DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks)
Compiled on Apr 14 2022 15:31:19
Current date and time: Mon Nov 25 13:25:59 2024
CPU: GenuineIntel Intel(R) Xeon(R) Gold 6258R CPU @ 2.70GHz
SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 
Logical CPU cores: 56
diann.exe --f "D:\Project_auto\XB08942DA_T\XB08942DA_LA1.mzML" --f "D:\Project_auto\XB08942DA_T\XB08942DA_LA2.mzML" --f "D:\Project_auto\XB08942DA_T\XB08942DA_LA4.mzML" --f "D:\Project_auto\XB08942DA_T\XB08942DA_LA6.mzML" --f "D:\Project_auto\XB08942DA_T\XB08942DA_LA7.mzML" --f "D:\Project_auto\XB08942DA_T\XB08942DA_CS1.mzML" --f "D:\Project_auto\XB08942DA_T\XB08942DA_CS2.mzML" --f "D:\Project_auto\XB08942DA_T\XB08942DA_CS4.mzML" --f "D:\Project_auto\XB08942DA_T\XB08942DA_CS6.mzML" --f "D:\Project_auto\XB08942DA_T\XB08942DA_CS7.mzML" --lib "\\192.168.200.201\smb\ProteinDB\SPECLIB\DA\Homo_sapiens_9606_SP_20231220.predicted.speclib" --threads 24 --verbose 1 --out "D:\Project_auto\XB08942DA_T\Results\report.tsv"  --qvalue 0.01 --matrices --out-lib "D:\Project_auto\XB08942DA_T\Results\report-lib.tsv"  --gen-spec-lib --reanalyse --relaxed-prot-inf --smart-profiling --peak-center --no-ifs-removal 

Thread number set to 24
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
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.

10 files will be processed
[0:00] Loading spectral library \\192.168.200.201\smb\ProteinDB\SPECLIB\DA\Homo_sapiens_9606_SP_20231220.predicted.speclib
[0:17] Library annotated with sequence database(s): C:\1_Project\LL\DIA_Lib\Homo_sapiens_9606_SP_20231220\Homo_sapiens_9606_SP_20231220.fasta
[0:17] Gene names missing for some isoforms
[0:17] Library contains 5043 proteins, and 5043 genes
[0:18] Spectral library loaded: 20412 protein isoforms, 29359 protein groups and 4637741 precursors in 1491709 elution groups.
[0:18] Initialising library

[0:23] First pass: generating a spectral library from DIA data
[0:23] File #1/10
[0:23] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_LA1.mzML
[2:47] 2740758 library precursors are potentially detectable
[2:49] Processing...
[5:22] RT window set to 1.30202
[5:22] Peak width: 2.772
[5:22] Scan window radius set to 6
[5:22] Recommended MS1 mass accuracy setting: 7.66798 ppm
[8:16] Optimised mass accuracy: 12.6773 ppm
[11:54] Removing low confidence identifications
[11:55] Removing interfering precursors
[11:59] Training neural networks: 71106 targets, 44071 decoys
[12:03] Number of IDs at 0.01 FDR: 23470
[12:04] Calculating protein q-values
[12:05] Number of genes identified at 1% FDR: 1596 (precursor-level), 1393 (protein-level) (inference performed using proteotypic peptides only)
[12:05] Quantification
[12:07] Quantification information saved to D:\Project_auto\XB08942DA_T\XB08942DA_LA1.mzML.quant.

[12:09] File #2/10
[12:09] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_LA2.mzML
[14:37] 2740758 library precursors are potentially detectable
[14:38] Processing...
[17:55] RT window set to 1.41032
[17:56] Recommended MS1 mass accuracy setting: 7.53862 ppm
[22:27] Removing low confidence identifications
[22:27] Removing interfering precursors
[22:29] Training neural networks: 53598 targets, 31821 decoys
[22:33] Number of IDs at 0.01 FDR: 17184
[22:33] Calculating protein q-values
[22:33] Number of genes identified at 1% FDR: 1330 (precursor-level), 1130 (protein-level) (inference performed using proteotypic peptides only)
[22:34] Quantification
[22:35] Quantification information saved to D:\Project_auto\XB08942DA_T\XB08942DA_LA2.mzML.quant.

