DIA-NN 1.9 (Data-Independent Acquisition by Neural Networks)
Compiled on Jun  8 2024 20:00:31
Current date and time: Sat Apr 12 23:44:25 2025
CPU: GenuineIntel Intel(R) Core(TM) i7-14700
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 
Logical CPU cores: 28
diann.exe --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_1_sh_p62_FLAGIP_timsHT_DIA_Slot2-10_1_4808.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_2_sh_p62_WT_FLAGIP_timsHT_DIA_Slot2-11_1_4810.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_3_sh_p62_dNES_FLAGIP_timsHT_DIA_Slot2-12_1_4812.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_4_sh_p62_dNLS_FLAGIP_timsHT_DIA_Slot2-13_1_4814.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_5_sh_p62_MG123_FLAGIP_timsHT_DIA_Slot2-14_1_4816.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_6_sh_p62_WT_MG123_FLAGIP_timsHT_DIA_Slot2-15_1_4818.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_7_sh_p62_dNES_MG123_FLAGIP_timsHT_DIA_Slot2-16_1_4820.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_8_sh_p62_dNLS_MG123_FLAGIP_timsHT_DIA_Slot2-17_1_4822.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_9_sh_p62_FLAGIP_timsHT_DIA_Slot2-18_1_4824.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_10_sh_p62_WT_FLAGIP_timsHT_DIA_Slot2-19_1_4826.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_11_sh_p62_dNES_FLAGIP_timsHT_DIA_Slot2-20_1_4828.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_12_sh_p62_dNLS_FLAGIP_timsHT_DIA_Slot2-21_1_4830.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_13_sh_p62_MG123_FLAGIP_timsHT_DIA_Slot2-22_1_4832.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_14_sh_p62_WT_MG123_FLAGIP_timsHT_DIA_Slot2-23_1_4834.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_15_sh_p62_dNES_MG123_FLAGIP_timsHT_DIA_Slot2-24_1_4836.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_16_sh_p62_dNLS_MG123_FLAGIP_timsHT_DIA_Slot2-25_1_4838.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_17_sh_p62_FLAGIP_timsHT_DIA_Slot2-26_1_4840.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_18_sh_p62_WT_FLAGIP_timsHT_DIA_Slot2-27_1_4842.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_19_sh_p62_dNES_FLAGIP_timsHT_DIA_Slot2-28_1_4844.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_20_sh_p62_dNLS_FLAGIP_timsHT_DIA_Slot2-29_1_4846.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_21_sh_p62_MG123_FLAGIP_timsHT_DIA_Slot2-30_1_4849.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_22_sh_p62_WT_MG123_FLAGIP_timsHT_DIA_Slot2-31_1_4851.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_23_sh_p62_dNES_MG123_FLAGIP_timsHT_DIA_Slot2-32_1_4853.d  --f D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_24_sh_p62_dNLS_MG123_FLAGIP_timsHT_DIA_Slot2-33_1_4855.d  --lib D:\fasta_SpecLib\DAINN19\human_DIANN19.predicted.speclib --threads 20 --verbose 1 --out D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result\report.tsv --qvalue 0.01 --matrices --out-lib D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result\report-lib.tsv --gen-spec-lib --reannotate --xic --fasta camprotR_240512_cRAP_20190401_full_tags.fasta --cont-quant-exclude cRAP- --fasta D:\fasta_SpecLib\human_uniprotkb_taxonomy_id_9606_AND_reviewed_2024_03_07.fasta --met-excision --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --cut K*,R* --missed-cleavages 1 --unimod4 --mass-acc 15 --mass-acc-ms1 15 --use-quant --reanalyse --relaxed-prot-inf --rt-profiling --global-norm 

