# ------------------------------------------------------------------
# SearchGUI 4.3.11 Report File
#
# Originally saved by: maatallah @ SH-1070-LAB02
# on: 02 Jan 2025, 16:01
# as: SearchGUI Report 2025-01-02 16.01.24.html
# ------------------------------------------------------------------
Thu Jan 02 15:55:31 CST 2025 Importing spectrum files.
Thu Jan 02 15:55:31 CST 2025 Importing spectrum file 20240530_10ng_DDA_1_20240607074110.mgf
Thu Jan 02 15:55:31 CST 2025 Importing spectrum file 20240530_10ng_DDA_2_20240607101044.mgf
Thu Jan 02 15:55:31 CST 2025 Importing spectrum file 20240530_10ng_DDA_3_20240607124013.mgf
Thu Jan 02 15:55:31 CST 2025 Importing spectrum files completed (53.0 milliseconds).
Thu Jan 02 15:55:31 CST 2025 Converting spectrum file 20240530_10ng_DDA_1_20240607074110.mgf to peak list.
Thu Jan 02 15:55:31 CST 2025 Processing 20240530_10ng_DDA_1_20240607074110.mgf with X!Tandem.
X! TANDEM Vengeance (2015.12.15.2)
Loading spectra| (mgf)...... loaded.
Spectra matching criteria = 10255
Starting threads .|.|.|.|.|.|.|. started.
Computing models:
Spectrum-to-sequence matching process in p
waiting for 2|3456|78| done.
sequences modelled = 41 ks
Model refinement:
partial cleavage done.
unanticipated cleavage done.
finishing refinement ... done.
waiting for 2|3|4|5|6|7|8| done.
Merging results:
from 2.3.4.5.6.7.8.
Creating report:
initial calculations ..... done.
sorting ..... done.
finding repeats ..... done.
evaluating results ..... done.
calculating expectations ..... done.
writing results ..... done.
Valid models = 0
Thu Jan 02 15:55:48 CST 2025 X!Tandem finished for 20240530_10ng_DDA_1_20240607074110.mgf (16.2 seconds).
Thu Jan 02 15:55:48 CST 2025 Processing 20240530_10ng_DDA_1_20240607074110.mgf with MS-GF+.
MS-GF+ Release (v2024.03.26) (26 March 2024)
Java 22.0.2 (Oracle Corporation)
Windows 11 (amd64, version 10.0)
Loading database files...
Warning: Sequence database contains 72 counts of letter 'U', which does not correspond to an amino acid.
Warning: Sequence database contains 134 counts of letter 'X', which does not correspond to an amino acid.
Creating the suffix array indexed file... Size: 22931769
AlphabetSize: 28
Suffix creation: 43.17% complete.
Suffix creation: 78.49% complete.
Sorting suffixes... Size: 17210368
Sorting: 34.28% complete.
Sorting: 66.82% complete.
Counting number of distinct peptides in UP000005640_9606_concatenated_target_decoy.csarr using UP000005640_9606_concatenated_target_decoy.cnlcp
Counting distinct peptides: 64.54% complete.
Loading database finished (elapsed time: 15.59 sec)
Reading spectra...
Opening Mascot MGF file 20240530_10ng_DDA_1_20240607074110.mgf
Spectrum index=0 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=1 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=2 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=3 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=4 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=5 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=6 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=7 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=8 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=9 activationMethod is unknown; Using HCD as specified in parameters.
...
Ignoring 0 profile spectra.
Ignoring 0 spectra having less than 10 peaks.
Reading spectra finished (elapsed time: 17.00 sec)
Using 8 threads.
Search Parameters:
PrecursorMassTolerance: 10.0 ppm
IsotopeError: 0,1
TargetDecoyAnalysis: false
FragmentationMethod: HCD
Instrument: HighRes (Orbitrap/FTICR/Lumos)
Enzyme: Tryp
Enzyme file: C:\Users\maatallah\Downloads\SearchGUI-4.3.11-windows\SearchGUI-4.3.11\resources\temp\search_engines\msgf\params\enzymes.txt
Enzyme info: Added new enzyme Trypsin_(no_P_rule) with target residues RK
Enzyme info: Added new enzyme CNBr with target residues M
Enzyme info: Added new enzyme Pepsin_A with target residues LF
Enzyme info: Added new enzyme Thermolysin with target residues AILMFV
Enzyme info: Added new enzyme Lys-C_(no_P_rule) with target residues K
Enzyme info: Added new enzyme Arg-C_(no_P_rule) with target residues R
Enzyme info: Added new enzyme Chymotrypsin_(no_P_rule) with target residues YLFW
Enzyme info: Added new enzyme Asp-N_(ambic) with target residues DE
Enzyme info: Added new enzyme Arg-N with target residues R
Enzyme info: Added new enzyme LysargiNase with target residues RK
Protocol: Standard
NumTolerableTermini: 2
IgnoreMetCleavage: false
MinPepLength: 8
MaxPepLength: 30
MinCharge: 2
MaxCharge: 4
NumMatchesPerSpec: 10
MaxMissedCleavages: 2
MaxNumModsPerPeptide: 2
ChargeCarrierMass: 1.00727649 (proton)
MinNumPeaksPerSpectrum: 10
NumIsoforms: 128
No static or dynamic post translational modifications are defined.
Spectrum 0-10297 (total: 10298)
Splitting work into 24 tasks.
