
DIA-NN 2.2.0 Academia  (Data-Independent Acquisition by Neural Networks)
Compiled on May 29 2025 21:29:29
Current date and time: Tue Sep 16 15:35:01 2025
CPU: AuthenticAMD AMD Ryzen 9 5950X 16-Core Processor
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 SSE4a 
Logical CPU cores: 32
diann.exe --f C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw  --f C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw  --f C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw  --f C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw  --f C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw  --f C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw  --lib C:\DIA-NN\2.2.0\report-lib.predicted.speclib --threads 16 --verbose 1 --out C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro\report.parquet --qvalue 0.01 --matrices --out-lib C:\DIA-NN\2.2.0\report-lib.parquet --gen-spec-lib --xic --fasta C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\ProteoBenchFASTA_MixedSpecies_HY.fasta --met-excision --cut K*,R* --missed-cleavages 1 --unimod4 --var-mods 1 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --peptidoforms --reanalyse --rt-profiling 

Thread number set to 16
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
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
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 1
Cysteine carbamidomethylation enabled as a fixed modification
Maximum number of variable modifications set to 1
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
Modification UniMod:1 with mass delta 42.0106 at *n will be considered as variable
Peptidoform scoring enabled
MBR enabled; .quant files will only be saved to disk during the first pass
The spectral library (if generated) will retain the original spectra but will include empirically-aligned RTs
DIA-NN will automatically optimise the mass accuracy for the first run of the experiment, use this mode for preliminary analyses only
The following variable modifications will be localised: UniMod:35 UniMod:1 

6 files will be processed
[0:00] Loading spectral library C:\DIA-NN\2.2.0\report-lib.predicted.speclib
[0:02] Library annotated with sequence database(s): C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\ProteoBenchFASTA_MixedSpecies_HY.fasta
[0:03] Spectral library loaded: 27447 protein isoforms, 46269 protein groups and 4807155 precursors in 2476899 elution groups.
[0:03] Loading protein annotations from FASTA C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\ProteoBenchFASTA_MixedSpecies_HY.fasta
[0:03] Annotating library proteins with information from the FASTA database
[0:03] Gene names missing for some isoforms
[0:03] Library contains 27297 proteins, and 0 genes
[0:06] Initialising library

First pass: generating a spectral library from DIA data

[0:14] File #1/6
[0:14] Loading run C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw
[0:18] Pre-processing...
[0:20] 1842 MS1 and 27799 MS2 scans in 1842 (inferred) and 1842 (encoded) cycles, 3546175 precursors in range
[0:20] Calibrating with mass accuracies 22 (MS1), 24 (MS2)
[1:35] RT window set to 1.49567
[1:35] Peak width: 3.056
[1:35] Scan window radius set to 6
[1:35] Recommended MS1 mass accuracy setting: 1.9 ppm
[3:00] Optimised mass accuracy: 6 ppm
[3:26] Searching decoys
[4:32] Main search
[6:43] Removing low confidence identifications
[6:52] Removing interfering precursors
[6:57] Training neural networks on 92243 target and 58183 decoy PSMs
[7:53] Training neural networks on 92243 target and 55358 decoy PSMs
[8:45] Number of IDs at 0.01 FDR: 37703
[8:46] Precursors at 1% peptidoform FDR: 35971
[8:46] Calculating protein q-values
[8:46] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[8:46] Quantification
[8:47] Precursors with scored PTMs at 1% FDR: 646 out of 716 considered
[8:47] Precursors with all scored PTM sites unoccupied at 1% FDR: 35325
[8:47] Precursors with PTMs localised (when required) with > 90% confidence: 635 out of 646
[8:47] Quantification information saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw.quant