Thread number set to 20
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
Library precursors will be reannotated using the FASTA database
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 300
Max precursor m/z set to 1800
Min precursor charge set to 1
Max precursor charge set to 4
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
Cysteine carbamidomethylation enabled as a fixed modification
Existing .quant files will be used
A spectral library will be created from the DIA runs and used to reanalyse them; .quant files will only be saved to disk during the first step
Heuristic protein grouping will be used, to reduce the number of protein groups obtained; this mode is recommended for benchmarking protein ID numbers, GO/pathway and system-scale analyses
The spectral library (if generated) will retain the original spectra but will include empirically-aligned RTs
Median-based local normalisation disabled
Mass accuracy will be fixed to 1.5e-05 (MS2) and 1.5e-05 (MS1)
WARNING: combining reuse of .quant files with automatic optimisation of mass accuracies or scan window will lead to results that are different from those of the original analysis that produced the .quant files and is therefore not recommended

24 files will be processed
[0:00] Loading spectral library D:\fasta_SpecLib\DAINN19\human_DIANN19.predicted.speclib
[0:05] Library annotated with sequence database(s): camprotR_240512_cRAP_20190401_full_tags.fasta; D:\fasta_SpecLib\human_uniprotkb_taxonomy_id_9606_AND_reviewed_2024_03_07.fasta
[0:05] Spectral library loaded: 20535 protein isoforms, 29338 protein groups and 4301869 precursors in 1339383 elution groups.
[0:05] Loading FASTA camprotR_240512_cRAP_20190401_full_tags.fasta
[0:05] Loading FASTA D:\fasta_SpecLib\human_uniprotkb_taxonomy_id_9606_AND_reviewed_2024_03_07.fasta
[0:19] Reannotating library precursors with information from the FASTA database
[0:23] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
[0:23] 4301869 precursors generated
[0:23] Gene names missing for some isoforms
[0:23] Library contains 20535 proteins, and 20288 genes
[0:24] Initialising library

First pass: generating a spectral library from DIA data
[0:31] Cross-run analysis
[0:31] Reading quantification information: 24 files
[0:35] Quantifying peptides
[0:36] Assembling protein groups
[0:38] Quantifying proteins
[0:38] Calculating q-values for protein and gene groups
[0:41] Calculating global q-values for protein and gene groups
[0:41] Protein groups with global q-value <= 0.01: 6010
[0:43] Compressed report saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result\report-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[0:43] Writing report
[0:59] Report saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result\report-first-pass.tsv.
[0:59] Saving precursor levels matrix
[1:00] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result\report-first-pass.pr_matrix.tsv.
[1:00] Stats report saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result\report-first-pass.stats.tsv
[1:00] Generating spectral library:
[1:00] Saving spectral library to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result\report-lib.tsv
[1:04] 43700 target and 437 decoy precursors saved

[1:05] Loading spectral library D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result\report-lib.tsv
[1:08] Spectral library loaded: 7061 protein isoforms, 6899 protein groups and 44137 precursors in 41686 elution groups.
[1:08] Loading protein annotations from FASTA camprotR_240512_cRAP_20190401_full_tags.fasta
[1:08] Loading protein annotations from FASTA D:\fasta_SpecLib\human_uniprotkb_taxonomy_id_9606_AND_reviewed_2024_03_07.fasta
[1:08] Annotating library proteins with information from the FASTA database
[1:08] Gene names missing for some isoforms
[1:08] Library contains 7061 proteins, and 7040 genes
[1:08] Initialising library
[1:08] Saving the library to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result\report-lib.tsv.skyline.speclib


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

[1:08] File #1/24
[1:08] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_1_sh_p62_FLAGIP_timsHT_DIA_Slot2-10_1_4808.d
[1:33] 43700 library precursors are potentially detectable
[1:34] Processing...
[1:36] RT window set to 1.27219
[1:36] Ion mobility window set to 0.016379
[1:36] Peak width: 3.42
[1:36] Scan window radius set to 7
[1:36] Recommended MS1 mass accuracy setting: 15.5666 ppm
[1:39] Removing low confidence identifications
[1:39] Removing interfering precursors
[1:39] Training neural networks: 37841 targets, 19694 decoys
[1:41] Number of IDs at 0.01 FDR: 31447
[1:41] Calculating protein q-values
[1:41] Number of genes identified at 1% FDR: 5047 (precursor-level), 4676 (protein-level) (inference performed using proteotypic peptides only)
[1:41] Quantification
[1:42] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_1_sh_p62_FLAGIP_timsHT_DIA_Slot2-10_1_4808.xic.parquet