Search progress: 0 / 24 tasks, 0.00% 0.00 seconds elapsed
Loading built-in param file: HCD_HighRes_Tryp.param
Loading built-in param file: HCD_HighRes_Tryp.param
Loading built-in param file: HCD_HighRes_Tryp.param
Loading built-in param file: HCD_HighRes_Tryp.param
Search progress: 1 / 24 tasks, 25.23% 14.47 seconds elapsed
Search progress: 2 / 24 tasks, 26.16% 14.89 seconds elapsed
Search progress: 3 / 24 tasks, 27.02% 15.28 seconds elapsed
Search progress: 4 / 24 tasks, 28.01% 15.65 seconds elapsed
Search progress: 4 / 24 tasks, 34.57% 19.72 seconds elapsed
Search progress: 6 / 24 tasks, 39.32% 19.92 seconds elapsed
Search progress: 7 / 24 tasks, 39.70% 20.01 seconds elapsed
Search progress: 8 / 24 tasks, 40.29% 20.17 seconds elapsed
Search progress: 9 / 24 tasks, 57.95% 27.53 seconds elapsed
Search progress: 10 / 24 tasks, 59.27% 28.05 seconds elapsed
Search progress: 11 / 24 tasks, 60.00% 28.44 seconds elapsed
Search progress: 12 / 24 tasks, 60.35% 28.53 seconds elapsed
Search progress: 13 / 24 tasks, 76.49% 36.94 seconds elapsed
Search progress: 14 / 24 tasks, 77.35% 37.20 seconds elapsed
Search progress: 15 / 24 tasks, 78.12% 37.40 seconds elapsed
Search progress: 16 / 24 tasks, 81.54% 38.34 seconds elapsed
Search progress: 17 / 24 tasks, 87.88% 40.98 seconds elapsed
Search progress: 18 / 24 tasks, 88.94% 42.08 seconds elapsed
Search progress: 19 / 24 tasks, 89.19% 42.14 seconds elapsed
Search progress: 20 / 24 tasks, 89.60% 42.39 seconds elapsed
Search progress: 21 / 24 tasks, 98.34% 48.51 seconds elapsed
Search progress: 22 / 24 tasks, 99.37% 49.72 seconds elapsed
Search progress: 23 / 24 tasks, 99.69% 49.92 seconds elapsed
Search progress: 24 / 24 tasks, 100.00% 50.22 seconds elapsed
Search progress: 24 / 24 tasks, 100.00% 50.22 seconds elapsed
Writing results...
Writing results finished (elapsed time: 6.89 sec)
File: C:\QC_20241005\Pioneer_test_spectral_library_generation\SearchGUI_output_1\SEARCH_GUI_3trial\.SearchGUI_temp\20240530_10ng_DDA_1_20240607074110.msgf.mzid
MS-GF+ complete (total elapsed time: 74.31 sec)
Thu Jan 02 15:57:02 CST 2025 MS-GF+ finished for 20240530_10ng_DDA_1_20240607074110.mgf (1 minute 15.0 seconds).
Thu Jan 02 15:57:02 CST 2025 Processing 20240530_10ng_DDA_1_20240607074110.mgf with Comet.
Comet version "2024.01 rev. 1"
Search start: 01/02/2025, 03:57:02 PM
- Input file: C:\QC_20241005\Pioneer_test_spectral_library_generation\20240530_10ng_DDA_1_20240607074110.mgf
- Reading all spectra into memory; set "spectrum_batch_size" if search terminates here.
- Load spectra: 10261
- Search progress: 1% 2% 3% 4% 6% 7% 8% 9% 10% 12% 13% 14% 15% 16% 18% 19% 20% 21% 22% 24% 25% 26% 27% 28% 30% 31% 32% 33% 34% 36% 37% 38% 39% 41% 42% 43% 44% 45% 47% 48% 49% 50% 51% 53% 54% 55% 56% 58% 59% 60% 61% 62% 63% 65% 66% 67% 69% 70% 71% 72% 73% 74% 76% 77% 78% 79% 80% 82% 83% 84% 85% 87% 88% 89% 90% 91% 93% 94% 95% 96% 97% 99%100%
- Post analysis: done
Search end: 01/02/2025, 03:57:14 PM, 0m:12s
Thu Jan 02 15:57:14 CST 2025 Comet finished for 20240530_10ng_DDA_1_20240607074110.mgf (11.8 seconds).
Thu Jan 02 15:57:14 CST 2025 Converting spectrum file 20240530_10ng_DDA_2_20240607101044.mgf to peak list.
Thu Jan 02 15:57:15 CST 2025 Processing 20240530_10ng_DDA_2_20240607101044.mgf with X!Tandem.
X! TANDEM Vengeance (2015.12.15.2)
Loading spectra| (mgf)...... loaded.
Spectra matching criteria = 10389
Starting threads .|.|.|.|.|.|.|. started.
Computing models:
Spectrum-to-sequence matching process in p
waiting for 23|4|5|6|7|8| done.
sequences modelled = 41 ks
Model refinement:
partial cleavage done.
unanticipated cleavage done.
finishing refinement ... done.
waiting for 2|3|4|5|6|7|8| done.
Merging results:
from 2.3.4.5.6.7.8.
Creating report:
initial calculations ..... done.
sorting ..... done.
finding repeats ..... done.
evaluating results ..... done.
calculating expectations ..... done.
writing results ..... done.
Valid models = 0
Thu Jan 02 15:57:32 CST 2025 X!Tandem finished for 20240530_10ng_DDA_2_20240607101044.mgf (17.3 seconds).