[22:42] File #3/10
[22:42] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_LA4.mzML
[24:50] 2740758 library precursors are potentially detectable
[24:50] Processing...
[28:24] RT window set to 1.30789
[28:25] Recommended MS1 mass accuracy setting: 7.48929 ppm
[32:54] Removing low confidence identifications
[32:54] Removing interfering precursors
[32:57] Training neural networks: 55592 targets, 32549 decoys
[33:01] Number of IDs at 0.01 FDR: 17324
[33:01] Calculating protein q-values
[33:02] Number of genes identified at 1% FDR: 1327 (precursor-level), 1123 (protein-level) (inference performed using proteotypic peptides only)
[33:03] Quantification
[33:04] Quantification information saved to D:\Project_auto\XB08942DA_T\XB08942DA_LA4.mzML.quant.

[33:07] File #4/10
[33:07] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_LA6.mzML
[35:44] 2740758 library precursors are potentially detectable
[35:45] Processing...
[37:42] RT window set to 1.26233
[37:43] Recommended MS1 mass accuracy setting: 6.49831 ppm
[41:53] Removing low confidence identifications
[41:54] Removing interfering precursors
[41:58] Training neural networks: 101754 targets, 61692 decoys
[42:04] Number of IDs at 0.01 FDR: 32787
[42:04] Calculating protein q-values
[42:05] Number of genes identified at 1% FDR: 1905 (precursor-level), 1664 (protein-level) (inference performed using proteotypic peptides only)
[42:05] Quantification
[42:07] Quantification information saved to D:\Project_auto\XB08942DA_T\XB08942DA_LA6.mzML.quant.

[42:14] File #5/10
[42:14] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_LA7.mzML
[44:21] 2740758 library precursors are potentially detectable
[44:22] Processing...
[46:33] RT window set to 1.29209
[46:34] Recommended MS1 mass accuracy setting: 6.18459 ppm
[51:00] Removing low confidence identifications
[51:00] Removing interfering precursors
[51:04] Training neural networks: 83864 targets, 49807 decoys
[51:09] Number of IDs at 0.01 FDR: 26405
[51:09] Calculating protein q-values
[51:10] Number of genes identified at 1% FDR: 1705 (precursor-level), 1479 (protein-level) (inference performed using proteotypic peptides only)
[51:10] Quantification
[51:13] Quantification information saved to D:\Project_auto\XB08942DA_T\XB08942DA_LA7.mzML.quant.

[51:16] File #6/10
[51:16] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_CS1.mzML
[53:47] 2740758 library precursors are potentially detectable
[53:47] Processing...
[73:35] RT window set to 1.54279
[73:37] Recommended MS1 mass accuracy setting: 5.9539 ppm
[79:42] Removing low confidence identifications
[79:42] Removing interfering precursors
[79:49] Training neural networks: 19192 targets, 11436 decoys
[79:51] Number of IDs at 0.01 FDR: 3541
[79:51] Calculating protein q-values
[79:53] Number of genes identified at 1% FDR: 578 (precursor-level), 444 (protein-level) (inference performed using proteotypic peptides only)
[79:53] Quantification
[79:56] Quantification information saved to D:\Project_auto\XB08942DA_T\XB08942DA_CS1.mzML.quant.

[79:59] File #7/10
[79:59] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_CS2.mzML
[82:14] 2740758 library precursors are potentially detectable
[82:14] Processing...
[98:08] RT window set to 1.35576
[98:09] Recommended MS1 mass accuracy setting: 5.69728 ppm
[104:16] Removing low confidence identifications
[104:16] Removing interfering precursors
[104:20] Training neural networks: 18117 targets, 10629 decoys
[104:21] Number of IDs at 0.01 FDR: 3806
[104:21] Calculating protein q-values
[104:22] Number of genes identified at 1% FDR: 576 (precursor-level), 469 (protein-level) (inference performed using proteotypic peptides only)
[104:22] Quantification
[104:23] Quantification information saved to D:\Project_auto\XB08942DA_T\XB08942DA_CS2.mzML.quant.

[104:26] File #8/10
[104:26] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_CS4.mzML
[106:46] 2740758 library precursors are potentially detectable
[106:46] Processing...
[123:09] RT window set to 1.32532
[123:10] Recommended MS1 mass accuracy setting: 5.46745 ppm
[127:12] Removing low confidence identifications
[127:13] Removing interfering precursors
[127:14] Training neural networks: 18104 targets, 10513 decoys
[127:15] Number of IDs at 0.01 FDR: 3477
[127:15] Calculating protein q-values
[127:16] Number of genes identified at 1% FDR: 576 (precursor-level), 391 (protein-level) (inference performed using proteotypic peptides only)
[127:16] Quantification
[127:17] Quantification information saved to D:\Project_auto\XB08942DA_T\XB08942DA_CS4.mzML.quant.