[1:42] File #2/24
[1:42] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_2_sh_p62_WT_FLAGIP_timsHT_DIA_Slot2-11_1_4810.d
[2:09] 43700 library precursors are potentially detectable
[2:09] Processing...
[2:11] RT window set to 1.26714
[2:11] Ion mobility window set to 0.0185381
[2:11] Recommended MS1 mass accuracy setting: 16.8268 ppm
[2:14] Removing low confidence identifications
[2:14] Removing interfering precursors
[2:15] Training neural networks: 37969 targets, 19790 decoys
[2:17] Number of IDs at 0.01 FDR: 30337
[2:17] Calculating protein q-values
[2:17] Number of genes identified at 1% FDR: 5134 (precursor-level), 4706 (protein-level) (inference performed using proteotypic peptides only)
[2:17] Quantification
[2:18] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_2_sh_p62_WT_FLAGIP_timsHT_DIA_Slot2-11_1_4810.xic.parquet

[2:18] File #3/24
[2:18] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_3_sh_p62_dNES_FLAGIP_timsHT_DIA_Slot2-12_1_4812.d
[2:44] 43700 library precursors are potentially detectable
[2:44] Processing...
[2:46] RT window set to 1.27289
[2:46] Ion mobility window set to 0.0168476
[2:46] Recommended MS1 mass accuracy setting: 15.111 ppm
[2:49] Removing low confidence identifications
[2:49] Removing interfering precursors
[2:49] Training neural networks: 37963 targets, 19746 decoys
[2:51] Number of IDs at 0.01 FDR: 30957
[2:52] Calculating protein q-values
[2:52] Number of genes identified at 1% FDR: 5211 (precursor-level), 4756 (protein-level) (inference performed using proteotypic peptides only)
[2:52] Quantification
[2:53] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_3_sh_p62_dNES_FLAGIP_timsHT_DIA_Slot2-12_1_4812.xic.parquet

[2:53] File #4/24
[2:53] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_4_sh_p62_dNLS_FLAGIP_timsHT_DIA_Slot2-13_1_4814.d
[3:20] 43700 library precursors are potentially detectable
[3:20] Processing...
[3:22] RT window set to 1.28292
[3:22] Ion mobility window set to 0.0151405
[3:22] Recommended MS1 mass accuracy setting: 16.0072 ppm
[3:25] Removing low confidence identifications
[3:26] Removing interfering precursors
[3:26] Training neural networks: 38670 targets, 20191 decoys
[3:28] Number of IDs at 0.01 FDR: 33030
[3:28] Calculating protein q-values
[3:28] Number of genes identified at 1% FDR: 5332 (precursor-level), 4872 (protein-level) (inference performed using proteotypic peptides only)
[3:28] Quantification
[3:29] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_4_sh_p62_dNLS_FLAGIP_timsHT_DIA_Slot2-13_1_4814.xic.parquet

[3:29] File #5/24
[3:29] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_5_sh_p62_MG123_FLAGIP_timsHT_DIA_Slot2-14_1_4816.d
[3:54] 43700 library precursors are potentially detectable
[3:54] Processing...
[3:57] RT window set to 1.19838
[3:57] Ion mobility window set to 0.018178
[3:57] Recommended MS1 mass accuracy setting: 14.6229 ppm
[3:59] Removing low confidence identifications
[4:00] Removing interfering precursors
[4:00] Training neural networks: 34548 targets, 18017 decoys
[4:02] Number of IDs at 0.01 FDR: 22237
[4:02] Calculating protein q-values
[4:02] Number of genes identified at 1% FDR: 4203 (precursor-level), 3915 (protein-level) (inference performed using proteotypic peptides only)
[4:02] Quantification
[4:03] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_5_sh_p62_MG123_FLAGIP_timsHT_DIA_Slot2-14_1_4816.xic.parquet

