DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks)
Compiled on Apr 14 2022 15:31:19
Current date and time: Fri Feb 16 11:19:06 2024
CPU: GenuineIntel Intel(R) Xeon(R) Silver 4214 CPU @ 2.20GHz
SIMD instructions: AVX AVX2 AVX512CD AVX512F FMA SSE4.1 SSE4.2 
Logical CPU cores: 48
diann.exe --f D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\1219474_PPI_Struc_Macrophages_A_T_DIA_1_19Jan24_Cicero_BEHCoA-24-01-13.mzML  --f D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\1219543_PPI_Struc_Macrophages_B_T_DIA_2_19Jan24_Cicero_BEHCoA-24-01-13.mzML  --f D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\1219561_PPI_Struc_Macrophages_C_T_DIA_3_19Jan24_Cicero_BEHCoA-24-01-13.mzML  --lib D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\library.tsv --threads 24 --verbose 1 --out D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\report.tsv --qvalue 0.01 --matrices --out-lib C:\DIA-NN\1.8.1\report-lib.tsv --gen-spec-lib --var-mods 1 --var-mod UniMod:35,15.994915,M --reanalyse --relaxed-prot-inf --smart-profiling --peak-center --no-ifs-removal 

Thread number set to 24
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
Maximum number of variable modifications set to 1
Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable
A spectral library will be created from the DIA runs and used to reanalyse them; .quant files will only be saved to disk during the first step
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
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.

3 files will be processed
[0:00] Loading spectral library D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\library.tsv
[0:03] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
[0:03] Spectral library loaded: 4291 protein isoforms, 4291 protein groups and 47926 precursors in 45214 elution groups.
[0:03] Initialising library
[0:03] Saving the library to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\library.tsv.speclib

[0:03] First pass: generating a spectral library from DIA data
[0:03] File #1/3
[0:03] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\1219474_PPI_Struc_Macrophages_A_T_DIA_1_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[0:20] 40086 library precursors are potentially detectable
[0:20] Processing...
[0:20] RT window set to 2.61295
[0:20] Peak width: 2.9
[0:20] Scan window radius set to 6
[0:20] Recommended MS1 mass accuracy setting: 5.53062 ppm
[0:21] Optimised mass accuracy: 12.4641 ppm
[0:23] Removing low confidence identifications
[0:23] Removing interfering precursors
[0:24] Training neural networks: 37762 targets, 23871 decoys
[0:27] Number of IDs at 0.01 FDR: 35371
[0:28] Calculating protein q-values
[0:28] Number of protein isoforms identified at 1% FDR: 3872 (precursor-level), 3820 (protein-level) (inference performed using proteotypic peptides only)
[0:28] Quantification
[0:28] Quantification information saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\1219474_PPI_Struc_Macrophages_A_T_DIA_1_19Jan24_Cicero_BEHCoA-24-01-13.mzML.quant.

[0:28] File #2/3
[0:28] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\1219543_PPI_Struc_Macrophages_B_T_DIA_2_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[0:45] 40086 library precursors are potentially detectable
[0:45] Processing...
[0:46] RT window set to 2.61183
[0:46] Recommended MS1 mass accuracy setting: 5.12039 ppm
[0:48] Removing low confidence identifications
[0:48] Removing interfering precursors
[0:49] Training neural networks: 38044 targets, 25223 decoys
[0:52] Number of IDs at 0.01 FDR: 35854
[0:53] Calculating protein q-values
[0:53] Number of protein isoforms identified at 1% FDR: 3906 (precursor-level), 3872 (protein-level) (inference performed using proteotypic peptides only)
[0:53] Quantification
[0:54] Quantification information saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\1219543_PPI_Struc_Macrophages_B_T_DIA_2_19Jan24_Cicero_BEHCoA-24-01-13.mzML.quant.

[0:54] File #3/3
[0:54] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\1219561_PPI_Struc_Macrophages_C_T_DIA_3_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[1:10] 40086 library precursors are potentially detectable
[1:10] Processing...
[1:11] RT window set to 2.61454
[1:11] Recommended MS1 mass accuracy setting: 4.53027 ppm
[1:12] Removing low confidence identifications
[1:12] Removing interfering precursors
[1:14] Training neural networks: 36400 targets, 22434 decoys
[1:16] Number of IDs at 0.01 FDR: 33329
[1:17] Calculating protein q-values
[1:17] Number of protein isoforms identified at 1% FDR: 3678 (precursor-level), 3620 (protein-level) (inference performed using proteotypic peptides only)
[1:17] Quantification
[1:17] Quantification information saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\1219561_PPI_Struc_Macrophages_C_T_DIA_3_19Jan24_Cicero_BEHCoA-24-01-13.mzML.quant.

