DIA-NN 1.7.12 (Data Independent Acquisition by Neural Networks)
Compiled on Oct  1 2020 21:36:38
Current date and time: Thu Jan 28 15:18:07 2021
CPU: GenuineIntel Intel(R) Xeon(R) CPU           E5620  @ 2.40GHz
SIMD instructions: SSE4.1 SSE4.2 
Logical CPU cores: 16
diann.exe --f Z:\Iwata\181201_Liver_Whole\SWATH\KI1.wiff.dia --f Z:\Iwata\181201_Liver_Whole\SWATH\KI2.wiff.dia --f Z:\Iwata\181201_Liver_Whole\SWATH\KI3.wiff.dia --f Z:\Iwata\181201_Liver_Whole\SWATH\KI4.wiff.dia --f Z:\Iwata\181201_Liver_Whole\SWATH\KI5.wiff.dia --f Z:\Iwata\181201_Liver_Whole\SWATH\WT1.wiff.dia --f Z:\Iwata\181201_Liver_Whole\SWATH\WT2.wiff.dia --f Z:\Iwata\181201_Liver_Whole\SWATH\WT3.wiff.dia --f Z:\Iwata\181201_Liver_Whole\SWATH\WT4.wiff.dia --f Z:\Iwata\181201_Liver_Whole\SWATH\WT5.wiff.dia --lib Z:\Iwata\210127_APP-KI_5month_Liver_Whole_re\Proein pilot\181201_Iwata_Liver_Wholemix.txt --threads 12 --verbose 1 --out Z:\Iwata\210127_APP-KI_5month_Liver_Whole_re\DIA-NN\APP-KI_5month_Liver_Whole_output.tsv --out-gene Z:\Iwata\210127_APP-KI_5month_Liver_Whole_re\DIA-NN\APP-KI_5month_Liver_Whole_output.genes.tsv --qvalue 0.01 --matrices --reannotate --fasta Z:\Proteome DB\UP000000589_10090_mouse_200403.fasta --met-excision --cut-after KR --missed-cleavages 1 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --unimod4 --var-mods 1 --rt-profiling 

Thread number set to 12
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
Library precursors will be reannotated using the FASTA database
N-terminal methionine excision enabled
WARNING: unrecognised option [--cut-after KR]
Maximum number of missed cleavages set to 1
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
Cysteine carbamidomethylation enabled as a fixed modification
Maximum number of variable modifications set to 1
RT profiling enabled

10 files will be processed
[0:00] Loading spectral library Z:\Iwata\210127_APP-KI_5month_Liver_Whole_re\Proein pilot\181201_Iwata_Liver_Wholemix.txt
WARNING: no neutral loss information found in the library - assuming fragments without losses
[0:03] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
[0:03] Spectral library loaded: 2223 protein isoforms, 2223 protein groups and 24756 precursors in 22743 elution groups.
[0:03] Loading FASTA Z:\Proteome DB\UP000000589_10090_mouse_200403.fasta
[0:33] Reannotating library precursors with information from the FASTA database
[0:34] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
[0:34] 24756 precursors generated
[0:34] Gene names missing for some isoforms
[0:34] Library contains 2626 proteins, and 2625 genes
[0:34] Initialising library
[0:34] Saving the library to Z:\Iwata\210127_APP-KI_5month_Liver_Whole_re\Proein pilot\181201_Iwata_Liver_Wholemix.txt.speclib

[0:35] First pass: collecting retention time information
[0:35] File #1/10
[0:35] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\KI1.wiff.dia
[1:19] 24754 library precursors are potentially detectable
[1:19] Processing...
[1:23] RT window set to 1.5233
[1:23] Peak width: 3.44
[1:23] Scan window radius set to 7
[1:33] Optimised mass accuracy: 36.612 ppm
[1:47] Removing interfering precursors
[1:49] Training the neural network: 22828 targets, 23222 decoys
[1:53] Number of IDs at 0.01 FDR: 21933
[1:54] Calculating protein q-values
[1:54] Number of genes identified at 1% FDR: 1995 (precursor-level), 1983 (protein-level) (inference performed using proteotypic peptides only)
[1:54] Quantification
[1:58] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\KI1.wiff.dia.quant.

[1:58] File #2/10
[1:58] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\KI2.wiff.dia
[2:35] 24754 library precursors are potentially detectable
[2:35] Processing...
[2:38] RT window set to 1.52896
[2:52] Removing interfering precursors
[2:54] Training the neural network: 22757 targets, 23356 decoys
[2:58] Number of IDs at 0.01 FDR: 21906
[2:59] Calculating protein q-values
[2:59] Number of genes identified at 1% FDR: 1983 (precursor-level), 1959 (protein-level) (inference performed using proteotypic peptides only)
[2:59] Quantification
[3:03] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\KI2.wiff.dia.quant.