[127:20] File #9/10
[127:20] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_CS6.mzML
[129:12] 2740758 library precursors are potentially detectable
[129:12] Processing...
[143:09] RT window set to 1.39702
[143:09] Recommended MS1 mass accuracy setting: 5.38696 ppm
[147:48] Removing low confidence identifications
[147:48] Removing interfering precursors
[147:50] Training neural networks: 18341 targets, 10610 decoys
[147:51] Number of IDs at 0.01 FDR: 3579
[147:51] Calculating protein q-values
[147:51] Number of genes identified at 1% FDR: 575 (precursor-level), 433 (protein-level) (inference performed using proteotypic peptides only)
[147:52] Quantification
[147:53] Quantification information saved to D:\Project_auto\XB08942DA_T\XB08942DA_CS6.mzML.quant.

[147:56] File #10/10
[147:56] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_CS7.mzML
[149:47] 2740758 library precursors are potentially detectable
[149:47] Processing...
[159:27] RT window set to 1.37604
[159:27] Recommended MS1 mass accuracy setting: 5.54857 ppm
[163:22] Removing low confidence identifications
[163:22] Removing interfering precursors
[163:24] Training neural networks: 22132 targets, 12821 decoys
[163:25] Number of IDs at 0.01 FDR: 4535
[163:25] Calculating protein q-values
[163:26] Number of genes identified at 1% FDR: 626 (precursor-level), 530 (protein-level) (inference performed using proteotypic peptides only)
[163:26] Quantification
[163:27] Quantification information saved to D:\Project_auto\XB08942DA_T\XB08942DA_CS7.mzML.quant.

[163:30] Cross-run analysis
[163:30] Reading quantification information: 10 files
[163:31] Quantifying peptides
[163:32] Assembling protein groups
[163:35] Quantifying proteins
[163:35] Calculating q-values for protein and gene groups
[163:36] Calculating global q-values for protein and gene groups
[163:36] Writing report
[163:45] Report saved to D:\Project_auto\XB08942DA_T\Results\report-first-pass.tsv.
[163:45] Saving precursor levels matrix
[163:45] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Project_auto\XB08942DA_T\Results\report-first-pass.pr_matrix.tsv.
[163:45] Saving protein group levels matrix
[163:45] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\Project_auto\XB08942DA_T\Results\report-first-pass.pg_matrix.tsv.
[163:45] Saving gene group levels matrix
[163:45] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to D:\Project_auto\XB08942DA_T\Results\report-first-pass.gg_matrix.tsv.
[163:45] Saving unique genes levels matrix
[163:45] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to D:\Project_auto\XB08942DA_T\Results\report-first-pass.unique_genes_matrix.tsv.
[163:45] Stats report saved to D:\Project_auto\XB08942DA_T\Results\report-first-pass.stats.tsv
[163:45] Generating spectral library:
[163:45] 37845 precursors passing the FDR threshold are to be extracted
[163:45] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_LA1.mzML
[165:35] 2740758 library precursors are potentially detectable
[165:36] 10156 spectra added to the library
[165:38] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_LA2.mzML
[167:27] 2740758 library precursors are potentially detectable
[167:27] 1048 spectra added to the library
[167:29] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_LA4.mzML
[169:19] 2740758 library precursors are potentially detectable
[169:20] 788 spectra added to the library
[169:22] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_LA6.mzML
[171:13] 2740758 library precursors are potentially detectable
[171:14] 8094 spectra added to the library
[171:17] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_LA7.mzML
[173:04] 2740758 library precursors are potentially detectable
[173:05] 5183 spectra added to the library
[173:07] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_CS1.mzML
[174:54] 2740758 library precursors are potentially detectable
[174:55] 167 spectra added to the library
[174:57] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_CS2.mzML
[176:44] 2740758 library precursors are potentially detectable
[176:44] 103 spectra added to the library
[176:46] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_CS4.mzML
[178:33] 2740758 library precursors are potentially detectable
[178:33] 13 spectra added to the library
[178:35] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_CS6.mzML
[180:23] 2740758 library precursors are potentially detectable
[180:23] 334 spectra added to the library
[180:25] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_CS7.mzML
[182:12] 2740758 library precursors are potentially detectable
[182:12] 889 spectra added to the library
[182:14] Saving spectral library to D:\Project_auto\XB08942DA_T\Results\report-lib.tsv
[182:18] 37845 precursors saved
[182:18] Loading the generated library and saving it in the .speclib format
[182:18] Loading spectral library D:\Project_auto\XB08942DA_T\Results\report-lib.tsv
[182:20] Spectral library loaded: 5441 protein isoforms, 5711 protein groups and 37845 precursors in 32679 elution groups.
[182:20] Protein names missing for some isoforms
[182:20] Gene names missing for some isoforms
[182:20] Library contains 0 proteins, and 0 genes
[182:20] Saving the library to D:\Project_auto\XB08942DA_T\Results\report-lib.tsv.speclib