Thu Jan 02 15:57:32 CST 2025 Processing 20240530_10ng_DDA_2_20240607101044.mgf with MS-GF+.
MS-GF+ Release (v2024.03.26) (26 March 2024)
Java 22.0.2 (Oracle Corporation)
Windows 11 (amd64, version 10.0)
Loading database files...
Warning: Sequence database contains 72 counts of letter 'U', which does not correspond to an amino acid.
Warning: Sequence database contains 134 counts of letter 'X', which does not correspond to an amino acid.
Counting number of distinct peptides in UP000005640_9606_concatenated_target_decoy.csarr using UP000005640_9606_concatenated_target_decoy.cnlcp
Counting distinct peptides: 59.74% complete.
Loading database finished (elapsed time: 3.90 sec)
Reading spectra...
Opening Mascot MGF file 20240530_10ng_DDA_2_20240607101044.mgf
Spectrum index=0 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=1 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=2 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=3 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=4 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=5 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=6 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=7 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=8 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=9 activationMethod is unknown; Using HCD as specified in parameters.
...
Ignoring 0 profile spectra.
Ignoring 0 spectra having less than 10 peaks.
Reading spectra finished (elapsed time: 5.31 sec)
Using 8 threads.
Search Parameters:
PrecursorMassTolerance: 10.0 ppm
IsotopeError: 0,1
TargetDecoyAnalysis: false
FragmentationMethod: HCD
Instrument: HighRes (Orbitrap/FTICR/Lumos)
Enzyme: Tryp
Enzyme file: C:\Users\maatallah\Downloads\SearchGUI-4.3.11-windows\SearchGUI-4.3.11\resources\temp\search_engines\msgf\params\enzymes.txt
Enzyme info: Added new enzyme Trypsin_(no_P_rule) with target residues RK
Enzyme info: Added new enzyme CNBr with target residues M
Enzyme info: Added new enzyme Pepsin_A with target residues LF
Enzyme info: Added new enzyme Thermolysin with target residues AILMFV
Enzyme info: Added new enzyme Lys-C_(no_P_rule) with target residues K
Enzyme info: Added new enzyme Arg-C_(no_P_rule) with target residues R
Enzyme info: Added new enzyme Chymotrypsin_(no_P_rule) with target residues YLFW
Enzyme info: Added new enzyme Asp-N_(ambic) with target residues DE
Enzyme info: Added new enzyme Arg-N with target residues R
Enzyme info: Added new enzyme LysargiNase with target residues RK
Protocol: Standard
NumTolerableTermini: 2
IgnoreMetCleavage: false
MinPepLength: 8
MaxPepLength: 30
MinCharge: 2
MaxCharge: 4
NumMatchesPerSpec: 10
MaxMissedCleavages: 2
MaxNumModsPerPeptide: 2
ChargeCarrierMass: 1.00727649 (proton)
MinNumPeaksPerSpectrum: 10
NumIsoforms: 128
No static or dynamic post translational modifications are defined.
Spectrum 0-10432 (total: 10433)
Splitting work into 24 tasks.
Search progress: 0 / 24 tasks, 0.00% 0.01 seconds elapsed
Loading built-in param file: HCD_HighRes_Tryp.param
Search progress: 1 / 24 tasks, 28.81% 17.80 seconds elapsed
Search progress: 2 / 24 tasks, 29.06% 17.82 seconds elapsed
Search progress: 3 / 24 tasks, 29.38% 17.87 seconds elapsed
Search progress: 4 / 24 tasks, 29.70% 17.92 seconds elapsed
Search progress: 5 / 24 tasks, 38.09% 21.04 seconds elapsed
Search progress: 6 / 24 tasks, 39.00% 21.63 seconds elapsed
Search progress: 7 / 24 tasks, 39.24% 21.67 seconds elapsed
Search progress: 8 / 24 tasks, 39.45% 21.68 seconds elapsed
Search progress: 9 / 24 tasks, 58.17% 29.88 seconds elapsed
Search progress: 10 / 24 tasks, 58.99% 30.44 seconds elapsed
Search progress: 11 / 24 tasks, 61.07% 31.63 seconds elapsed
Search progress: 12 / 24 tasks, 62.81% 32.26 seconds elapsed
Search progress: 13 / 24 tasks, 74.98% 38.39 seconds elapsed
Search progress: 14 / 24 tasks, 76.76% 39.73 seconds elapsed
Search progress: 15 / 24 tasks, 77.80% 40.20 seconds elapsed
Search progress: 16 / 24 tasks, 78.26% 40.31 seconds elapsed
Search progress: 17 / 24 tasks, 88.09% 44.75 seconds elapsed
Search progress: 18 / 24 tasks, 89.12% 45.44 seconds elapsed
Search progress: 19 / 24 tasks, 90.27% 46.06 seconds elapsed
Search progress: 20 / 24 tasks, 91.80% 46.55 seconds elapsed
Search progress: 21 / 24 tasks, 98.33% 52.25 seconds elapsed
Search progress: 22 / 24 tasks, 99.44% 53.79 seconds elapsed
Search progress: 23 / 24 tasks, 99.73% 54.00 seconds elapsed
Search progress: 24 / 24 tasks, 100.00% 54.12 seconds elapsed
Search progress: 24 / 24 tasks, 100.00% 54.12 seconds elapsed
Writing results...
