DIA-NN 1.8 (Data-Independent Acquisition by Neural Networks)
Compiled on Jun 28 2021 14:55:31
Current date and time: Thu Oct 20 23:06:00 2022
CPU: GenuineIntel Intel(R) Xeon(R) W-3225 CPU @ 3.70GHz
SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 
Logical CPU cores: 16
C:\DIA-NN\1.8\diann.exe --f D:\Data\raw\M221020_025_1_1_14726.d --lib C:\DIA-NN\PaSER_Plasma_Fractions_K562_TIMScore.tsv --threads 8 --verbose 1 --out D:\Data\raw\M221020_025_1_1_14726.d\M221020_025_1_1_14726_dia-NN.tsv  --qvalue 0.01 --matrices --min-corr 1.0 --corr-diff 1.0 --time-corr-only --fasta C:\DIA-NN\20211001_Human-isoforms_Swissprot.fasta --met-excision --cut K*,R* --no-prot-inf --rt-profiling --peak-center --no-ifs-removal 

Thread number set to 8
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
Only peaks with correlation sum exceeding 1 will be considered
Peaks with correlation sum below 1 from maximum will not be considered
A single score will be used until RT alignment to save memory; this can potentially lead to slower search
N-terminal methionine excision enabled
In silico digest will involve cuts at K*,R*
Protein inference will not be performed
The spectral library (if generated) will retain the original spectra but will include empirically-aligned RTs
Fixed-width center of each elution peak will be used for quantification
Interference removal from fragment elution curves disabled
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 C:\DIA-NN\PaSER_Plasma_Fractions_K562_TIMScore.tsv
[0:10] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
[0:11] Spectral library loaded: 9249 protein isoforms, 9249 protein groups and 112306 precursors in 99255 elution groups.
[0:11] Loading protein annotations from FASTA C:\DIA-NN\20211001_Human-isoforms_Swissprot.fasta
[0:32] Annotating library proteins with information from the FASTA database
[0:32] Protein names missing for some isoforms
[0:32] Gene names missing for some isoforms
[0:32] Library contains 7837 proteins, and 7824 genes
[0:33] Initialising library
[0:33] Saving the library to C:\DIA-NN\PaSER_Plasma_Fractions_K562_TIMScore.tsv.speclib

[0:33] File #1/1
[0:33] Loading run D:\Data\raw\M221020_025_1_1_14726.d
For most diaPASEF datasets it is better to manually fix both the MS1 and MS2 mass accuracies to 10 ppm.
[1:01] 105538 library precursors are potentially detectable
[1:01] Processing...
[1:36] RT window set to 0.987282
[1:36] Ion mobility window set to 0.0541778
[1:36] Peak width: 4.236
[1:36] Scan window radius set to 9
[1:36] Recommended MS1 mass accuracy setting: 34.4528 ppm
[3:13] Optimised mass accuracy: 23.3348 ppm
[3:49] Removing low confidence identifications
[3:49] Removing interfering precursors
[3:50] Training neural networks: 8256 targets, 5672 decoys
[3:51] Number of IDs at 0.01 FDR: 2716
[3:51] Calculating protein q-values
[3:51] Number of genes identified at 1% FDR: 286 (precursor-level), 216 (protein-level) (inference performed using proteotypic peptides only)
[3:51] Quantification
[3:51] Quantification information saved to D:\Data\raw\M221020_025_1_1_14726.d.quant.

[3:52] Cross-run analysis
[3:52] Reading quantification information: 1 files
[3:52] Quantifying peptides
[3:52] Quantifying proteins
[3:52] Calculating q-values for protein and gene groups
[3:52] Calculating global q-values for protein and gene groups
[3:52] Writing report
[3:52] Report saved to D:\Data\raw\M221020_025_1_1_14726.d\M221020_025_1_1_14726_dia-NN.tsv.
[3:52] Saving precursor levels matrix
[3:52] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Data\raw\M221020_025_1_1_14726.d\M221020_025_1_1_14726_dia-NN.pr_matrix.tsv.
[3:52] Saving protein group levels matrix
[3:52] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\Data\raw\M221020_025_1_1_14726.d\M221020_025_1_1_14726_dia-NN.pg_matrix.tsv.
[3:52] Saving gene group levels matrix
[3:52] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to D:\Data\raw\M221020_025_1_1_14726.d\M221020_025_1_1_14726_dia-NN.gg_matrix.tsv.
[3:52] Saving unique genes levels matrix
[3:52] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to D:\Data\raw\M221020_025_1_1_14726.d\M221020_025_1_1_14726_dia-NN.unique_genes_matrix.tsv.
[3:53] Stats report saved to D:\Data\raw\M221020_025_1_1_14726.d\M221020_025_1_1_14726_dia-NN.stats.tsv