[3:03] File #3/10
[3:03] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\KI3.wiff.dia
[3:32] 24754 library precursors are potentially detectable
[3:32] Processing...
[3:36] RT window set to 1.51439
[3:49] Removing interfering precursors
[3:52] Training the neural network: 22999 targets, 23286 decoys
[3:56] Number of IDs at 0.01 FDR: 22142
[3:56] Calculating protein q-values
[3:56] Number of genes identified at 1% FDR: 1993 (precursor-level), 1959 (protein-level) (inference performed using proteotypic peptides only)
[3:56] Quantification
[4:00] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\KI3.wiff.dia.quant.

[4:00] File #4/10
[4:00] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\KI4.wiff.dia
[4:24] 24754 library precursors are potentially detectable
[4:24] Processing...
[4:27] RT window set to 1.50475
[4:40] Removing interfering precursors
[4:43] Training the neural network: 22916 targets, 23263 decoys
[4:47] Number of IDs at 0.01 FDR: 21992
[4:48] Calculating protein q-values
[4:48] Number of genes identified at 1% FDR: 1984 (precursor-level), 1969 (protein-level) (inference performed using proteotypic peptides only)
[4:48] Quantification
[4:51] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\KI4.wiff.dia.quant.

[4:51] File #5/10
[4:51] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\KI5.wiff.dia
[5:18] 24754 library precursors are potentially detectable
[5:18] Processing...
[5:21] RT window set to 1.51854
[5:35] Removing interfering precursors
[5:37] Training the neural network: 23393 targets, 23179 decoys
[5:42] Number of IDs at 0.01 FDR: 22889
[5:42] Calculating protein q-values
[5:42] Number of genes identified at 1% FDR: 2024 (precursor-level), 2018 (protein-level) (inference performed using proteotypic peptides only)
[5:42] Quantification
[5:46] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\KI5.wiff.dia.quant.

[5:46] File #6/10
[5:46] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\WT1.wiff.dia
[6:15] 24754 library precursors are potentially detectable
[6:15] Processing...
[6:19] RT window set to 1.53841
[6:32] Removing interfering precursors
[6:35] Training the neural network: 23010 targets, 23322 decoys
[6:39] Number of IDs at 0.01 FDR: 22292
[6:40] Calculating protein q-values
[6:40] Number of genes identified at 1% FDR: 1998 (precursor-level), 1984 (protein-level) (inference performed using proteotypic peptides only)
[6:40] Quantification
[6:43] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\WT1.wiff.dia.quant.

[6:44] File #7/10
[6:44] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\WT2.wiff.dia
[7:13] 24754 library precursors are potentially detectable
[7:13] Processing...
[7:17] RT window set to 1.53804
[7:30] Removing interfering precursors
[7:33] Training the neural network: 23113 targets, 23305 decoys
[7:37] Number of IDs at 0.01 FDR: 22319
[7:38] Calculating protein q-values
[7:38] Number of genes identified at 1% FDR: 1988 (precursor-level), 1964 (protein-level) (inference performed using proteotypic peptides only)
[7:38] Quantification
[7:42] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\WT2.wiff.dia.quant.

[7:42] File #8/10
[7:42] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\WT3.wiff.dia
[8:09] 24754 library precursors are potentially detectable
[8:09] Processing...
[8:13] RT window set to 1.53925
[8:26] Removing interfering precursors
[8:29] Training the neural network: 23419 targets, 23281 decoys
[8:33] Number of IDs at 0.01 FDR: 22892
[8:34] Calculating protein q-values
[8:34] Number of genes identified at 1% FDR: 2008 (precursor-level), 1980 (protein-level) (inference performed using proteotypic peptides only)
[8:34] Quantification
[8:37] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\WT3.wiff.dia.quant.

[8:37] File #9/10
[8:37] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\WT4.wiff.dia
[9:13] 24754 library precursors are potentially detectable
[9:13] Processing...
[9:17] RT window set to 1.51677
[9:30] Removing interfering precursors
[9:33] Training the neural network: 23130 targets, 23266 decoys
[9:37] Number of IDs at 0.01 FDR: 22371
[9:37] Calculating protein q-values
[9:37] Number of genes identified at 1% FDR: 1993 (precursor-level), 1973 (protein-level) (inference performed using proteotypic peptides only)
[9:37] Quantification
[9:41] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\WT4.wiff.dia.quant.