[4:03] File #6/24
[4:03] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_6_sh_p62_WT_MG123_FLAGIP_timsHT_DIA_Slot2-15_1_4818.d
[4:28] 43700 library precursors are potentially detectable
[4:28] Processing...
[4:31] RT window set to 1.23354
[4:31] Ion mobility window set to 0.0184059
[4:31] Recommended MS1 mass accuracy setting: 15.8298 ppm
[4:34] Removing low confidence identifications
[4:34] Removing interfering precursors
[4:34] Training neural networks: 37429 targets, 19432 decoys
[4:36] Number of IDs at 0.01 FDR: 26859
[4:36] Calculating protein q-values
[4:36] Number of genes identified at 1% FDR: 5150 (precursor-level), 4751 (protein-level) (inference performed using proteotypic peptides only)
[4:36] Quantification
[4:37] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_6_sh_p62_WT_MG123_FLAGIP_timsHT_DIA_Slot2-15_1_4818.xic.parquet

[4:38] File #7/24
[4:38] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_7_sh_p62_dNES_MG123_FLAGIP_timsHT_DIA_Slot2-16_1_4820.d
[5:05] 43700 library precursors are potentially detectable
[5:05] Processing...
[5:08] RT window set to 1.23746
[5:08] Ion mobility window set to 0.0191128
[5:08] Recommended MS1 mass accuracy setting: 14.0186 ppm
[5:10] Removing low confidence identifications
[5:10] Removing interfering precursors
[5:11] Training neural networks: 35324 targets, 18338 decoys
[5:13] Number of IDs at 0.01 FDR: 22915
[5:13] Calculating protein q-values
[5:13] Number of genes identified at 1% FDR: 4839 (precursor-level), 4523 (protein-level) (inference performed using proteotypic peptides only)
[5:13] Quantification
[5:14] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_7_sh_p62_dNES_MG123_FLAGIP_timsHT_DIA_Slot2-16_1_4820.xic.parquet

[5:14] File #8/24
[5:14] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_8_sh_p62_dNLS_MG123_FLAGIP_timsHT_DIA_Slot2-17_1_4822.d
[5:40] 43700 library precursors are potentially detectable
[5:40] Processing...
[5:43] RT window set to 1.23367
[5:43] Ion mobility window set to 0.0168941
[5:43] Recommended MS1 mass accuracy setting: 14.7061 ppm
[5:46] Removing low confidence identifications
[5:46] Removing interfering precursors
[5:47] Training neural networks: 39056 targets, 20300 decoys
[5:48] Number of IDs at 0.01 FDR: 33726
[5:49] Calculating protein q-values
[5:49] Number of genes identified at 1% FDR: 5771 (precursor-level), 5336 (protein-level) (inference performed using proteotypic peptides only)
[5:49] Quantification
[5:50] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_8_sh_p62_dNLS_MG123_FLAGIP_timsHT_DIA_Slot2-17_1_4822.xic.parquet

[5:50] File #9/24
[5:50] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_9_sh_p62_FLAGIP_timsHT_DIA_Slot2-18_1_4824.d
[6:15] 43700 library precursors are potentially detectable
[6:15] Processing...
[6:17] RT window set to 1.24546
[6:17] Ion mobility window set to 0.0170508
[6:17] Recommended MS1 mass accuracy setting: 13.3661 ppm
[6:19] Removing low confidence identifications
[6:19] Removing interfering precursors
[6:20] Training neural networks: 36942 targets, 19255 decoys
[6:21] Number of IDs at 0.01 FDR: 27967
[6:21] Calculating protein q-values
[6:21] Number of genes identified at 1% FDR: 4858 (precursor-level), 4411 (protein-level) (inference performed using proteotypic peptides only)
[6:21] Quantification
[6:22] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_9_sh_p62_FLAGIP_timsHT_DIA_Slot2-18_1_4824.xic.parquet