Writing results finished (elapsed time: 6.86 sec)
File: C:\QC_20241005\Pioneer_test_spectral_library_generation\SearchGUI_output_1\SEARCH_GUI_3trial\.SearchGUI_temp\20240530_10ng_DDA_2_20240607101044.msgf.mzid
MS-GF+ complete (total elapsed time: 66.47 sec)
Thu Jan 02 15:58:39 CST 2025 MS-GF+ finished for 20240530_10ng_DDA_2_20240607101044.mgf (1 minute 7.0 seconds).
Thu Jan 02 15:58:39 CST 2025 Processing 20240530_10ng_DDA_2_20240607101044.mgf with Comet.
Comet version "2024.01 rev. 1"
Search start: 01/02/2025, 03:58:39 PM
- Input file: C:\QC_20241005\Pioneer_test_spectral_library_generation\20240530_10ng_DDA_2_20240607101044.mgf
- Reading all spectra into memory; set "spectrum_batch_size" if search terminates here.
- Load spectra: 10399
- Search progress: 1% 2% 3% 4% 6% 7% 8% 9% 10% 12% 13% 14% 15% 16% 18% 19% 20% 21% 22% 24% 25% 26% 27% 28% 30% 31% 32% 33% 34% 36% 37% 38% 39% 41% 42% 43% 44% 45% 47% 48% 49% 50% 51% 53% 54% 55% 56% 58% 59% 60% 61% 62% 63% 65% 66% 67% 69% 70% 71% 72% 73% 74% 76% 77% 78% 79% 80% 82% 83% 84% 85% 87% 88% 89% 90% 91% 93% 94% 95% 96% 97% 99%100%
- Post analysis: done
Search end: 01/02/2025, 03:58:51 PM, 0m:12s
Thu Jan 02 15:58:51 CST 2025 Comet finished for 20240530_10ng_DDA_2_20240607101044.mgf (12.3 seconds).
Thu Jan 02 15:58:51 CST 2025 Converting spectrum file 20240530_10ng_DDA_3_20240607124013.mgf to peak list.
Thu Jan 02 15:58:52 CST 2025 Processing 20240530_10ng_DDA_3_20240607124013.mgf with X!Tandem.
X! TANDEM Vengeance (2015.12.15.2)
Loading spectra| (mgf)...... loaded.
Spectra matching criteria = 10347
Starting threads .|.|.|.|.|.|.|. started.
Computing models:
Spectrum-to-sequence matching process in p
waiting for 2|3|456|78| done.
sequences modelled = 41 ks
Model refinement:
partial cleavage done.
unanticipated cleavage done.
finishing refinement ... done.
waiting for 2|3|4|5|6|7|8| done.
Merging results:
from 2.3.4.5.6.7.8.
Creating report:
initial calculations ..... done.
sorting ..... done.
finding repeats ..... done.
evaluating results ..... done.
calculating expectations ..... done.
writing results ..... done.
Valid models = 0
Thu Jan 02 15:59:09 CST 2025 X!Tandem finished for 20240530_10ng_DDA_3_20240607124013.mgf (17.4 seconds).
Thu Jan 02 15:59:09 CST 2025 Processing 20240530_10ng_DDA_3_20240607124013.mgf with MS-GF+.
MS-GF+ Release (v2024.03.26) (26 March 2024)
Java 22.0.2 (Oracle Corporation)
Windows 11 (amd64, version 10.0)
Loading database files...
Warning: Sequence database contains 72 counts of letter 'U', which does not correspond to an amino acid.
Warning: Sequence database contains 134 counts of letter 'X', which does not correspond to an amino acid.
Counting number of distinct peptides in UP000005640_9606_concatenated_target_decoy.csarr using UP000005640_9606_concatenated_target_decoy.cnlcp
Counting distinct peptides: 56.25% complete.
Loading database finished (elapsed time: 3.90 sec)
Reading spectra...
Opening Mascot MGF file 20240530_10ng_DDA_3_20240607124013.mgf
Spectrum index=0 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=1 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=2 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=3 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=4 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=5 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=6 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=7 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=8 activationMethod is unknown; Using HCD as specified in parameters.
Spectrum index=9 activationMethod is unknown; Using HCD as specified in parameters.
...
Ignoring 0 profile spectra.
Ignoring 0 spectra having less than 10 peaks.
Reading spectra finished (elapsed time: 5.29 sec)
Using 8 threads.
Search Parameters:
PrecursorMassTolerance: 10.0 ppm
IsotopeError: 0,1
TargetDecoyAnalysis: false
FragmentationMethod: HCD
Instrument: HighRes (Orbitrap/FTICR/Lumos)
Enzyme: Tryp
Enzyme file: C:\Users\maatallah\Downloads\SearchGUI-4.3.11-windows\SearchGUI-4.3.11\resources\temp\search_engines\msgf\params\enzymes.txt
Enzyme info: Added new enzyme Trypsin_(no_P_rule) with target residues RK
Enzyme info: Added new enzyme CNBr with target residues M
Enzyme info: Added new enzyme Pepsin_A with target residues LF
Enzyme info: Added new enzyme Thermolysin with target residues AILMFV
Enzyme info: Added new enzyme Lys-C_(no_P_rule) with target residues K
Enzyme info: Added new enzyme Arg-C_(no_P_rule) with target residues R
Enzyme info: Added new enzyme Chymotrypsin_(no_P_rule) with target residues YLFW
Enzyme info: Added new enzyme Asp-N_(ambic) with target residues DE
Enzyme info: Added new enzyme Arg-N with target residues R
Enzyme info: Added new enzyme LysargiNase with target residues RK
Protocol: Standard
NumTolerableTermini: 2
IgnoreMetCleavage: false
MinPepLength: 8
MaxPepLength: 30
MinCharge: 2
MaxCharge: 4
NumMatchesPerSpec: 10
MaxMissedCleavages: 2
MaxNumModsPerPeptide: 2
ChargeCarrierMass: 1.00727649 (proton)
MinNumPeaksPerSpectrum: 10
NumIsoforms: 128
No static or dynamic post translational modifications are defined.