[9:41] File #10/10
[9:41] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\WT5.wiff.dia
[10:10] 24754 library precursors are potentially detectable
[10:10] Processing...
[10:14] RT window set to 1.52612
[10:27] Removing interfering precursors
[10:29] Training the neural network: 23415 targets, 23187 decoys
[10:34] Number of IDs at 0.01 FDR: 22873
[10:34] Calculating protein q-values
[10:34] Number of genes identified at 1% FDR: 2013 (precursor-level), 1991 (protein-level) (inference performed using proteotypic peptides only)
[10:34] Quantification
[10:38] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\WT5.wiff.dia.quant.

[10:38] Second pass: indentification and quantification
[10:39] Second pass: file #1/10
[10:39] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\KI1.wiff.dia
[11:15] 24754 library precursors are potentially detectable
[11:15] Processing...
[11:19] RT window set to 1.52327
[11:32] Removing interfering precursors
[11:35] Training the neural network: 23265 targets, 23197 decoys
[11:39] Number of IDs at 0.01 FDR: 22639
[11:40] Calculating protein q-values
[11:40] Number of genes identified at 1% FDR: 2011 (precursor-level), 2005 (protein-level) (inference performed using proteotypic peptides only)
[11:40] Quantification
[11:44] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\KI1.wiff.dia.quant.

[11:44] Second pass: file #2/10
[11:44] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\KI2.wiff.dia
[12:11] 24754 library precursors are potentially detectable
[12:11] Processing...
[12:15] RT window set to 1.52896
[12:28] Removing interfering precursors
[12:31] Training the neural network: 23240 targets, 23199 decoys
[12:35] Number of IDs at 0.01 FDR: 22594
[12:36] Calculating protein q-values
[12:36] Number of genes identified at 1% FDR: 1997 (precursor-level), 1988 (protein-level) (inference performed using proteotypic peptides only)
[12:36] Quantification
[12:39] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\KI2.wiff.dia.quant.

[12:40] Second pass: file #3/10
[12:40] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\KI3.wiff.dia
[13:10] 24754 library precursors are potentially detectable
[13:10] Processing...
[13:14] RT window set to 1.51439
[13:27] Removing interfering precursors
[13:30] Training the neural network: 23397 targets, 23152 decoys
[13:34] Number of IDs at 0.01 FDR: 22857
[13:35] Calculating protein q-values
[13:35] Number of genes identified at 1% FDR: 2006 (precursor-level), 1980 (protein-level) (inference performed using proteotypic peptides only)
[13:35] Quantification
[13:39] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\KI3.wiff.dia.quant.

[13:39] Second pass: file #4/10
[13:39] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\KI4.wiff.dia
[14:09] 24754 library precursors are potentially detectable
[14:09] Processing...
[14:12] RT window set to 1.50475
[14:26] Removing interfering precursors
[14:28] Training the neural network: 22734 targets, 23317 decoys
[14:32] Number of IDs at 0.01 FDR: 21780
[14:33] Calculating protein q-values
[14:33] Number of genes identified at 1% FDR: 1990 (precursor-level), 1977 (protein-level) (inference performed using proteotypic peptides only)
[14:33] Quantification
[14:36] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\KI4.wiff.dia.quant.

[14:37] Second pass: file #5/10
[14:37] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\KI5.wiff.dia
[15:03] 24754 library precursors are potentially detectable
[15:03] Processing...
[15:07] RT window set to 1.51854
[15:21] Removing interfering precursors
[15:23] Training the neural network: 23408 targets, 23187 decoys
[15:27] Number of IDs at 0.01 FDR: 22899
[15:28] Calculating protein q-values
[15:28] Number of genes identified at 1% FDR: 2019 (precursor-level), 2010 (protein-level) (inference performed using proteotypic peptides only)
[15:28] Quantification
[15:32] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\KI5.wiff.dia.quant.

[15:32] Second pass: file #6/10
[15:32] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\WT1.wiff.dia
[15:58] 24754 library precursors are potentially detectable
[15:58] Processing...
[16:02] RT window set to 1.53841
[16:15] Removing interfering precursors
[16:18] Training the neural network: 23387 targets, 23261 decoys
[16:22] Number of IDs at 0.01 FDR: 22865
[16:23] Calculating protein q-values
[16:23] Number of genes identified at 1% FDR: 2010 (precursor-level), 1995 (protein-level) (inference performed using proteotypic peptides only)
[16:23] Quantification
[16:26] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\WT1.wiff.dia.quant.

