DIA-NN 1.9.2 (Data-Independent Acquisition by Neural Networks)
Compiled on Oct 17 2024 21:58:43
Current date and time: Sun May 18 15:10:15 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_dia_1.9.2\Mix15-16.wiff.dia  --lib \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250514_diann_1.9.2_lib_isoform\Mix-8_lib.predicted.speclib --threads 32 --verbose 1 --out \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250514_SearchResult_diann_1.9.2 _isoform\Mix-8.tsv --qvalue 0.01 --matrices --out-lib \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250514_SearchResult_diann_1.9.2 _isoform\Mix-8_lib.parquet --gen-spec-lib --reannotate --fasta \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250511_FASTA_input\clean_Mix-8.fasta --min-pep-len 7 --max-pep-len 30 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --cut K*,R* --missed-cleavages 0 --unimod4 --relaxed-prot-inf --rt-profiling --pg-level 0 --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
Library precursors will be reannotated using the FASTA database
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
In silico digest will involve cuts at K*,R*
Maximum number of missed cleavages set to 0
Cysteine carbamidomethylation enabled as a fixed modification
Heuristic protein grouping will be used, to reduce the number of protein groups obtained; this mode is recommended for benchmarking protein ID numbers, GO/pathway and system-scale analyses
The spectral library (if generated) will retain the original spectra but will include empirically-aligned RTs
Implicit protein grouping: isoform IDs; this determines which peptides are considered 'proteotypic' and thus affects protein FDR calculation
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.

1 files will be processed
[0:00] Loading spectral library \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250514_diann_1.9.2_lib_isoform\Mix-8_lib.predicted.speclib
[0:03] Library annotated with sequence database(s): \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250511_FASTA_input\clean_Mix-8.fasta
[0:03] Spectral library loaded: 18130 protein isoforms, 21886 protein groups and 1114496 precursors in 353481 elution groups.
[0:03] Loading FASTA \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250511_FASTA_input\clean_Mix-8.fasta
[0:08] Reannotating library precursors with information from the FASTA database
[0:09] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
[0:09] 1114496 precursors generated
[0:09] Protein names missing for some isoforms
[0:09] Gene names missing for some isoforms
[0:09] Library contains 0 proteins, and 0 genes
[0:09] Initialising library
WARNING: it is strongly recommended to enable MBR when analysing with a large library, if this is a quantitative analysis

[0:12] File #1/1
[0:12] Loading run \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\RawFiles\diann_dia_1.9.2\Mix15-16.wiff.dia
[0:28] 981072 library precursors are potentially detectable
[0:28] Calibrating with mass accuracies 30 (MS1), 20 (MS2)
[1:03] RT window set to 3.52647
[1:03] Peak width: 3.056
[1:03] Scan window radius set to 6
[1:03] Recommended MS1 mass accuracy setting: 28.1102 ppm
[2:31] Optimised mass accuracy: 39.7256 ppm
[4:12] Removing low confidence identifications
[4:12] Removing interfering precursors
[4:13] Training neural networks on 52659 PSMs
[4:15] Number of IDs at 0.01 FDR: 15609
[4:15] Calculating protein q-values
[4:15] Number of protein isoforms identified at 1% FDR: 2001 (precursor-level), 1816 (protein-level) (inference performed using proteotypic peptides only)
[4:15] Quantification
[4:16] Quantification information saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\RawFiles\diann_dia_1.9.2\Mix15-16.wiff.dia.quant

[4:17] Cross-run analysis
[4:17] Reading quantification information: 1 files
[4:17] Quantifying peptides
[4:17] Assembling protein groups
[4:17] Quantifying proteins
[4:17] Calculating q-values for protein and gene groups
[4:17] Calculating global q-values for protein and gene groups
[4:17] Protein groups with global q-value <= 0.01: 1864
[4:17] Compressed report saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250514_SearchResult_diann_1.9.2 _isoform\Mix-8.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[4:17] Writing report
[4:19] Report saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250514_SearchResult_diann_1.9.2 _isoform\Mix-8.tsv.
[4:19] Saving precursor levels matrix
[4:19] Precursor levels matrix (1% precursor and protein group FDR) saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250514_SearchResult_diann_1.9.2 _isoform\Mix-8.pr_matrix.tsv.
[4:19] Saving protein group levels matrix
[4:19] 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\250514_SearchResult_diann_1.9.2 _isoform\Mix-8.pg_matrix.tsv.
[4:19] Saving gene group levels matrix
[4:19] 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\250514_SearchResult_diann_1.9.2 _isoform\Mix-8.gg_matrix.tsv.
[4:19] Saving unique genes levels matrix
[4:19] 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\250514_SearchResult_diann_1.9.2 _isoform\Mix-8.unique_genes_matrix.tsv.
[4:19] Manifest saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250514_SearchResult_diann_1.9.2 _isoform\Mix-8.manifest.txt
[4:19] Stats report saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250514_SearchResult_diann_1.9.2 _isoform\Mix-8.stats.tsv
[4:19] Generating spectral library:
[4:19] 15604 target and 156 decoy precursors saved
[4:19] Spectral library saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250514_SearchResult_diann_1.9.2 _isoform\Mix-8_lib.parquet