Spectrum 0-10390 (total: 10391)
Splitting work into 24 tasks.
Search progress: 0 / 24 tasks, 0.00% 0.01 seconds elapsed
Loading built-in param file: HCD_HighRes_Tryp.param
Loading built-in param file: HCD_HighRes_Tryp.param
Search progress: 1 / 24 tasks, 26.23% 14.99 seconds elapsed
Search progress: 2 / 24 tasks, 26.64% 15.07 seconds elapsed
Search progress: 3 / 24 tasks, 27.28% 15.20 seconds elapsed
Search progress: 4 / 24 tasks, 28.59% 15.50 seconds elapsed
Search progress: 5 / 24 tasks, 37.64% 18.02 seconds elapsed
Search progress: 6 / 24 tasks, 38.82% 18.84 seconds elapsed
Search progress: 6 / 24 tasks, 35.34% 19.16 seconds elapsed
Search progress: 8 / 24 tasks, 40.36% 19.48 seconds elapsed
Search progress: 9 / 24 tasks, 59.30% 28.30 seconds elapsed
Search progress: 10 / 24 tasks, 59.51% 28.31 seconds elapsed
Search progress: 11 / 24 tasks, 60.33% 28.67 seconds elapsed
Search progress: 12 / 24 tasks, 61.05% 28.94 seconds elapsed
Search progress: 13 / 24 tasks, 70.89% 33.90 seconds elapsed
Search progress: 14 / 24 tasks, 73.91% 35.67 seconds elapsed
Search progress: 16 / 24 tasks, 74.49% 35.81 seconds elapsed
Search progress: 16 / 24 tasks, 74.49% 35.81 seconds elapsed
Search progress: 17 / 24 tasks, 85.26% 40.97 seconds elapsed
Search progress: 18 / 24 tasks, 93.51% 45.38 seconds elapsed
Search progress: 19 / 24 tasks, 93.98% 45.54 seconds elapsed
Search progress: 20 / 24 tasks, 94.24% 45.59 seconds elapsed
Search progress: 21 / 24 tasks, 98.16% 48.04 seconds elapsed
Search progress: 22 / 24 tasks, 99.50% 49.65 seconds elapsed
Search progress: 23 / 24 tasks, 99.79% 49.78 seconds elapsed
Search progress: 24 / 24 tasks, 100.00% 49.79 seconds elapsed
Search progress: 24 / 24 tasks, 100.00% 49.79 seconds elapsed
Writing results...
Writing results finished (elapsed time: 6.64 sec)
File: C:\QC_20241005\Pioneer_test_spectral_library_generation\SearchGUI_output_1\SEARCH_GUI_3trial\.SearchGUI_temp\20240530_10ng_DDA_3_20240607124013.msgf.mzid
MS-GF+ complete (total elapsed time: 61.88 sec)
Thu Jan 02 16:00:11 CST 2025 MS-GF+ finished for 20240530_10ng_DDA_3_20240607124013.mgf (1 minute 2.0 seconds).
Thu Jan 02 16:00:11 CST 2025 Processing 20240530_10ng_DDA_3_20240607124013.mgf with Comet.
Comet version "2024.01 rev. 1"
Search start: 01/02/2025, 04:00:11 PM
- Input file: C:\QC_20241005\Pioneer_test_spectral_library_generation\20240530_10ng_DDA_3_20240607124013.mgf
- Reading all spectra into memory; set "spectrum_batch_size" if search terminates here.
- Load spectra: 10356
- Search progress: 1% 2% 3% 4% 6% 7% 8% 9% 10% 12% 13% 14% 15% 16% 18% 19% 20% 21% 22% 24% 25% 26% 27% 28% 30% 31% 32% 33% 34% 36% 37% 38% 39% 41% 42% 43% 44% 45% 47% 48% 49% 50% 51% 53% 54% 55% 56% 58% 59% 60% 61% 62% 63% 65% 66% 67% 69% 70% 71% 72% 73% 74% 76% 77% 78% 79% 80% 82% 83% 84% 85% 87% 88% 89% 90% 91% 93% 94% 95% 96% 97% 99%100%
- Post analysis: done
Search end: 01/02/2025, 04:00:23 PM, 0m:12s
Thu Jan 02 16:00:23 CST 2025 Comet finished for 20240530_10ng_DDA_3_20240607124013.mgf (12.1 seconds).
Thu Jan 02 16:00:23 CST 2025 Zipping output files.
Thu Jan 02 16:00:28 CST 2025 Processing identification files with PeptideShaker.
Thu Jan 02 16:00:45 CST 2025 PeptideShaker processing failed. See the PeptideShaker log for details.
Thu Jan 02 16:00:45 CST 2025 Searching Canceled!
Thu Jan 02 16:01:24 CST 2025 The search or processing did not finish properly!