[8:47] File #2/6
[8:47] Loading run C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw
[8:51] Pre-processing...
[8:53] 1859 MS1 and 28183 MS2 scans in 1859 (inferred) and 1859 (encoded) cycles, 3546175 precursors in range
[8:54] Calibrating with mass accuracies 22 (MS1), 24 (MS2)
[10:07] RT window set to 1.50027
[10:07] Recommended MS1 mass accuracy setting: 2 ppm
[10:31] Searching decoys
[11:41] Main search
[14:00] Removing low confidence identifications
[14:10] Removing interfering precursors
[14:14] Training neural networks on 92300 target and 56097 decoy PSMs
[15:10] Training neural networks on 92300 target and 53632 decoy PSMs
[16:00] Number of IDs at 0.01 FDR: 40410
[16:01] Precursors at 1% peptidoform FDR: 38624
[16:01] Calculating protein q-values
[16:01] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[16:02] Quantification
[16:02] Precursors with scored PTMs at 1% FDR: 2093 out of 2248 considered
[16:02] Precursors with all scored PTM sites unoccupied at 1% FDR: 36531
[16:02] Precursors with PTMs localised (when required) with > 90% confidence: 2061 out of 2093
[16:02] Quantification information saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw.quant

[16:02] File #3/6
[16:02] Loading run C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw
[16:06] Pre-processing...
[16:08] 1856 MS1 and 28105 MS2 scans in 1856 (inferred) and 1856 (encoded) cycles, 3546175 precursors in range
[16:09] Calibrating with mass accuracies 22 (MS1), 24 (MS2)
[17:24] RT window set to 1.7084
[17:25] Recommended MS1 mass accuracy setting: 2 ppm
[17:49] Searching decoys
[19:04] Main search
[21:29] Removing low confidence identifications
[21:40] Removing interfering precursors
[21:44] Training neural networks on 88803 target and 53049 decoy PSMs
[22:38] Training neural networks on 88803 target and 50511 decoy PSMs
[23:27] Number of IDs at 0.01 FDR: 39534
[23:27] Precursors at 1% peptidoform FDR: 37876
[23:28] Calculating protein q-values
[23:28] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[23:28] Quantification
[23:29] Precursors with scored PTMs at 1% FDR: 2266 out of 2443 considered
[23:29] Precursors with all scored PTM sites unoccupied at 1% FDR: 35610
[23:29] Precursors with PTMs localised (when required) with > 90% confidence: 2238 out of 2266
[23:29] Quantification information saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw.quant

[23:29] File #4/6
[23:29] Loading run C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw
[23:32] Pre-processing...
[23:34] 1827 MS1 and 27525 MS2 scans in 1827 (inferred) and 1827 (encoded) cycles, 3546175 precursors in range
[23:35] Calibrating with mass accuracies 22 (MS1), 24 (MS2)
[25:00] RT window set to 1.5535
[25:01] Recommended MS1 mass accuracy setting: 2 ppm
[25:27] Searching decoys
[26:20] Main search
[28:02] Removing low confidence identifications
[28:11] Removing interfering precursors
[28:15] Training neural networks on 83409 target and 50926 decoy PSMs
[29:06] Training neural networks on 83409 target and 48526 decoy PSMs
[29:52] Number of IDs at 0.01 FDR: 36058
[29:53] Precursors at 1% peptidoform FDR: 34610
[29:53] Calculating protein q-values
[29:53] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[29:54] Quantification
[29:54] Precursors with scored PTMs at 1% FDR: 737 out of 804 considered
[29:54] Precursors with all scored PTM sites unoccupied at 1% FDR: 33873
[29:54] Precursors with PTMs localised (when required) with > 90% confidence: 714 out of 737
[29:54] Quantification information saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw.quant

[29:54] File #5/6
[29:54] Loading run C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw
[29:57] Pre-processing...
[29:59] 1831 MS1 and 27624 MS2 scans in 1831 (inferred) and 1831 (encoded) cycles, 3546175 precursors in range
[30:00] Calibrating with mass accuracies 22 (MS1), 24 (MS2)
[31:26] RT window set to 1.58483
[31:26] Recommended MS1 mass accuracy setting: 1.9 ppm
[31:47] Searching decoys
[32:48] Main search
[34:48] Removing low confidence identifications
[34:56] Removing interfering precursors
[35:01] Training neural networks on 87449 target and 55165 decoy PSMs
[35:54] Training neural networks on 87449 target and 52486 decoy PSMs
[36:44] Number of IDs at 0.01 FDR: 36585
[36:44] Precursors at 1% peptidoform FDR: 34995
[36:45] Calculating protein q-values
[36:45] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[36:45] Quantification
[36:45] Precursors with scored PTMs at 1% FDR: 911 out of 985 considered
[36:45] Precursors with all scored PTM sites unoccupied at 1% FDR: 34084
[36:45] Precursors with PTMs localised (when required) with > 90% confidence: 888 out of 911
[36:46] Quantification information saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw.quant

