DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks)
Compiled on Apr 14 2022 15:31:19
Current date and time: Tue Apr  9 12:36:57 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_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML  --f D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML  --f D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML  --lib D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\library.tsv --threads 24 --verbose 1 --out D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\report.tsv --qvalue 0.01 --matrices --out-lib D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\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\DIA_DD_MZML\library.tsv
[0:07] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
[0:07] Spectral library loaded: 4536 protein isoforms, 4536 protein groups and 81235 precursors in 71894 elution groups.
[0:07] Initialising library
[0:07] Saving the library to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\library.tsv.speclib

[0:07] First pass: generating a spectral library from DIA data
[0:07] File #1/3
[0:07] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[0:27] 81235 library precursors are potentially detectable
[0:27] Processing...
[0:28] RT window set to 2.6337
[0:28] Peak width: 2.912
[0:28] Scan window radius set to 6
[0:28] Recommended MS1 mass accuracy setting: 6.41857 ppm
[0:29] Optimised mass accuracy: 13.2572 ppm
[0:33] Removing low confidence identifications
[0:33] Removing interfering precursors
[0:36] Training neural networks: 68072 targets, 51011 decoys
[0:42] Number of IDs at 0.01 FDR: 63943
[0:43] Calculating protein q-values
[0:43] Number of protein isoforms identified at 1% FDR: 4255 (precursor-level), 4204 (protein-level) (inference performed using proteotypic peptides only)
[0:43] Quantification
[0:44] Quantification information saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML.quant.

[0:45] File #2/3
[0:45] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[1:02] 81235 library precursors are potentially detectable
[1:02] Processing...
[1:03] RT window set to 2.62889
[1:03] Recommended MS1 mass accuracy setting: 5.90253 ppm
[1:06] Removing low confidence identifications
[1:06] Removing interfering precursors
[1:10] Training neural networks: 67661 targets, 47202 decoys
[1:15] Number of IDs at 0.01 FDR: 63818
[1:17] Calculating protein q-values
[1:17] Number of protein isoforms identified at 1% FDR: 4229 (precursor-level), 4165 (protein-level) (inference performed using proteotypic peptides only)
[1:17] Quantification
[1:18] Quantification information saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML.quant.

[1:18] File #3/3
[1:18] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[1:37] 81235 library precursors are potentially detectable
[1:37] Processing...
[1:38] RT window set to 2.63663
[1:38] Recommended MS1 mass accuracy setting: 5.9477 ppm
[1:41] Removing low confidence identifications
[1:41] Removing interfering precursors
[1:44] Training neural networks: 65262 targets, 47980 decoys
[1:49] Number of IDs at 0.01 FDR: 58549
[1:51] Calculating protein q-values
[1:51] Number of protein isoforms identified at 1% FDR: 4089 (precursor-level), 3988 (protein-level) (inference performed using proteotypic peptides only)
[1:51] Quantification
[1:52] Quantification information saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML.quant.

[1:52] Cross-run analysis
[1:52] Reading quantification information: 3 files
[1:53] Quantifying peptides
[1:57] Assembling protein groups
[1:57] Quantifying proteins
[1:57] Calculating q-values for protein and gene groups
[1:57] Calculating global q-values for protein and gene groups
[1:57] Writing report
[2:13] Report saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\report-first-pass.tsv.
[2:13] Saving precursor levels matrix
[2:14] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\report-first-pass.pr_matrix.tsv.
[2:14] Saving protein group levels matrix
[2:14] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\report-first-pass.pg_matrix.tsv.
[2:14] Saving gene group levels matrix
[2:14] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\report-first-pass.gg_matrix.tsv.
[2:14] Saving unique genes levels matrix
[2:14] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\report-first-pass.unique_genes_matrix.tsv.
[2:14] Stats report saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\report-first-pass.stats.tsv
[2:14] Generating spectral library:
[2:14] 75675 precursors passing the FDR threshold are to be extracted
[2:14] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[2:33] 81235 library precursors are potentially detectable
[2:36] 34617 spectra added to the library
[2:37] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[2:55] 81235 library precursors are potentially detectable
[2:56] 17167 spectra added to the library
[2:56] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[3:17] 81235 library precursors are potentially detectable
[3:20] 23694 spectra added to the library
[3:20] Saving spectral library to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\report-lib.tsv
[3:33] 75675 precursors saved
[3:33] Loading the generated library and saving it in the .speclib format
[3:33] Loading spectral library D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\report-lib.tsv
[3:41] Spectral library loaded: 4509 protein isoforms, 4509 protein groups and 75675 precursors in 66808 elution groups.
[3:41] Protein names missing for some isoforms
[3:41] Gene names missing for some isoforms
[3:41] Library contains 0 proteins, and 0 genes
[3:41] Saving the library to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\report-lib.tsv.speclib

