DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks)
Compiled on Apr 14 2022 15:31:19
Current date and time: Mon Jun  3 09:59:53 2024
CPU: GenuineIntel 13th Gen Intel(R) Core(TM) i7-1355U
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 
Logical CPU cores: 12
diann.exe --f D:\1_KK2601_IP-DIA\MS data\KK2601-1_WT.raw  --f D:\1_KK2601_IP-DIA\MS data\KK2601-2_RK.raw  --lib Z:\Prosit\240401_GC_Mouse_UP000000589_E21709\DIA-NN\GC_240401_Mouse_UP000000589_E21709_pep7-45_z2-4_mz495-745_Car_Trypsin_miss1_Contami.predicted.speclib --threads 10 --verbose 1 --out D:\1_KK2601_IP-DIA\DIA-NN\KK2601.tsv --qvalue 0.01 --matrices --out-lib D:\1_KK2601_IP-DIA\DIA-NN\KK2601_SL.tsv --gen-spec-lib --fasta Z:\Prosit\240401_GC_Mouse_UP000000589_E21709\240401_GC_Mouse_UP000000589_E21709_Contami.fasta --met-excision --cut K*,R*,!*P --mass-acc 10 --mass-acc-ms1 10 --individual-mass-acc --individual-windows --relaxed-prot-inf --smart-profiling --peak-center --no-ifs-removal --no-norm --protein-qvalue 0.01  --mass-acc-cal 10  --matrix-qvalue 0.01  --matrix-spec-q 

Thread number set to 10
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
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
But excluding cuts at *P
Mass accuracy will be determined separately for different runs
Scan windows will be inferred separately for different runs
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
Normalisation disabled
Output will be filtered at 0.01 protein-level FDR
Calibration mass accuracy set to 1e-05
Precursor/protein x sample matrices will be filtered at 0.01 precursor & protein-level FDR
Protein x sample matrices will be also filtered using run-specific protein q-value
Mass accuracy will be fixed to 1e-05 (MS2) and 1e-05 (MS1)

2 files will be processed
[0:00] Loading spectral library Z:\Prosit\240401_GC_Mouse_UP000000589_E21709\DIA-NN\GC_240401_Mouse_UP000000589_E21709_pep7-45_z2-4_mz495-745_Car_Trypsin_miss1_Contami.predicted.speclib
[0:05] Library annotated with sequence database(s): Z:\Prosit\240401_GC_Mouse_UP000000589_E21709\240401_GC_Mouse_UP000000589_E21709_Contami.fasta
[0:05] Spectral library loaded: 22004 protein isoforms, 29752 protein groups and 1102750 precursors in 990857 elution groups.
[0:05] Loading protein annotations from FASTA Z:\Prosit\240401_GC_Mouse_UP000000589_E21709\240401_GC_Mouse_UP000000589_E21709_Contami.fasta
[0:06] Annotating library proteins with information from the FASTA database
[0:06] Gene names missing for some isoforms
[0:06] Library contains 21978 proteins, and 21638 genes
[0:06] Initialising library

[0:06] File #1/2
[0:06] Loading run D:\1_KK2601_IP-DIA\MS data\KK2601-1_WT.raw
[0:30] 1057415 library precursors are potentially detectable
[0:30] Processing...
[0:56] RT window set to 5.36039
[0:56] Peak width: 3.152
[0:56] Scan window radius set to 6
[0:56] Recommended MS1 mass accuracy setting: 19.3029 ppm
[2:21] Removing low confidence identifications
[2:21] Removing interfering precursors
[2:24] Training neural networks: 70789 targets, 45996 decoys
[2:33] Number of IDs at 0.01 FDR: 32529
[2:34] Calculating protein q-values
[2:34] Number of genes identified at 1% FDR: 5954 (precursor-level), 5602 (protein-level) (inference performed using proteotypic peptides only)
[2:34] Quantification
[2:36] Quantification information saved to D:\1_KK2601_IP-DIA\MS data\KK2601-1_WT.raw.quant.

[2:36] File #2/2
[2:36] Loading run D:\1_KK2601_IP-DIA\MS data\KK2601-2_RK.raw
[3:00] 1057415 library precursors are potentially detectable
[3:00] Processing...
[3:26] RT window set to 5.1378
[3:26] Peak width: 3.136
[3:26] Scan window radius set to 6
[3:26] Recommended MS1 mass accuracy setting: 19.0499 ppm
[4:53] Removing low confidence identifications
[4:53] Removing interfering precursors
[4:56] Training neural networks: 70041 targets, 45363 decoys
[5:08] Number of IDs at 0.01 FDR: 32834
[5:09] Calculating protein q-values
[5:09] Number of genes identified at 1% FDR: 5998 (precursor-level), 5615 (protein-level) (inference performed using proteotypic peptides only)
[5:09] Quantification
[5:10] Quantification information saved to D:\1_KK2601_IP-DIA\MS data\KK2601-2_RK.raw.quant.

[5:10] Cross-run analysis
[5:10] Reading quantification information: 2 files
[5:10] Averaged recommended settings for this experiment: Mass accuracy = 10ppm, MS1 accuracy = 10ppm, Scan window = 6
[5:10] Quantifying peptides
[5:10] Assembling protein groups
[5:12] Quantifying proteins
[5:12] Calculating q-values for protein and gene groups
[5:12] Calculating global q-values for protein and gene groups
[5:12] Writing report
[5:18] Report saved to D:\1_KK2601_IP-DIA\DIA-NN\KK2601.tsv.
[5:18] Saving precursor levels matrix
[5:18] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\1_KK2601_IP-DIA\DIA-NN\KK2601.pr_matrix.tsv.
[5:18] Saving protein group levels matrix
[5:18] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\1_KK2601_IP-DIA\DIA-NN\KK2601.pg_matrix.tsv.
[5:18] Saving gene group levels matrix
[5:18] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to D:\1_KK2601_IP-DIA\DIA-NN\KK2601.gg_matrix.tsv.
[5:18] Saving unique genes levels matrix
[5:19] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to D:\1_KK2601_IP-DIA\DIA-NN\KK2601.unique_genes_matrix.tsv.
[5:19] Stats report saved to D:\1_KK2601_IP-DIA\DIA-NN\KK2601.stats.tsv
[5:19] Generating spectral library:
[5:19] 36899 precursors passing the FDR threshold are to be extracted
[5:19] Loading run D:\1_KK2601_IP-DIA\MS data\KK2601-1_WT.raw
[5:35] 1057415 library precursors are potentially detectable
[5:36] 12107 spectra added to the library
[5:36] Loading run D:\1_KK2601_IP-DIA\MS data\KK2601-2_RK.raw
[5:52] 1057415 library precursors are potentially detectable
[5:53] 16802 spectra added to the library
[5:53] Saving spectral library to D:\1_KK2601_IP-DIA\DIA-NN\KK2601_SL.tsv
[6:00] 36899 precursors saved
[6:00] Loading the generated library and saving it in the .speclib format
[6:00] Loading spectral library D:\1_KK2601_IP-DIA\DIA-NN\KK2601_SL.tsv
[6:02] Spectral library loaded: 7139 protein isoforms, 7268 protein groups and 36899 precursors in 36429 elution groups.
[6:02] Loading protein annotations from FASTA Z:\Prosit\240401_GC_Mouse_UP000000589_E21709\240401_GC_Mouse_UP000000589_E21709_Contami.fasta
[6:03] Gene names missing for some isoforms
[6:03] Library contains 7119 proteins, and 7087 genes
[6:03] Saving the library to D:\1_KK2601_IP-DIA\DIA-NN\KK2601_SL.tsv.speclib

Finished