DIA-NN 2.1.0 Academia  (Data-Independent Acquisition by Neural Networks)
Compiled on Mar 25 2025 10:59:54
Current date and time: Sat May 17 23:06:33 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_2.1\Mix7-8.wiff.dia  --lib \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_diann_2.1_isoform_lib\Mix-4_lib.predicted.speclib --threads 32 --verbose 1 --out \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_2.1_isoform\Mix-4.parquet --qvalue 0.01 --matrices --out-lib \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_2.1_isoform\Mix-4_lib.parquet --gen-spec-lib --reannotate --fasta \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250511_FASTA_input\clean_Mix-4.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 --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
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 automatically optimise the mass accuracy for the first run of the experiment, use this mode for preliminary analyses only

1 files will be processed
[0:00] Loading spectral library \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_diann_2.1_isoform_lib\Mix-4_lib.predicted.speclib
[0:02] Library annotated with sequence database(s): \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250511_FASTA_input\clean_Mix-4.fasta
[0:02] Spectral library loaded: 18137 protein isoforms, 21927 protein groups and 1114496 precursors in 353481 elution groups.
[0:02] Loading FASTA \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250511_FASTA_input\clean_Mix-4.fasta
[0:07] Reannotating library precursors with information from the FASTA database
[0:08] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
[0:08] 1114496 precursors generated
[0:08] Protein names missing for some isoforms
[0:08] Gene names missing for some isoforms
[0:08] Library contains 0 proteins, and 0 genes
[0:09] Initialising library

[0:11] File #1/1
[0:11] Loading run \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\RawFiles\diann_dia_2.1\Mix7-8.wiff.dia
[0:26] Pre-processing...
[0:28] 1704 MS1 and 124392 MS2 scans in 1704 (inferred) and 1704 (encoded) cycles, 981072 precursors in range
[0:28] Calibrating with mass accuracies 24 (MS1), 25 (MS2)
[1:01] RT window set to 4.94975
[1:01] Peak width: 3.104
[1:01] Scan window radius set to 6
[1:01] Recommended MS1 mass accuracy setting: 31 ppm
[3:23] Optimised mass accuracy: 37 ppm
[4:13] Main search
[5:47] Removing low confidence identifications
[5:49] Removing interfering precursors
[5:50] Training neural networks on 34058 target and 21088 decoy PSMs
[6:04] Number of IDs at 0.01 FDR: 15352
[6:05] Calculating protein q-values
[6:05] Number of protein isoforms identified at 1% FDR: 1939 (precursor-level), 1825 (protein-level) (inference performed using proteotypic peptides only)
[6:05] Quantification
[6:06] Quantification information saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\RawFiles\diann_dia_2.1\Mix7-8.wiff.dia.quant

[6:07] Cross-run analysis
[6:07] Reading quantification information: 1 files
[6:08] Quantifying peptides
[6:08] Assembling protein groups
[6:08] Quantifying proteins
[6:08] Calculating q-values for protein and gene groups
[6:08] Calculating global q-values for protein and gene groups
[6:08] Protein groups with global q-value <= 0.01: 1870
[6:08] Compressed report saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_2.1_isoform\Mix-4.parquet. Use R 'arrow' or Python 'PyArrow' package to process
[6:09] Saving precursor levels matrix
[6:09] 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_2.1_isoform\Mix-4.pr_matrix.tsv.
[6:09] Saving protein group levels matrix
[6:09] Protein groups matrix saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_2.1_isoform\Mix-4.pg_matrix.tsv.
[6:09] Saving gene group levels matrix
[6:09] Gene groups matrix saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_2.1_isoform\Mix-4.gg_matrix.tsv.
[6:09] Saving unique genes levels matrix
[6:09] Unique genes matrix saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_2.1_isoform\Mix-4.unique_genes_matrix.tsv.
[6:09] Manifest saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_2.1_isoform\Mix-4.manifest.txt
[6:09] Stats report saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_2.1_isoform\Mix-4.stats.tsv
[6:09] Generating spectral library:
[6:09] 15347 target and 153 decoy precursors saved
[6:09] Spectral library saved to \\YBisei-Server\Bisei-lab\AD_MS-DATA\Ko\2.TrueFDR\250511_Revised\250513_SearchResult_diann_2.1_isoform\Mix-4_lib.parquet