DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks)
Compiled on Apr 14 2022 15:31:19
Current date and time: Sun May 18 21:35:50 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 \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\RawFiles\diann_dian_1.8.1\Mix5-6.wiff.dia  --lib  --threads 32 --verbose 1 --out \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_1.8.1_isoform\Mix-3.tsv --qvalue 0.01 --matrices --out-lib \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_1.8.1_isoform\Mix-3_lib.tsv --gen-spec-lib --predictor --fasta \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250511_FASTA_input\clean_Mix-3.fasta --fasta-search --min-fr-mz 200 --max-fr-mz 1800 --cut K*,R* --missed-cleavages 0 --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --unimod4 --relaxed-prot-inf --smart-profiling --pg-level 0 --peak-center --no-ifs-removal --cut  --duplicate-proteins 

Thread number set to 32
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
Library-free search enabled
Min fragment m/z set to 200
Max fragment m/z set to 1800
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 0
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
Min precursor charge set to 1
Max precursor charge set to 4
Cysteine carbamidomethylation enabled as a fixed modification
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
Implicit protein grouping: isoform IDs; this determines which peptides are considered 'proteotypic' and thus affects protein FDR calculation
Fixed-width center of each elution peak will be used for quantification
Interference removal from fragment elution curves disabled
Duplicate proteins in FASTA files will not be skipped
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.
Exclusion of fragments shared between heavy and light peptides from quantification is not supported in FASTA digest mode - disabled; to enable, generate an in silico predicted spectral library and analyse with this library

1 files will be processed
[0:00] Loading FASTA \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250511_FASTA_input\clean_Mix-3.fasta
[0:03] Processing FASTA
[0:04] Assembling elution groups
[0:05] 1070614 precursors generated
[0:05] Protein names missing for some isoforms
[0:05] Gene names missing for some isoforms
[0:05] Library contains 0 proteins, and 0 genes
[0:05] [0:07] [3:42] [4:00] [4:01] [4:01] Saving the library to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_1.8.1_isoform\Mix-3_lib.predicted.speclib
[4:27] Initialising library

[4:27] File #1/1
[4:27] Loading run \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\RawFiles\diann_dian_1.8.1\Mix5-6.wiff.dia
[4:45] 942438 library precursors are potentially detectable
[4:45] Processing...
[5:23] RT window set to 5.42791
[5:23] Peak width: 3.24
[5:23] Scan window radius set to 7
[5:23] Recommended MS1 mass accuracy setting: 24.8623 ppm
[6:31] Optimised mass accuracy: 34.6983 ppm
[8:12] Removing low confidence identifications
[8:12] Removing interfering precursors
[8:13] Training neural networks: 35236 targets, 22336 decoys
[8:14] Number of IDs at 0.01 FDR: 15728
[8:14] Calculating protein q-values
[8:14] Number of protein isoforms identified at 1% FDR: 2141 (precursor-level), 1882 (protein-level) (inference performed using proteotypic peptides only)
[8:14] Quantification
[8:16] Quantification information saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\RawFiles\diann_dian_1.8.1\Mix5-6.wiff.dia.quant.

[8:16] Cross-run analysis
[8:16] Reading quantification information: 1 files
[8:16] Quantifying peptides
[8:16] Assembling protein groups
[8:17] Quantifying proteins
[8:17] Calculating q-values for protein and gene groups
[8:17] Calculating global q-values for protein and gene groups
[8:17] Writing report
[8:18] Report saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_1.8.1_isoform\Mix-3.tsv.
[8:18] Saving precursor levels matrix
[8:18] Precursor levels matrix (1% precursor and protein group FDR) saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_1.8.1_isoform\Mix-3.pr_matrix.tsv.
[8:18] Saving protein group levels matrix
[8:19] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_1.8.1_isoform\Mix-3.pg_matrix.tsv.
[8:19] Saving gene group levels matrix
[8:19] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_1.8.1_isoform\Mix-3.gg_matrix.tsv.
[8:19] Saving unique genes levels matrix
[8:19] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_1.8.1_isoform\Mix-3.unique_genes_matrix.tsv.
[8:19] Stats report saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_1.8.1_isoform\Mix-3.stats.tsv
[8:19] Generating spectral library:
[8:19] 15728 precursors passing the FDR threshold are to be extracted
[8:19] Loading run \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\RawFiles\diann_dian_1.8.1\Mix5-6.wiff.dia
[8:37] 942438 library precursors are potentially detectable
[8:38] 10737 spectra added to the library
[8:38] Saving spectral library to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_1.8.1_isoform\Mix-3_lib.tsv
[8:43] 15728 precursors saved
[8:43] Loading the generated library and saving it in the .speclib format
[8:43] Loading spectral library \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_1.8.1_isoform\Mix-3_lib.tsv
[8:43] Spectral library loaded: 2311 protein isoforms, 2284 protein groups and 15728 precursors in 12812 elution groups.
[8:43] Loading protein annotations from FASTA \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250511_FASTA_input\clean_Mix-3.fasta
[8:46] Protein names missing for some isoforms
[8:46] Gene names missing for some isoforms
[8:46] Library contains 0 proteins, and 0 genes
[8:46] Saving the library to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_1.8.1_isoform\Mix-3_lib.tsv.speclib

Finished