[1:18] Cross-run analysis
[1:18] Reading quantification information: 3 files
[1:18] Quantifying peptides
[1:20] Assembling protein groups
[1:20] Quantifying proteins
[1:20] Calculating q-values for protein and gene groups
[1:20] Calculating global q-values for protein and gene groups
[1:20] Writing report
[1:28] Report saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\report-first-pass.tsv.
[1:28] Saving precursor levels matrix
[1:28] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\report-first-pass.pr_matrix.tsv.
[1:28] Saving protein group levels matrix
[1:28] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\report-first-pass.pg_matrix.tsv.
[1:28] Saving gene group levels matrix
[1:28] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\report-first-pass.gg_matrix.tsv.
[1:28] Saving unique genes levels matrix
[1:28] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\report-first-pass.unique_genes_matrix.tsv.
[1:28] Stats report saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\report-first-pass.stats.tsv
[1:28] Generating spectral library:
[1:28] 39494 precursors passing the FDR threshold are to be extracted
[1:28] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\1219474_PPI_Struc_Macrophages_A_T_DIA_1_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[1:45] 40086 library precursors are potentially detectable
[1:46] 12782 spectra added to the library
[1:46] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\1219543_PPI_Struc_Macrophages_B_T_DIA_2_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[2:03] 40086 library precursors are potentially detectable
[2:05] 18084 spectra added to the library
[2:05] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\1219561_PPI_Struc_Macrophages_C_T_DIA_3_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[2:21] 40086 library precursors are potentially detectable
[2:22] 7949 spectra added to the library
[2:22] Saving spectral library to C:\DIA-NN\1.8.1\report-lib.tsv
[2:27] 39494 precursors saved
[2:27] Loading the generated library and saving it in the .speclib format
[2:27] Loading spectral library C:\DIA-NN\1.8.1\report-lib.tsv
[2:31] Spectral library loaded: 4132 protein isoforms, 4132 protein groups and 39494 precursors in 37815 elution groups.
[2:31] Protein names missing for some isoforms
[2:31] Gene names missing for some isoforms
[2:31] Library contains 0 proteins, and 0 genes
[2:31] Saving the library to C:\DIA-NN\1.8.1\report-lib.tsv.speclib

[2:31] Second pass: using the newly created spectral library to reanalyse the data
[2:31] File #1/3
[2:31] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\1219474_PPI_Struc_Macrophages_A_T_DIA_1_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[2:48] 39494 library precursors are potentially detectable
[2:48] Processing...
[2:48] RT window set to 2.60609
[2:48] Recommended MS1 mass accuracy setting: 5.30839 ppm
[2:50] Removing low confidence identifications
[2:50] Removing interfering precursors
[2:51] Training neural networks: 37490 targets, 23144 decoys
[2:54] Number of IDs at 0.01 FDR: 35247
[2:55] Calculating protein q-values
[2:55] Number of protein isoforms identified at 1% FDR: 3877 (precursor-level), 3822 (protein-level) (inference performed using proteotypic peptides only)
[2:55] Quantification

[2:55] File #2/3
[2:55] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\1219543_PPI_Struc_Macrophages_B_T_DIA_2_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[3:12] 39494 library precursors are potentially detectable
[3:12] Processing...
[3:13] RT window set to 2.64037
[3:13] Recommended MS1 mass accuracy setting: 4.9902 ppm
[3:14] Removing low confidence identifications
[3:14] Removing interfering precursors
[3:15] Training neural networks: 37857 targets, 24710 decoys
[3:18] Number of IDs at 0.01 FDR: 35913
[3:19] Calculating protein q-values
[3:19] Number of protein isoforms identified at 1% FDR: 3924 (precursor-level), 3890 (protein-level) (inference performed using proteotypic peptides only)
[3:19] Quantification

[3:20] File #3/3
[3:20] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\1219561_PPI_Struc_Macrophages_C_T_DIA_3_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[3:36] 39494 library precursors are potentially detectable
[3:36] Processing...
[3:37] RT window set to 2.62676
[3:37] Recommended MS1 mass accuracy setting: 4.44874 ppm
[3:38] Removing low confidence identifications
[3:38] Removing interfering precursors
[3:40] Training neural networks: 36074 targets, 21834 decoys
[3:42] Number of IDs at 0.01 FDR: 33014
[3:43] Calculating protein q-values
[3:43] Number of protein isoforms identified at 1% FDR: 3668 (precursor-level), 3615 (protein-level) (inference performed using proteotypic peptides only)
[3:43] Quantification

[3:44] Cross-run analysis
[3:44] Reading quantification information: 3 files
[3:44] Quantifying peptides
[3:46] Quantifying proteins
[3:46] Calculating q-values for protein and gene groups
[3:46] Calculating global q-values for protein and gene groups
[3:46] Writing report
[3:54] Report saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\report.tsv.
[3:54] Saving precursor levels matrix
[3:54] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\report.pr_matrix.tsv.
[3:54] Saving protein group levels matrix
[3:54] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\report.pg_matrix.tsv.
[3:54] Saving gene group levels matrix
[3:54] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\report.gg_matrix.tsv.
[3:54] Saving unique genes levels matrix
[3:54] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\report.unique_genes_matrix.tsv.
[3:54] Stats report saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_T_MZML\report.stats.tsv

Finished

