
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 Oct 21 00:24:29 2025
CPU: AuthenticAMD AMD EPYC 9334 32-Core Processor
SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 SSE4a 
Logical CPU cores: 64
diann.exe --f C:\Data\Adi\2025-10-15_BTK_PD_53\P4_1.raw  --f C:\Data\Adi\2025-10-15_BTK_PD_53\P4_2.raw  --f C:\Data\Adi\2025-10-15_BTK_PD_53\P4_3.raw  --f C:\Data\Adi\2025-10-15_BTK_PD_53\P4_4.raw  --lib C:\Data\Adi\2025-10-15_BTK_PD_53\DIANN\Predicted.predicted.speclib --threads 64 --verbose 1 --out C:\Data\Adi\2025-10-15_BTK_PD_53\DIANN\P4\P4.parquet --qvalue 0.01 --matrices --out-lib C:\Data\Adi\2025-10-15_BTK_PD_53\DIANN\P4\P4_library.parquet --gen-spec-lib --predictor --fasta C:\Data\Human_proteome_05_2025_strep.fasta --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --met-excision --min-pep-len 7 --max-pep-len 30 --min-pr-mz 370 --max-pr-mz 1000 --min-pr-charge 2 --max-pr-charge 4 --cut K*,R* --missed-cleavages 1 --unimod4 --individual-mass-acc --individual-windows --reanalyse --rt-profiling 

Thread number set to 64
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
Deep learning will be used to generate a new in silico spectral library from peptides provided
DIA-NN will carry out FASTA digest for in silico lib generation
Min fragment m/z set to 200
Max fragment m/z set to 1800
N-terminal methionine excision enabled
Min peptide length set to 7
Max peptide length set to 30
Min precursor m/z set to 370
Max precursor m/z set to 1000
Min precursor charge set to 2
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
Mass accuracy will be determined separately for different runs
Scan windows will be inferred separately for different runs
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
ERROR: cannot read .raw files, please download and install .NET Runtime .NET SDK 8.0.407 or later https://dotnet.microsoft.com/en-us/download/dotnet/8.0
WARNING: spectral library is provided, FASTA digest will therefore be disabled
WARNING: MBR turned off, at least two files are required

0 files will be processed
[0:00] Loading spectral library C:\Data\Adi\2025-10-15_BTK_PD_53\DIANN\Predicted.predicted.speclib
[0:02] Library annotated with sequence database(s): C:\Data\Human_proteome_05_2025_strep.fasta
[0:03] Spectral library loaded: 20620 protein isoforms, 29339 protein groups and 2552273 precursors in 1327597 elution groups.
[0:03] Loading protein annotations from FASTA C:\Data\Human_proteome_05_2025_strep.fasta
[0:03] Annotating library proteins with information from the FASTA database
[0:03] Gene names missing for some isoforms
[0:03] Library contains 20620 proteins, and 20372 genes
[0:05] [0:12] [1:48] [2:01] [2:02] [2:04] Saving the library to C:\Data\Adi\2025-10-15_BTK_PD_53\DIANN\P4\P4_library.predicted.speclib
[2:07] Initialising library