[6:22] File #10/24
[6:22] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_10_sh_p62_WT_FLAGIP_timsHT_DIA_Slot2-19_1_4826.d
[6:48] 43700 library precursors are potentially detectable
[6:48] Processing...
[6:51] RT window set to 1.27165
[6:51] Ion mobility window set to 0.0171021
[6:51] Recommended MS1 mass accuracy setting: 15.0916 ppm
[6:54] Removing low confidence identifications
[6:54] Removing interfering precursors
[6:54] Training neural networks: 38652 targets, 20156 decoys
[6:56] Number of IDs at 0.01 FDR: 32971
[6:56] Calculating protein q-values
[6:56] Number of genes identified at 1% FDR: 5410 (precursor-level), 5010 (protein-level) (inference performed using proteotypic peptides only)
[6:56] Quantification
[6:57] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_10_sh_p62_WT_FLAGIP_timsHT_DIA_Slot2-19_1_4826.xic.parquet

[6:57] File #11/24
[6:57] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_11_sh_p62_dNES_FLAGIP_timsHT_DIA_Slot2-20_1_4828.d
[7:22] 43700 library precursors are potentially detectable
[7:22] Processing...
[7:24] RT window set to 1.23167
[7:24] Ion mobility window set to 0.0170157
[7:24] Recommended MS1 mass accuracy setting: 15.22 ppm
[7:27] Removing low confidence identifications
[7:27] Removing interfering precursors
[7:27] Training neural networks: 36226 targets, 18802 decoys
[7:29] Number of IDs at 0.01 FDR: 25404
[7:29] Calculating protein q-values
[7:29] Number of genes identified at 1% FDR: 4837 (precursor-level), 4429 (protein-level) (inference performed using proteotypic peptides only)
[7:29] Quantification
[7:30] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_11_sh_p62_dNES_FLAGIP_timsHT_DIA_Slot2-20_1_4828.xic.parquet

[7:30] File #12/24
[7:30] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_12_sh_p62_dNLS_FLAGIP_timsHT_DIA_Slot2-21_1_4830.d
[7:55] 43700 library precursors are potentially detectable
[7:55] Processing...
[7:57] RT window set to 1.24824
[7:57] Ion mobility window set to 0.0179425
[7:57] Recommended MS1 mass accuracy setting: 14.9303 ppm
[8:00] Removing low confidence identifications
[8:00] Removing interfering precursors
[8:00] Training neural networks: 36674 targets, 19015 decoys
[8:02] Number of IDs at 0.01 FDR: 26735
[8:02] Calculating protein q-values
[8:02] Number of genes identified at 1% FDR: 4934 (precursor-level), 4608 (protein-level) (inference performed using proteotypic peptides only)
[8:02] Quantification
[8:03] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_12_sh_p62_dNLS_FLAGIP_timsHT_DIA_Slot2-21_1_4830.xic.parquet

[8:03] File #13/24
[8:03] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_13_sh_p62_MG123_FLAGIP_timsHT_DIA_Slot2-22_1_4832.d
[8:28] 43700 library precursors are potentially detectable
[8:28] Processing...
[8:30] RT window set to 1.24627
[8:30] Ion mobility window set to 0.0181962
[8:30] Recommended MS1 mass accuracy setting: 14.0856 ppm
[8:32] Removing low confidence identifications
[8:32] Removing interfering precursors
[8:33] Training neural networks: 36465 targets, 18903 decoys
[8:34] Number of IDs at 0.01 FDR: 25429
[8:34] Calculating protein q-values
[8:34] Number of genes identified at 1% FDR: 4599 (precursor-level), 4279 (protein-level) (inference performed using proteotypic peptides only)
[8:34] Quantification
[8:35] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_13_sh_p62_MG123_FLAGIP_timsHT_DIA_Slot2-22_1_4832.xic.parquet