[36:46] File #6/6
[36:46] Loading run C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw
[36:49] Pre-processing...
[36:50] 1831 MS1 and 27589 MS2 scans in 1831 (inferred) and 1831 (encoded) cycles, 3546175 precursors in range
[36:51] Calibrating with mass accuracies 22 (MS1), 24 (MS2)
[38:01] RT window set to 1.66568
[38:02] Recommended MS1 mass accuracy setting: 1.9 ppm
[38:24] Searching decoys
[39:27] Main search
[41:29] Removing low confidence identifications
[41:38] Removing interfering precursors
[41:42] Training neural networks on 84149 target and 51405 decoy PSMs
[42:34] Training neural networks on 84149 target and 48801 decoy PSMs
[43:20] Number of IDs at 0.01 FDR: 36913
[43:21] Precursors at 1% peptidoform FDR: 35166
[43:21] Calculating protein q-values
[43:21] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[43:21] Quantification
[43:22] Precursors with scored PTMs at 1% FDR: 836 out of 928 considered
[43:22] Precursors with all scored PTM sites unoccupied at 1% FDR: 34330
[43:22] Precursors with PTMs localised (when required) with > 90% confidence: 812 out of 836
[43:22] Quantification information saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw.quant

[43:22] Cross-run analysis
[43:22] Reading quantification information: 6 files
[43:32] Quantifying peptides
[44:02] Assembling protein groups
[44:03] Quantifying proteins
[44:04] Calculating q-values for protein and gene groups
[44:04] Calculating global q-values for protein and gene groups
[44:05] Protein groups with global q-value <= 0.01: 8391
[44:06] Compressed report saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro\report-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[44:06] Site report saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro\report-first-pass.site_report.parquet
[44:06] Saving precursor levels matrix
[44:06] Precursor levels matrix (1% precursor and protein group FDR) saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro\report-first-pass.pr_matrix.tsv.
[44:06] Manifest saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro\report-first-pass.manifest.txt
[44:06] Stats report saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro\report-first-pass.stats.tsv
[44:06] Generating spectral library:
[44:07] 50066 target and 499 decoy precursors saved
[44:07] Spectral library saved to C:\DIA-NN\2.2.0\report-lib.parquet

[44:07] Loading spectral library C:\DIA-NN\2.2.0\report-lib.parquet
[44:08] Spectral library loaded: 9636 protein isoforms, 9380 protein groups and 50565 precursors in 49597 elution groups.
[44:08] Loading protein annotations from FASTA C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\ProteoBenchFASTA_MixedSpecies_HY.fasta
[44:08] Annotating library proteins with information from the FASTA database
[44:08] Gene names missing for some isoforms
[44:08] Library contains 9617 proteins, and 0 genes
[44:08] Initialising library
[44:09] Saving the library to C:\DIA-NN\2.2.0\report-lib.parquet.skyline.speclib


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

[44:09] File #1/6
[44:09] Loading run C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw
[44:12] Pre-processing...
[44:13] 1842 MS1 and 27799 MS2 scans in 1842 (inferred) and 1842 (encoded) cycles, 50066 precursors in range
[44:13] Calibrating with mass accuracies 22 (MS1), 24 (MS2)
[44:13] RT window set to 0.445111
[44:13] Recommended MS1 mass accuracy setting: 2.2 ppm
[44:14] Searching decoys
[44:14] Main search
[44:16] Removing low confidence identifications
[44:18] Removing interfering precursors
[44:19] Training neural networks on 46828 target and 24603 decoy PSMs
[44:43] Training neural networks on 46797 target and 25962 decoy PSMs
[45:09] Number of IDs at 0.01 FDR: 41713
[45:09] Precursors at 1% peptidoform FDR: 40201
[45:09] Calculating protein q-values
[45:09] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[45:09] Quantification
[45:10] Precursors with scored PTMs at 1% FDR: 1208 out of 1308 considered
[45:10] Precursors with all scored PTM sites unoccupied at 1% FDR: 38993
[45:10] Precursors with PTMs localised (when required) with > 90% confidence: 1182 out of 1208
[45:12] XICs saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro/report_xic/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.xic.parquet

