS1 mass accuracy setting: 12.7659 ppm
[2709:59] Removing low confidence identifications
[2709:59] Searching PTM decoys
[2709:59] Removing interfering precursors
[2710:01] Training neural networks: 33597 targets, 27183 decoys
[2710:07] Number of IDs at 0.01 FDR: 25531
[2710:07] Calculating protein q-values
[2710:07] Number of genes identified at 1% FDR: 4113 (precursor-level), 3425 (protein-level) (inference performed using proteotypic peptides only)
[2710:07] Quantification

[2710:14] File #14/15
[2710:14] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPS2_11042025_S1-B3_1_1197.d
[2711:32] 35934 library precursors are potentially detectable
[2711:32] Processing...
[2711:58] RT window set to 0.943447
[2711:58] Ion mobility window set to 0.01
[2711:58] Recommended MS1 mass accuracy setting: 12.839 ppm
[2712:11] Removing low confidence identifications
[2712:11] Searching PTM decoys
[2712:11] Removing interfering precursors
[2712:13] Training neural networks: 32762 targets, 25313 decoys
[2712:18] Number of IDs at 0.01 FDR: 23985
[2712:19] Calculating protein q-values
[2712:19] Number of genes identified at 1% FDR: 3974 (precursor-level), 3317 (protein-level) (inference performed using proteotypic peptides only)
[2712:19] Quantification

[2712:25] File #15/15
[2712:25] Loading run G:\Shaswati_timsTOF\16042025_CSP_CM\CSPS3_11042025_S1-B4_1_1198.d
[2713:41] 35934 library precursors are potentially detectable
[2713:41] Processing...
[2714:06] RT window set to 0.931166
[2714:06] Ion mobility window set to 0.0100653
[2714:06] Recommended MS1 mass accuracy setting: 12.5962 ppm
[2714:20] Removing low confidence identifications
[2714:20] Searching PTM decoys
[2714:20] Removing interfering precursors
[2714:22] Training neural networks: 32528 targets, 24794 decoys
[2714:28] Number of IDs at 0.01 FDR: 23821
[2714:28] Calculating protein q-values
[2714:28] Number of genes identified at 1% FDR: 3953 (precursor-level), 3218 (protein-level) (inference performed using proteotypic peptides only)
[2714:28] Quantification

[2714:34] Cross-run analysis
[2714:34] Reading quantification information: 15 files
[2714:35] Quantifying peptides
[2714:41] Quantifying proteins
[2714:43] Calculating q-values for protein and gene groups
[2714:44] Calculating global q-values for protein and gene groups
[2714:44] Writing report
[2715:19] Report saved to G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report.tsv.
[2715:19] Saving precursor levels matrix
[2715:21] Precursor levels matrix (1% precursor and protein group FDR) saved to G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report.pr_matrix.tsv.
[2715:21] Saving protein group levels matrix
[2715:21] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report.pg_matrix.tsv.
[2715:21] Saving gene group levels matrix
[2715:21] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report.gg_matrix.tsv.
[2715:21] Saving unique genes levels matrix
[2715:21] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report.unique_genes_matrix.tsv.
[2715:21] Stats report saved to G:\Shaswati_timsTOF\16042025_CSP_CM\Output\report.stats.tsv

Finished