[8:35] File #14/24
[8:35] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_14_sh_p62_WT_MG123_FLAGIP_timsHT_DIA_Slot2-23_1_4834.d
[9:01] 43700 library precursors are potentially detectable
[9:01] Processing...
[9:03] RT window set to 1.24261
[9:03] Ion mobility window set to 0.0166455
[9:03] Recommended MS1 mass accuracy setting: 17.3069 ppm
[9:06] Removing low confidence identifications
[9:06] Removing interfering precursors
[9:06] Training neural networks: 38051 targets, 19743 decoys
[9:08] Number of IDs at 0.01 FDR: 31303
[9:08] Calculating protein q-values
[9:08] Number of genes identified at 1% FDR: 5615 (precursor-level), 5211 (protein-level) (inference performed using proteotypic peptides only)
[9:08] Quantification
[9:09] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_14_sh_p62_WT_MG123_FLAGIP_timsHT_DIA_Slot2-23_1_4834.xic.parquet

[9:09] File #15/24
[9:09] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_15_sh_p62_dNES_MG123_FLAGIP_timsHT_DIA_Slot2-24_1_4836.d
[9:34] 43700 library precursors are potentially detectable
[9:34] Processing...
[9:37] RT window set to 1.25005
[9:37] Ion mobility window set to 0.0187419
[9:37] Recommended MS1 mass accuracy setting: 13.9264 ppm
[9:39] Removing low confidence identifications
[9:39] Removing interfering precursors
[9:40] Training neural networks: 37215 targets, 19222 decoys
[9:41] Number of IDs at 0.01 FDR: 26963
[9:41] Calculating protein q-values
[9:41] Number of genes identified at 1% FDR: 5292 (precursor-level), 4915 (protein-level) (inference performed using proteotypic peptides only)
[9:41] Quantification
[9:42] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_15_sh_p62_dNES_MG123_FLAGIP_timsHT_DIA_Slot2-24_1_4836.xic.parquet

[9:42] File #16/24
[9:42] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_16_sh_p62_dNLS_MG123_FLAGIP_timsHT_DIA_Slot2-25_1_4838.d
[10:08] 43700 library precursors are potentially detectable
[10:08] Processing...
[10:10] RT window set to 1.2467
[10:10] Ion mobility window set to 0.0178601
[10:10] Recommended MS1 mass accuracy setting: 14.7274 ppm
[10:13] Removing low confidence identifications
[10:13] Removing interfering precursors
[10:13] Training neural networks: 37741 targets, 19544 decoys
[10:15] Number of IDs at 0.01 FDR: 30030
[10:15] Calculating protein q-values
[10:15] Number of genes identified at 1% FDR: 5523 (precursor-level), 5053 (protein-level) (inference performed using proteotypic peptides only)
[10:15] Quantification
[10:16] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_16_sh_p62_dNLS_MG123_FLAGIP_timsHT_DIA_Slot2-25_1_4838.xic.parquet

[10:16] File #17/24
[10:16] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_17_sh_p62_FLAGIP_timsHT_DIA_Slot2-26_1_4840.d
[10:41] 43700 library precursors are potentially detectable
[10:41] Processing...
[10:43] RT window set to 1.19946
[10:43] Ion mobility window set to 0.0191646
[10:43] Recommended MS1 mass accuracy setting: 13.6669 ppm
[10:46] Removing low confidence identifications
[10:46] Removing interfering precursors
[10:46] Training neural networks: 30883 targets, 15969 decoys
[10:47] Number of IDs at 0.01 FDR: 17415
[10:48] Calculating protein q-values
[10:48] Number of genes identified at 1% FDR: 3753 (precursor-level), 3462 (protein-level) (inference performed using proteotypic peptides only)
[10:48] Quantification
[10:48] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_17_sh_p62_FLAGIP_timsHT_DIA_Slot2-26_1_4840.xic.parquet