[16:26] Second pass: file #7/10
[16:26] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\WT2.wiff.dia
[17:07] 24754 library precursors are potentially detectable
[17:07] Processing...
[17:10] RT window set to 1.53804
[17:24] Removing interfering precursors
[17:27] Training the neural network: 23409 targets, 23248 decoys
[17:31] Number of IDs at 0.01 FDR: 22822
[17:32] Calculating protein q-values
[17:32] Number of genes identified at 1% FDR: 2002 (precursor-level), 1992 (protein-level) (inference performed using proteotypic peptides only)
[17:32] Quantification
[17:35] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\WT2.wiff.dia.quant.

[17:36] Second pass: file #8/10
[17:36] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\WT3.wiff.dia
[18:02] 24754 library precursors are potentially detectable
[18:02] Processing...
[18:06] RT window set to 1.53925
[18:19] Removing interfering precursors
[18:22] Training the neural network: 23444 targets, 23268 decoys
[18:26] Number of IDs at 0.01 FDR: 22928
[18:27] Calculating protein q-values
[18:27] Number of genes identified at 1% FDR: 2013 (precursor-level), 1991 (protein-level) (inference performed using proteotypic peptides only)
[18:27] Quantification
[18:30] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\WT3.wiff.dia.quant.

[18:31] Second pass: file #9/10
[18:31] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\WT4.wiff.dia
[19:00] 24754 library precursors are potentially detectable
[19:00] Processing...
[19:03] RT window set to 1.51677
[19:17] Removing interfering precursors
[19:19] Training the neural network: 23427 targets, 23219 decoys
[19:24] Number of IDs at 0.01 FDR: 22872
[19:24] Calculating protein q-values
[19:24] Number of genes identified at 1% FDR: 2004 (precursor-level), 1988 (protein-level) (inference performed using proteotypic peptides only)
[19:24] Quantification
[19:28] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\WT4.wiff.dia.quant.

[19:28] Second pass: file #10/10
[19:28] Loading run Z:\Iwata\181201_Liver_Whole\SWATH\WT5.wiff.dia
[19:57] 24754 library precursors are potentially detectable
[19:57] Processing...
[20:00] RT window set to 1.52612
[20:14] Removing interfering precursors
[20:16] Training the neural network: 23452 targets, 23216 decoys
[20:20] Number of IDs at 0.01 FDR: 22986
[20:21] Calculating protein q-values
[20:21] Number of genes identified at 1% FDR: 2015 (precursor-level), 1993 (protein-level) (inference performed using proteotypic peptides only)
[20:21] Quantification
[20:25] Quantification information saved to Z:\Iwata\181201_Liver_Whole\SWATH\WT5.wiff.dia.quant.

[20:25] Cross-run analysis
[20:25] Reading quantification information: 10 files
[20:26] Quantifying peptides
[20:34] Assembling protein groups
[20:34] Quantifying proteins
[20:34] Calculating q-values for protein and gene groups
[20:34] Writing report
[21:03] Report saved to Z:\Iwata\210127_APP-KI_5month_Liver_Whole_re\DIA-NN\APP-KI_5month_Liver_Whole_output.tsv.
[21:03] Saving precursor levels matrix
[21:05] Precursor levels matrix (1% precursor and protein group FDR) saved to Z:\Iwata\210127_APP-KI_5month_Liver_Whole_re\DIA-NN\APP-KI_5month_Liver_Whole_output.pr_matrix.tsv.
[21:05] Saving protein group levels matrix
[21:05] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to Z:\Iwata\210127_APP-KI_5month_Liver_Whole_re\DIA-NN\APP-KI_5month_Liver_Whole_output.pg_matrix.tsv.
[21:05] Saving gene group levels matrix
[21:05] Gene groups levels matrix (1% precursor FDR and gene group FDR) saved to Z:\Iwata\210127_APP-KI_5month_Liver_Whole_re\DIA-NN\APP-KI_5month_Liver_Whole_output.gg_matrix.tsv.
[21:05] Saving unique genes levels matrix
[21:05] Unique genes levels matrix (1% precursor FDR and unique protein FDR) saved to Z:\Iwata\210127_APP-KI_5month_Liver_Whole_re\DIA-NN\APP-KI_5month_Liver_Whole_output.unique_genes_matrix.tsv.
[21:05] Stats report saved to Z:\Iwata\210127_APP-KI_5month_Liver_Whole_re\DIA-NN\APP-KI_5month_Liver_Whole_output.stats.tsv
[21:05] Writing gene report
[21:06] Gene report saved to Z:\Iwata\210127_APP-KI_5month_Liver_Whole_re\DIA-NN\APP-KI_5month_Liver_Whole_output.genes.tsv.