[182:24] Second pass: using the newly created spectral library to reanalyse the data
[182:24] File #1/10
[182:24] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_LA1.mzML
[184:06] 37845 library precursors are potentially detectable
[184:06] Processing...
[184:08] RT window set to 0.427473
[184:08] Recommended MS1 mass accuracy setting: 7.90225 ppm
[184:08] Removing low confidence identifications
[184:08] Removing interfering precursors
[184:09] Training neural networks: 35093 targets, 19895 decoys
[184:11] Number of IDs at 0.01 FDR: 29942
[184:11] Calculating protein q-values
[184:11] Number of genes identified at 1% FDR: 1772 (precursor-level), 1534 (protein-level) (inference performed using proteotypic peptides only)
[184:11] Quantification

[184:14] File #2/10
[184:14] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_LA2.mzML
[185:57] 37845 library precursors are potentially detectable
[185:57] Processing...
[186:00] RT window set to 0.426867
[186:00] Recommended MS1 mass accuracy setting: 7.22739 ppm
[186:01] Removing low confidence identifications
[186:01] Removing interfering precursors
[186:01] Training neural networks: 33163 targets, 18381 decoys
[186:03] Number of IDs at 0.01 FDR: 25217
[186:03] Calculating protein q-values
[186:03] Number of genes identified at 1% FDR: 1651 (precursor-level), 1332 (protein-level) (inference performed using proteotypic peptides only)
[186:03] Quantification

[186:06] File #3/10
[186:06] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_LA4.mzML
[187:50] 37845 library precursors are potentially detectable
[187:50] Processing...
[187:53] RT window set to 0.426862
[187:53] Recommended MS1 mass accuracy setting: 7.63043 ppm
[187:54] Removing low confidence identifications
[187:54] Removing interfering precursors
[187:55] Training neural networks: 34028 targets, 20849 decoys
[187:56] Number of IDs at 0.01 FDR: 25204
[187:56] Calculating protein q-values
[187:56] Number of genes identified at 1% FDR: 1629 (precursor-level), 1360 (protein-level) (inference performed using proteotypic peptides only)
[187:56] Quantification

[187:59] File #4/10
[187:59] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_LA6.mzML
[189:46] 37845 library precursors are potentially detectable
[189:46] Processing...
[189:47] RT window set to 0.427977
[189:47] Recommended MS1 mass accuracy setting: 7.38249 ppm
[189:48] Removing low confidence identifications
[189:48] Removing interfering precursors
[189:49] Training neural networks: 36612 targets, 24512 decoys
[189:51] Number of IDs at 0.01 FDR: 33769
[189:51] Calculating protein q-values
[189:51] Number of genes identified at 1% FDR: 1895 (precursor-level), 1590 (protein-level) (inference performed using proteotypic peptides only)
[189:51] Quantification

[189:54] File #5/10
[189:54] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_LA7.mzML
[191:39] 37845 library precursors are potentially detectable
[191:39] Processing...
[191:41] RT window set to 0.429089
[191:41] Recommended MS1 mass accuracy setting: 6.64126 ppm
[191:42] Removing low confidence identifications
[191:42] Removing interfering precursors
[191:43] Training neural networks: 36044 targets, 22971 decoys
[191:44] Number of IDs at 0.01 FDR: 31355
[191:45] Calculating protein q-values
[191:45] Number of genes identified at 1% FDR: 1807 (precursor-level), 1526 (protein-level) (inference performed using proteotypic peptides only)
[191:45] Quantification