[10:48] File #18/24
[10:48] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_18_sh_p62_WT_FLAGIP_timsHT_DIA_Slot2-27_1_4842.d
[11:14] 43700 library precursors are potentially detectable
[11:14] Processing...
[11:16] RT window set to 1.2775
[11:16] Ion mobility window set to 0.0167342
[11:16] Recommended MS1 mass accuracy setting: 16.5499 ppm
[11:19] Removing low confidence identifications
[11:19] Removing interfering precursors
[11:20] Training neural networks: 38641 targets, 20079 decoys
[11:21] Number of IDs at 0.01 FDR: 32237
[11:21] Calculating protein q-values
[11:21] Number of genes identified at 1% FDR: 5416 (precursor-level), 4962 (protein-level) (inference performed using proteotypic peptides only)
[11:21] Quantification
[11:22] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_18_sh_p62_WT_FLAGIP_timsHT_DIA_Slot2-27_1_4842.xic.parquet

[11:23] File #19/24
[11:23] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_19_sh_p62_dNES_FLAGIP_timsHT_DIA_Slot2-28_1_4844.d
[11:48] 43700 library precursors are potentially detectable
[11:48] Processing...
[11:49] RT window set to 1.2426
[11:49] Ion mobility window set to 0.0164352
[11:49] Recommended MS1 mass accuracy setting: 15.7648 ppm
[11:52] Removing low confidence identifications
[11:52] Removing interfering precursors
[11:52] Training neural networks: 37047 targets, 19205 decoys
[11:54] Number of IDs at 0.01 FDR: 28223
[11:54] Calculating protein q-values
[11:54] Number of genes identified at 1% FDR: 5151 (precursor-level), 4695 (protein-level) (inference performed using proteotypic peptides only)
[11:54] Quantification
[11:55] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_19_sh_p62_dNES_FLAGIP_timsHT_DIA_Slot2-28_1_4844.xic.parquet

[11:55] File #20/24
[11:55] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_20_sh_p62_dNLS_FLAGIP_timsHT_DIA_Slot2-29_1_4846.d
[12:21] 43700 library precursors are potentially detectable
[12:21] Processing...
[12:23] RT window set to 1.23502
[12:23] Ion mobility window set to 0.0167818
[12:23] Recommended MS1 mass accuracy setting: 14.1113 ppm
[12:25] Removing low confidence identifications
[12:25] Removing interfering precursors
[12:25] Training neural networks: 36402 targets, 18847 decoys
[12:27] Number of IDs at 0.01 FDR: 27143
[12:27] Calculating protein q-values
[12:27] Number of genes identified at 1% FDR: 4983 (precursor-level), 4508 (protein-level) (inference performed using proteotypic peptides only)
[12:27] Quantification
[12:28] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_20_sh_p62_dNLS_FLAGIP_timsHT_DIA_Slot2-29_1_4846.xic.parquet

[12:28] File #21/24
[12:28] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_21_sh_p62_MG123_FLAGIP_timsHT_DIA_Slot2-30_1_4849.d
[12:52] 43700 library precursors are potentially detectable
[12:52] Processing...
[12:55] RT window set to 1.26103
[12:55] Ion mobility window set to 0.0200232
[12:55] Recommended MS1 mass accuracy setting: 14.0505 ppm
[12:57] Removing low confidence identifications
[12:57] Removing interfering precursors
[12:57] Training neural networks: 31128 targets, 16116 decoys
[12:59] Number of IDs at 0.01 FDR: 16246
[12:59] Calculating protein q-values
[12:59] Number of genes identified at 1% FDR: 3547 (precursor-level), 3367 (protein-level) (inference performed using proteotypic peptides only)
[12:59] Quantification
[13:00] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_21_sh_p62_MG123_FLAGIP_timsHT_DIA_Slot2-30_1_4849.xic.parquet