# ------------------------------------------------------------------
# General Search Parameters
# ------------------------------------------------------------------
ENZYME0=Trypsin, Specific, 2 missed cleavages
FIXED_MODIFICATIONS=
VARIABLE_MODIFICATIONS=
REFINEMENT_FIXED_MODIFICATIONS=
REFINEMENT_VARIABLE_MODIFICATIONS=
PRECURSOR_MASS_TOLERANCE=10.0
PRECURSOR_MASS_TOLERANCE_UNIT=ppm
FRAGMENT_MASS_TOLERANCE=10.0
FRAGMENT_MASS_TOLERANCE_UNIT=ppm
PPM_TO_DA_CONVERSION_REF_MASS=2000.0
FORWARD_FRAGMENT_ION_TYPE=b
FRAGMENT_ION_TYPE_2=y
PRECURSOR_CHARGE_LOWER_BOUND=2
PRECURSOR_CHARGE_UPPER_BOUND=4
ISOTOPIC_CORRECTION_LOWER_BOUND=0
ISOTOPIC_CORRECTION_UPPER_BOUND=1
# ------------------------------------------------------------------
# OMSSA Specific Parameters
# ------------------------------------------------------------------
EVALUE_CUTOFF=100.0
MAXIMUM_HITLIST_LENGTH=10
PRECURSOR_ELIMINATION=false
PRECURSOR_SCALING=true
MINIMAL_PEPTIDE_SIZE=8
MAXIMAL_PEPTIDE_SIZE=30
PRECURSOR_CHARGE_TO_CONSIDER_MULTIPLY_CHARGED_FRAGMENTS=3
CHARGE_ESTIMATION=true
OUTPUT_TYPE=OMX
MEMORY_MAPPED_SEQUENCES=false
MASS_TO_CONSIDER_EXACT_NEUTRON_MASS=1446.94
LOW_INTENSITY_CUTOFF=0.0
HIGH_INTENSITY_CUTOFF=0.2
INTENSITY_INCREMENT=5.0E-4
SINGLE_CHARGE_WINDOW_WIDTH=27
DOUBLE_CHARGE_WINDOW_WIDTH=14
SINGLE_CHARGE_WINDOW_NPEAKS=2
DOUBLE_CHARGE_WINDOW_NPEAKS=2
MAX_HITS_PER_SPECTRUM_PER_CHARGE=30
MIN_ANNOTATED_INTENSE_PEAKS=6
MIN_ANNOTATED_PEAKS=2
MIN_PEAKS=4
CLEAVE_TERMINAL_METHIONINE=true
MAX_MZ_LADDERS=128
MAX_FRAGMENT_CHARGE=2
FRACTION_PEAKS_FOR_CHARGE_1_ESTIMATION=0.95
AUTO_DETERMINE_CHARGE_ONE=true
SEARCH_POSITIVE_IONS=true
MIN_PERCURSORS_PER_SPECTRUM=1
FORWARD_FRAGMENTS_FIRST=false
REWIND_FRAGMENTS=true
FRAGMENTS_PER_SERIES=100
CORRELATION_CORRECTION_SCORE=true
CONSECUTIVE_ION_PROBABILITY=0.5
ITERATIVE_SEARCH_SEQUENCE_EVALUE=0.0
ITERATIVE_SEARCH_SPECTRUM_EVALUE=0.01
ITERATIVE_SEARCH_REPLACEMENT_EVALUE=0.0
# ------------------------------------------------------------------
# MetaMorpheus Specific Parameters
# ------------------------------------------------------------------
MIN_PEPTIDE_LENGTH=8
MAX_PEPTIDE_LENGTH=30
SEARCH_TYPE=Classic
NUM_PARTITIONS=1
DISSOCIATION_TYPE=HCD
MAX_MODS_FOR_PEPTIDE=2
INITIATOR_METHIONINE_BEHAVIOR=Variable
SCORE_CUTOFF=5.0
USE_DELTA_SCORE=false
FRAGMENTATION_TERMINUS=Both
MAX_FRAGMENTATION_SIZE=30000.0
MIN_ALLOWED_INTERNAL_FRAGMENT_LENGTH=0
MASS_DIFF_ACCEPTOR_TYPE=OneMM
WRITE_MZID=true
WRITE_PEPXML=false
USE_PROVIDED_PRECURSOR=true
DO_PREC_DECONVOLUTION=true
DECONVOLUTION_INT_RATIO=3.0
DECONVOLUTION_MASS_TOL=4.0
DECONVOLUTION_MASS_TOL_TYPE=PPM
TRIM_MS1_PEAKS=false
TRIM_MSMS_PEAKS=true
NUM_PEAKS_PER_WINDOWS=200
MIN_ALLOWED_INT_RATIO_TO_BASE_PEAK=0.01
WINDOW_WITH_THOMPSON=null
NUM_WINDOWS=null
NORMALIZE_PEAKS_ACROSS_ALL_WINDOWS=false
MOD_PEPTIDES_ARE_DIFFERENT=false
NO_ONE_HIT_WONDERS=false
SEARCH_TARGET=true
DECOY_TYPE=None
MAX_MOD_ISOFORMS=1024
MIN_VARIANT_DEPTH=1
MAX_HETROZYGOUS_VARIANTS=4
RUN_GPTM=false
GPTMS=Common Biological, Common Artifact, Metal
# ------------------------------------------------------------------
# X!Tandem Specific Parameters
# ------------------------------------------------------------------
DYNAMIC_RANGE=100.0
NUMBER_OF_PEAKS=50
MIN_FRAG_MASS=200.0
MIN_NUMBER_OF_PEAKS=5
NOISE_SUPPRESSION=YES
PARENT_MONOISOTOPIC_MASS_ISOTOPE_ERROR=YES