[3:41] Second pass: using the newly created spectral library to reanalyse the data
[3:41] File #1/3
[3:41] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219601_PPI_Struc_Macrophages_A_DD_DIA_4_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[4:02] 75675 library precursors are potentially detectable
[4:02] Processing...
[4:03] RT window set to 2.64062
[4:03] Recommended MS1 mass accuracy setting: 6.44612 ppm
[4:05] Removing low confidence identifications
[4:05] Removing interfering precursors
[4:10] Training neural networks: 68032 targets, 46986 decoys
[4:15] Number of IDs at 0.01 FDR: 63594
[4:17] Calculating protein q-values
[4:17] Number of protein isoforms identified at 1% FDR: 4237 (precursor-level), 4185 (protein-level) (inference performed using proteotypic peptides only)
[4:17] Quantification

[4:18] File #2/3
[4:18] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219653_PPI_Struc_Macrophages_B_DD_DIA_5_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[4:37] 75675 library precursors are potentially detectable
[4:37] Processing...
[4:38] RT window set to 2.62147
[4:38] Recommended MS1 mass accuracy setting: 6.24344 ppm
[4:41] Removing low confidence identifications
[4:41] Removing interfering precursors
[4:44] Training neural networks: 67478 targets, 43475 decoys
[4:49] Number of IDs at 0.01 FDR: 63419
[4:51] Calculating protein q-values
[4:51] Number of protein isoforms identified at 1% FDR: 4200 (precursor-level), 4135 (protein-level) (inference performed using proteotypic peptides only)
[4:51] Quantification

[4:52] File #3/3
[4:52] Loading run D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\1219705_PPI_Struc_Macrophages_C_DD_DIA_6_19Jan24_Cicero_BEHCoA-24-01-13.mzML
[5:11] 75675 library precursors are potentially detectable
[5:11] Processing...
[5:12] RT window set to 2.62929
[5:12] Recommended MS1 mass accuracy setting: 5.36284 ppm
[5:14] Removing low confidence identifications
[5:14] Removing interfering precursors
[5:17] Training neural networks: 64953 targets, 43988 decoys
[5:22] Number of IDs at 0.01 FDR: 58136
[5:24] Calculating protein q-values
[5:24] Number of protein isoforms identified at 1% FDR: 4058 (precursor-level), 3963 (protein-level) (inference performed using proteotypic peptides only)
[5:24] Quantification

[5:25] Cross-run analysis
[5:25] Reading quantification information: 3 files
[5:25] Quantifying peptides
[5:29] Quantifying proteins
[5:30] Calculating q-values for protein and gene groups
[5:30] Calculating global q-values for protein and gene groups
[5:30] Writing report
[5:46] Report saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\report.tsv.
[5:46] Saving precursor levels matrix
[5:47] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\report.pr_matrix.tsv.
[5:47] Saving protein group levels matrix
[5:47] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\report.pg_matrix.tsv.
[5:47] Saving gene group levels matrix
[5:47] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\report.gg_matrix.tsv.
[5:47] Saving unique genes levels matrix
[5:47] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\report.unique_genes_matrix.tsv.
[5:47] Stats report saved to D:\Public\Snigdha\Lung_macro\DIA\DIA_MZML\DIA_DD_MZML\report.stats.tsv

Finished