[45:12] File #2/6
[45:12] Loading run C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw
[45:16] Pre-processing...
[45:16] 1859 MS1 and 28183 MS2 scans in 1859 (inferred) and 1859 (encoded) cycles, 50066 precursors in range
[45:16] Calibrating with mass accuracies 22 (MS1), 24 (MS2)
[45:17] RT window set to 0.446882
[45:17] Recommended MS1 mass accuracy setting: 2.3 ppm
[45:18] Searching decoys
[45:18] Main search
[45:20] Removing low confidence identifications
[45:22] Removing interfering precursors
[45:23] Training neural networks on 47134 target and 24355 decoy PSMs
[45:47] Training neural networks on 47107 target and 26078 decoy PSMs
[46:12] Number of IDs at 0.01 FDR: 43609
[46:12] Precursors at 1% peptidoform FDR: 41875
[46:12] Calculating protein q-values
[46:12] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[46:12] Quantification
[46:12] Precursors with scored PTMs at 1% FDR: 2058 out of 2132 considered
[46:12] Precursors with all scored PTM sites unoccupied at 1% FDR: 39817
[46:12] Precursors with PTMs localised (when required) with > 90% confidence: 2034 out of 2058
[46:15] XICs saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro/report_xic/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.xic.parquet

[46:15] File #3/6
[46:15] Loading run C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw
[46:19] Pre-processing...
[46:19] 1856 MS1 and 28105 MS2 scans in 1856 (inferred) and 1856 (encoded) cycles, 50066 precursors in range
[46:19] Calibrating with mass accuracies 22 (MS1), 24 (MS2)
[46:20] RT window set to 0.448502
[46:20] Recommended MS1 mass accuracy setting: 2.4 ppm
[46:21] Searching decoys
[46:21] Main search
[46:23] Removing low confidence identifications
[46:25] Removing interfering precursors
[46:25] Training neural networks on 46967 target and 24634 decoy PSMs
[46:50] Training neural networks on 46942 target and 25993 decoy PSMs
[47:14] Number of IDs at 0.01 FDR: 43056
[47:14] Precursors at 1% peptidoform FDR: 41449
[47:14] Calculating protein q-values
[47:14] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[47:14] Quantification
[47:14] Precursors with scored PTMs at 1% FDR: 2115 out of 2165 considered
[47:14] Precursors with all scored PTM sites unoccupied at 1% FDR: 39334
[47:14] Precursors with PTMs localised (when required) with > 90% confidence: 2090 out of 2115
[47:17] XICs saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro/report_xic/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.xic.parquet

[47:17] File #4/6
[47:17] Loading run C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw
[47:19] Pre-processing...
[47:20] 1827 MS1 and 27525 MS2 scans in 1827 (inferred) and 1827 (encoded) cycles, 50066 precursors in range
[47:20] Calibrating with mass accuracies 22 (MS1), 24 (MS2)
[47:21] RT window set to 0.451288
[47:21] Recommended MS1 mass accuracy setting: 2.2 ppm
[47:21] Searching decoys
[47:21] Main search
[47:23] Removing low confidence identifications
[47:25] Removing interfering precursors
[47:25] Training neural networks on 45975 target and 24062 decoy PSMs
[47:49] Training neural networks on 45951 target and 25074 decoy PSMs
[48:13] Number of IDs at 0.01 FDR: 39960
[48:13] Precursors at 1% peptidoform FDR: 38263
[48:13] Calculating protein q-values
[48:13] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[48:13] Quantification
[48:13] Precursors with scored PTMs at 1% FDR: 1145 out of 1235 considered
[48:13] Precursors with all scored PTM sites unoccupied at 1% FDR: 37118
[48:13] Precursors with PTMs localised (when required) with > 90% confidence: 1118 out of 1145
[48:16] XICs saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro/report_xic/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.xic.parquet