[13:00] File #22/24
[13:00] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_22_sh_p62_WT_MG123_FLAGIP_timsHT_DIA_Slot2-31_1_4851.d
[13:25] 43700 library precursors are potentially detectable
[13:25] Processing...
[13:28] RT window set to 1.25896
[13:28] Ion mobility window set to 0.0164445
[13:28] Recommended MS1 mass accuracy setting: 15.3335 ppm
[13:30] Removing low confidence identifications
[13:31] Removing interfering precursors
[13:31] Training neural networks: 39571 targets, 20570 decoys
[13:33] Number of IDs at 0.01 FDR: 33909
[13:33] Calculating protein q-values
[13:33] Number of genes identified at 1% FDR: 5750 (precursor-level), 5338 (protein-level) (inference performed using proteotypic peptides only)
[13:33] Quantification
[13:34] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_22_sh_p62_WT_MG123_FLAGIP_timsHT_DIA_Slot2-31_1_4851.xic.parquet

[13:34] File #23/24
[13:34] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_23_sh_p62_dNES_MG123_FLAGIP_timsHT_DIA_Slot2-32_1_4853.d
[13:59] 43700 library precursors are potentially detectable
[13:59] Processing...
[14:01] RT window set to 1.24301
[14:01] Ion mobility window set to 0.0179337
[14:01] Recommended MS1 mass accuracy setting: 14.1173 ppm
[14:04] Removing low confidence identifications
[14:04] Removing interfering precursors
[14:04] Training neural networks: 38875 targets, 20175 decoys
[14:06] Number of IDs at 0.01 FDR: 31862
[14:06] Calculating protein q-values
[14:06] Number of genes identified at 1% FDR: 5642 (precursor-level), 5227 (protein-level) (inference performed using proteotypic peptides only)
[14:06] Quantification
[14:07] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_23_sh_p62_dNES_MG123_FLAGIP_timsHT_DIA_Slot2-32_1_4853.xic.parquet

[14:07] File #24/24
[14:07] Loading run D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\PJ1647_Aaron_24_sh_p62_dNLS_MG123_FLAGIP_timsHT_DIA_Slot2-33_1_4855.d
[14:33] 43700 library precursors are potentially detectable
[14:33] Processing...
[14:35] RT window set to 1.243
[14:35] Ion mobility window set to 0.0168336
[14:35] Recommended MS1 mass accuracy setting: 14.7154 ppm
[14:38] Removing low confidence identifications
[14:38] Removing interfering precursors
[14:38] Training neural networks: 39524 targets, 20572 decoys
[14:40] Number of IDs at 0.01 FDR: 34762
[14:40] Calculating protein q-values
[14:40] Number of genes identified at 1% FDR: 5849 (precursor-level), 5476 (protein-level) (inference performed using proteotypic peptides only)
[14:40] Quantification
[14:41] XICs saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result/report_xic/PJ1647_Aaron_24_sh_p62_dNLS_MG123_FLAGIP_timsHT_DIA_Slot2-33_1_4855.xic.parquet

[14:41] Cross-run analysis
[14:41] Reading quantification information: 24 files
[14:43] Quantifying peptides
[15:59] Quantification parameters: 0.388247, 0.0013775, 0.00345749, 0.0614984, 0.389316, 0.22457, 0.195097, 0.240135, 0.2404, 0.132052, 0.143379, 0.147602, 0.662107, 0.507089, 0.506453, 0.200325
[16:01] Quantifying proteins
[16:01] Calculating q-values for protein and gene groups
[16:01] Calculating global q-values for protein and gene groups
[16:01] Protein groups with global q-value <= 0.01: 5723
[16:04] Compressed report saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result\report.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[16:04] Writing report
[16:26] Report saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result\report.tsv.
[16:26] Saving precursor levels matrix
[16:27] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result\report.pr_matrix.tsv.
[16:27] Saving protein group levels matrix
[16:27] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result\report.pg_matrix.tsv.
[16:27] Saving gene group levels matrix
[16:27] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result\report.gg_matrix.tsv.
[16:27] Saving unique genes levels matrix
[16:27] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result\report.unique_genes_matrix.tsv.
[16:27] Stats report saved to D:\timsTOF_HT\PJ1647_250409_Aaron_FLAGIP_timsHT_DIA\result\report.stats.tsv