MIN_PREC_MASS=500.0
PROTEIN_QUICK_ACETYL=YES
QUICK_PYROLIDONE=YES
PROTEIN_PTM_COMPLEXITY=6.0
STP_BIAS=NO
REFINE=YES
REFINE_SEMI=NO
REFINE_POINT_MUTATIONS=NO
REFINE_SPECTRUM_SYNTHESIS=YES
REFINE_UNANTICIPATED_CLEABAGES=YES
REFINE_SNAPS=YES
REFINE_MAX_EVALUE=0.01
POTENTIAL_MODIFICATIONS_FOR_FULL_REFINEMENT=NO
EVALUE_CUTOFF=0.01
SKYLINE_PATH=
OUTPUT_RESULTS=all
OUTPUT_PROTEINS=YES
OUTPUT_SEQUENCES=NO
OUTPUT_SPECTRA=YES
OUTPUT_HISTOGRAMS=NO
# ------------------------------------------------------------------
# PepNovo+ Specific Parameters
# ------------------------------------------------------------------
HIT_LIST_LENGTH=10
CORRECT_PRECURSOR_MASS=false
DISCARD_LOW_QUALITY_SPECTRA=true
FRAGMENTATION_MODEL=CID_IT_TRYP
GENERATE_QUERY=false
# ------------------------------------------------------------------
# Andromeda Specific Parameters
# ------------------------------------------------------------------
MIN_PEPTIDE_LENGHT_NO_ENZYME=8
MAX_PEPTIDE_LENGHT_NO_ENZYME=30
MAX_PEPTIDE_MASS=4600.0
NUMBER_SPECTRUM_MATCHES=10
MAX_PTMS=5
FRAGMENTATION_METHOD=CID
WATER_LOSS=true
AMMONIA_LOSS=true
SEQUENCE_DEPENDENT_NEUTRAL_LOSS=true
EQUAL_IL=false
FRAGMENT_ALL=false
EMPERICAL_CORRECTION=true
HIGHER_CHARGE=true
MAX_COMBINATIONS=250
TOP_PEAKS=8
TOP_PEAKS_WINDOW=100
DECOY_MODE=none
# ------------------------------------------------------------------
# Sage Specific Parameters
# ------------------------------------------------------------------
BUCKET_SIZE=32768
MIN_PEP_LENGTH=8
MAX_PEP_LENGTH=30
MIN_FRAGMENT_MZ=200.0
MAX_FRAGMENT_MZ=2000.0
MIN_PEPTIDE_MASS=600.0
MAX_PEPTIDE_MASS=5000.0
MIN_ION_INDEX=2
MAX_VARIABLE_MODS=2
GENERATE_DECOYS=false
TMT_TYPE=null
TMT_LEVEL=3
TMT_SN=false
LFQ=false
LFQ_PEAK_SCORING=Hybrid
LFQ_INTEGRATION=Sum
LFQ_SPECTRAL_ANGLE=0.7
LFQ_PPM_TOLERANCE=5.0
LFQ_COMBINE_CHARGE_STATES=true
DEISOTOPE=false
CHIMERA=false
WIDE_WINDOW=false
PREDICT_RT=true
MIN_PEAKS=15
MAX_PEAKS=150
MIN_MATCHED_PEAKS=4
MAX_FRAGMENT_CHARGE=null
NUM_PSMS_PER_SPECTRUM=1
BATCH_SIZE=null
# ------------------------------------------------------------------
# MS Amanda Specific Parameters
# ------------------------------------------------------------------
SEARCH_DECOY=false
REPORT_BOTH_BEST_HITS_FOR_TD=true
INSTRUMENT_ID=b, y
MONOISOTOPIC=true
MAX_RANK=10
PERFORM_DEISOTOPING=true
MAX_MODIFICATIONS=3
MAX_VARIABLE_MODIFICATIONS=4
MAX_MODIFICATIONS_SITES=6
MAX_NEUTRAL_LOSSES=1
MAX_NEUTRAL_LOSSES_PER_MODIFICATION=2
MIN_PEPTIDE_LENGTH=8
MAX_PEPTIDE_LENGTH=30
MAX_LOADED_PROTEINS=100000
MAX_LOADED_SPECTRA=2000
OUTPUT_FORMAT=csv
MAX_ALLOWED_CHARGE_STATE=+2
MIN_PEAK_DEPTH=1
MAX_PEAK_DEPTH=10
PERFORM_SECOND_SEARCH=false
KEEP_Y1_ION=true
REMOVE_WATER_LOSSES=true
REMOVE_AMMONIA_LOSSES=true
EXCLUDE_FIRST_PRECURSOR=true
MAX_MULTIPLE_PRECURSORS=5
CONSIDERED_CHARGES_FOR_PRECURSORS=+2,+3
COMBINE_CHARGE_STATES=true
RUN_PERCOLATOR=false
GENERATE_PIN_FILE=false
# ------------------------------------------------------------------
# MS-GF+ Specific Parameters
# ------------------------------------------------------------------
SEARCH_DECOY=false
INSTRUMENT_ID=1
FRAGMENTATION_ID=3
PROTOCOL_ID=0
MIN_PEP_LENGTH=8
MAX_PEP_LENGTH=30
NUMBER_SPECTRUM_MATCHES=10
ADDITIONAL_OUTPUT=false
NUMBER_OF_TOLERABLE_TERMINI=2
MAX_NUMBER_MODIFICATIONS=2
NUMBER_TASKS=null