[48:16] File #5/6
[48:16] Loading run C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw
[48:19] Pre-processing...
[48:19] 1831 MS1 and 27624 MS2 scans in 1831 (inferred) and 1831 (encoded) cycles, 50066 precursors in range
[48:19] Calibrating with mass accuracies 22 (MS1), 24 (MS2)
[48:20] RT window set to 0.45244
[48:20] Recommended MS1 mass accuracy setting: 2.1 ppm
[48:20] Searching decoys
[48:21] Main search
[48:22] Removing low confidence identifications
[48:24] Removing interfering precursors
[48:25] Training neural networks on 46073 target and 24296 decoy PSMs
[48:49] Training neural networks on 46048 target and 25482 decoy PSMs
[49:13] Number of IDs at 0.01 FDR: 40134
[49:13] Precursors at 1% peptidoform FDR: 38507
[49:13] Calculating protein q-values
[49:13] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[49:13] Quantification
[49:14] Precursors with scored PTMs at 1% FDR: 1320 out of 1409 considered
[49:14] Precursors with all scored PTM sites unoccupied at 1% FDR: 37187
[49:14] Precursors with PTMs localised (when required) with > 90% confidence: 1294 out of 1320
[49:16] XICs saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro/report_xic/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.xic.parquet

[49:16] File #6/6
[49:16] Loading run C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw
[49:19] Pre-processing...
[49:19] 1831 MS1 and 27589 MS2 scans in 1831 (inferred) and 1831 (encoded) cycles, 50066 precursors in range
[49:19] Calibrating with mass accuracies 22 (MS1), 24 (MS2)
[49:20] RT window set to 0.454637
[49:20] Recommended MS1 mass accuracy setting: 2.2 ppm
[49:20] Searching decoys
[49:21] Main search
[49:22] Removing low confidence identifications
[49:25] Removing interfering precursors
[49:25] Training neural networks on 46032 target and 23676 decoy PSMs
[49:50] Training neural networks on 46010 target and 24901 decoy PSMs
[50:15] Number of IDs at 0.01 FDR: 40302
[50:15] Precursors at 1% peptidoform FDR: 38742
[50:15] Calculating protein q-values
[50:15] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only)
[50:15] Quantification
[50:16] Precursors with scored PTMs at 1% FDR: 1269 out of 1375 considered
[50:16] Precursors with all scored PTM sites unoccupied at 1% FDR: 37473
[50:16] Precursors with PTMs localised (when required) with > 90% confidence: 1239 out of 1269
[50:18] XICs saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro/report_xic/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.xic.parquet

[50:18] Cross-run analysis
[50:18] Reading quantification information: 6 files
[50:18] Quantifying peptides
[51:05] Quantification parameters: 0.368599, 0.00212583, 0.0174338, 0.0129567, 0.0125331, 0.0127771, 0.309889, 0.225363, 0.220844, 0.0132533, 0.0141915, 0.014066, 0.505004, 0.153646, 0.227969, 0.0119107
[51:19] Quantifying proteins
[51:19] Calculating q-values for protein and gene groups
[51:19] Calculating global q-values for protein and gene groups
[51:19] Protein groups with global q-value <= 0.01: 8100
[51:20] Compressed report saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro\report.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[51:20] Site report saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro\report.site_report.parquet
[51:20] Saving precursor levels matrix
[51:20] Precursor levels matrix (1% precursor and protein group FDR) saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro\report.pr_matrix.tsv.
[51:20] Saving protein group levels matrix
[51:20] Protein groups matrix saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro\report.pg_matrix.tsv.
[51:20] Saving gene group levels matrix
[51:20] Gene groups matrix saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro\report.gg_matrix.tsv.
[51:20] Saving unique genes levels matrix
[51:20] Unique genes matrix saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro\report.unique_genes_matrix.tsv.
[51:20] Manifest saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro\report.manifest.txt
[51:20] Stats report saved to C:\Users\cajac\Documents\ExampleFiles\ProteoBench\Single_cell_run\results 1\diann\default_parameters_caro\report.stats.tsv