[191:48] File #6/10
[191:48] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_CS1.mzML
[193:32] 37845 library precursors are potentially detectable
[193:32] Processing...
[193:38] RT window set to 0.425733
[193:38] Recommended MS1 mass accuracy setting: 5.73847 ppm
[193:40] Removing low confidence identifications
[193:40] Removing interfering precursors
[193:40] Training neural networks: 24143 targets, 18759 decoys
[193:41] Number of IDs at 0.01 FDR: 5362
[193:41] Calculating protein q-values
[193:41] Number of genes identified at 1% FDR: 768 (precursor-level), 530 (protein-level) (inference performed using proteotypic peptides only)
[193:41] Quantification

[193:44] File #7/10
[193:44] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_CS2.mzML
[195:29] 37845 library precursors are potentially detectable
[195:29] Processing...
[195:36] RT window set to 0.427996
[195:36] Recommended MS1 mass accuracy setting: 5.80593 ppm
[195:37] Removing low confidence identifications
[195:37] Removing interfering precursors
[195:37] Training neural networks: 25248 targets, 19778 decoys
[195:39] Number of IDs at 0.01 FDR: 5815
[195:39] Calculating protein q-values
[195:39] Number of genes identified at 1% FDR: 779 (precursor-level), 557 (protein-level) (inference performed using proteotypic peptides only)
[195:39] Quantification

[195:42] File #8/10
[195:42] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_CS4.mzML
[197:27] 37845 library precursors are potentially detectable
[197:27] Processing...
[197:33] RT window set to 0.421886
[197:33] Recommended MS1 mass accuracy setting: 5.09548 ppm
[197:34] Removing low confidence identifications
[197:34] Removing interfering precursors
[197:35] Training neural networks: 24036 targets, 18883 decoys
[197:36] Number of IDs at 0.01 FDR: 5172
[197:36] Calculating protein q-values
[197:36] Number of genes identified at 1% FDR: 773 (precursor-level), 520 (protein-level) (inference performed using proteotypic peptides only)
[197:36] Quantification

[197:39] File #9/10
[197:39] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_CS6.mzML
[199:24] 37845 library precursors are potentially detectable
[199:24] Processing...
[199:30] RT window set to 0.425471
[199:30] Recommended MS1 mass accuracy setting: 5.37943 ppm
[199:31] Removing low confidence identifications
[199:31] Removing interfering precursors
[199:32] Training neural networks: 24296 targets, 19173 decoys
[199:33] Number of IDs at 0.01 FDR: 5202
[199:33] Calculating protein q-values
[199:33] Number of genes identified at 1% FDR: 770 (precursor-level), 491 (protein-level) (inference performed using proteotypic peptides only)
[199:33] Quantification

[199:36] File #10/10
[199:36] Loading run D:\Project_auto\XB08942DA_T\XB08942DA_CS7.mzML
[201:20] 37845 library precursors are potentially detectable
[201:20] Processing...
[201:25] RT window set to 0.430321
[201:25] Recommended MS1 mass accuracy setting: 5.2645 ppm
[201:26] Removing low confidence identifications
[201:26] Removing interfering precursors
[201:27] Training neural networks: 24415 targets, 18422 decoys
[201:28] Number of IDs at 0.01 FDR: 6232
[201:28] Calculating protein q-values
[201:28] Number of genes identified at 1% FDR: 833 (precursor-level), 552 (protein-level) (inference performed using proteotypic peptides only)
[201:28] Quantification

[201:31] Cross-run analysis
[201:31] Reading quantification information: 10 files
[201:31] Quantifying peptides
[201:33] Quantifying proteins
[201:33] Calculating q-values for protein and gene groups
[201:34] Calculating global q-values for protein and gene groups
[201:34] Writing report
[201:43] Report saved to D:\Project_auto\XB08942DA_T\Results\report.tsv.
[201:43] Saving precursor levels matrix
[201:43] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Project_auto\XB08942DA_T\Results\report.pr_matrix.tsv.
[201:43] Saving protein group levels matrix
[201:43] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\Project_auto\XB08942DA_T\Results\report.pg_matrix.tsv.
[201:43] Saving gene group levels matrix
[201:43] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to D:\Project_auto\XB08942DA_T\Results\report.gg_matrix.tsv.
[201:43] Saving unique genes levels matrix
[201:43] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to D:\Project_auto\XB08942DA_T\Results\report.unique_genes_matrix.tsv.
[201:43] Stats report saved to D:\Project_auto\XB08942DA_T\Results\report.stats.tsv

Finished