# ------------------------------------------------------------------
# DirecTag Specific Parameters
# ------------------------------------------------------------------
TIC_CUTOFF_PERCENTAGE=100.0
MAX_PEAK_COUNT=100
NUM_INTENSITY_CLASSES=3
ADJUST_PRECURSOR_MASS=false
MIN_PRECUSOR_ADJUSTMENT=-0.5
MAX_PRECUSOR_ADJUSTMENT=1.5
PRECUSOR_ADJUSTMENT_STEP=0.1
NUM_CHARGE_STATES=3
OUTPUT_SUFFIX=
USE_CHARGE_STATE_FROM_MS=true
DUPLICATE_SPECTRA=true
DEISOTOPING_MODE=0
ISOTOPE_MZ_TOLERANCE=0.25
COMPLEMENT_MZ_TOLERANCE=0.1
TAG_LENGTH=4
MAX_DYNAMIC_MODS=2
MAX_TAG_COUNT=10
INTENSITY_SCORE_WEIGHT=1.0
MZ_FIDELITY_SCORE_WEIGHT=1.0
COMPLEMENT_SCORE_WEIGHT=1.0
# ------------------------------------------------------------------
# Comet Specific Parameters
# ------------------------------------------------------------------
NUMBER_SPECTRUM_MATCHES=10
MAX_VARIABLE_MODS=10
REQUIRE_VARIABLE_MODS=false
MIN_PEAKS=10
MIN_PEAKS_INTENSITY=0.0
REMOVE_PRECURSOR=0
REMOVE_PRECURSOR_TOLERANCE=1.5
LOWER_CLEAR_MZ_RANGE=0.0
UPPER_CLEAR_MZ_RANGE=0.0
ENZYME_TYPE=2
ISOTOPE_CORRECTION=1
MIN_PRECURSOR_MASS=600.0
MAX_PRECURSOR_MASS=5000.0
MIN_PEP_LENGTH=8
MAX_PEP_LENGTH=30
MAX_FRAGMENT_CHARGE=3
REMOVE_METHIONINE=false
BATCH_SIZE=0
THEORETICAL_FRAGMENT_IONS_SUM_ONLY=false
FRAGMENT_BIN_OFFSET=0.01
USE_SPARSE_MATRIX=true
OUTPUT_FORAMT=PepXML
PRINT_EXPECT_SCORE=true
# ------------------------------------------------------------------
# MyriMatch Specific Parameters
# ------------------------------------------------------------------
MIN_PEP_LENGTH=8
MAX_PEP_LENGTH=30
NUMBER_SPECTRUM_MATCHES=10
TIC_CUTOFF_PERCENTAGE=0.98
MAX_DYNMIC_MODS=2
MIN_TERMINI_CLEAVAGES=2
MIN_PRECURSOR_MASS=600.0
MAX_PRECURSOR_MASS=5000.0
USE_SMART_PLUS_THREE_MODEL=false
COMPUTE_XCORR=false
NUM_INTENSITY_CLASSES=3
CLASS_SIZE_MULTIPLIER=2
NUM_BATCHES=50
FRAGMENTATION_RULE=CID
MAX_PEAK_COUNT=300
OUTPUT_FORMAT=mzIdentML
# ------------------------------------------------------------------
# pNovo+ Specific Parameters
# ------------------------------------------------------------------
NUMBER_PEPTIDES=10
LOWER_PRECURSOR_MASS=300
UPPER_PRECURSOR_MASS=5000
ACTIVATION_TYPE=HCD
# ------------------------------------------------------------------
# Tide Specific Parameters
# ------------------------------------------------------------------
MIN_PEP_LENGTH=6
MAX_PEP_LENGTH=30
MIN_PRECURSOR_MASS=200.0
MAX_PRECURSOR_MASS=7200.0
MAX_VARIABLE_MODIFICATIONS_PER_TYPE_PER_PEPTIDE=2
MAX_VARIABLE_MODIFICATIONS_PER_PEPTID=255
DECOY_FORMAT=none
KEEP_TERMINAL_AMINO_ACIDS=NC
DECOY_SEED=1
OUTPUT_FOLDER_NAME=crux-output
PRINT_PEPTIDES=false
VERBOSITY=30
MONOISOTOPIC_PRECURSOR=true
CLIP_NTERM_METHIONINE=false
DIGESTION_TYPE=full-digest
COMPUTE_SP_SCORE=false
NUMBER_SPECTRUM_MATCHES=10
COMPUTE_EXACT_P_VALUES=false
MIN_SPECTRUM_MZ=0.0
MAX_SPECTRUM_MZ=null
MIN_SPECTRUM_PEAKS=20
REMOVE_PRECURSOR=false
REMOVE_PRECURSOR_TOLERANCE=1.5
PRINT_PROGRESS_INDICATOR_SIZE=1000
USE_FLANKING_PEAKS=false
USE_NEUTRAL_LOSS_PEAKS=false
MZ_BIN_WIDTH=0.02
MZ_BIN_OFFSET=0.0
CONCATENATE_TARGET_DECOY=false
STORE_SPECTRA_FILE_NAME=null
TEXT_OUTPUT=true
SQT_OUTPUT=false
PEPXML_OUTPUT=false
MZID_OUTPUT=false
PERCOLATOR_OUTPUT=false
# ------------------------------------------------------------------
# Novor Specific Parameters
# ------------------------------------------------------------------
FRAGMENTATION=HCD
MASS_ANALYZER=FT