System OS: Windows 11, Architecture: AMD64
Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium
.NET Core Info: 6.0.35


Version info:
FragPipe version 22.0
MSFragger version 4.1
IonQuant version 1.10.27
diaTracer version 1.1.5
Philosopher version 5.1.1


LCMS files:
  Experiment/Group: 
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - D:\20240927_SW-KF\PLD_method\raw\20240927_SW-KF_S1_PLD_Slot2-38_1_8058.d	DIA
  - D:\20240927_SW-KF\PLD_method\raw\20240927_SW-KF_S1_sup_Slot2-37_1_8056.d	DIA
  - D:\20240927_SW-KF\PLD_method\raw\20240927_SW-KF_S1_total_Slot2-36_1_8055.d	DIA
  - D:\20240927_SW-KF\PLD_method\raw\20240927_SW-KF_S2_PLD_Slot2-41_1_8063.d	DIA
  - D:\20240927_SW-KF\PLD_method\raw\20240927_SW-KF_S2_sup_Slot2-40_1_8061.d	DIA
  - D:\20240927_SW-KF\PLD_method\raw\20240927_SW-KF_S2_total_Slot2-39_1_8060.d	DIA


5 commands to execute:
CheckCentroid
C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -Xmx47G -cp C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid D:\20240927_SW-KF\PLD_method\raw\20240927_SW-KF_S1_PLD_Slot2-38_1_8058.d 20
DIA-NN [Work dir: D:\20240927_SW-KF\PLD_method\output]
C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib library.tsv --threads 20 --verbose 1 --out diann-output\report.tsv --qvalue 0.01 --matrices --no-prot-inf --smart-profiling --no-quant-files --peak-center --no-ifs-removal --report-lib-info --var-mod PS,87.03203,DE --var-mod PE,43.0422,DE --peptidoforms --cfg D:\20240927_SW-KF\PLD_method\output\filelist_diann.txt
DIA-NN [Work dir: D:\20240927_SW-KF\PLD_method\output]
C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\tools\diann\1.8.2_beta_8\win\dia-nn-plotter.exe diann-output\report.stats.tsv diann-output\report.tsv diann-output\report.pdf
DIA-NN: Propagate information [Work dir: D:\20240927_SW-KF\PLD_method\output\diann-output]
C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\tools\batmass-io-1.33.4.jar;C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.Propagation D:\20240927_SW-KF\PLD_method\output
DIA-NN: Convert DIA-NN output to MSstats.csv [Work dir: D:\20240927_SW-KF\PLD_method\output\diann-output]
C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\lib\commons-io-2.15.1.jar;C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.DiannToMsstats report.tsv ./ D:\20240927_SW-KF\PLD_method\output\psm.tsv 0.01 1 0.01 0.01 D:\20240927_SW-KF\PLD_method\output\fragpipe-files.fp-manifest
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [D:\20240927_SW-KF\PLD_method\output]
    Cmd: [CheckCentroid], Work dir: [D:\20240927_SW-KF\PLD_method\output]
    Cmd: [DIA-NN], Work dir: [D:\20240927_SW-KF\PLD_method\output]

~~~~~~~~~~~~~~~~~~~~~~

~~~~~~Sample of D:\20240927_SW-KF\sequence\2024-10-03-decoys-contam-UP000005640.fas~~~~~~~
>contam_sp|O77727|K1C15_SHEEP Keratin, type I cytoskeletal 15 OS=Ovis aries OX=9940 GN=KRT15 PE=2 SV=1
>rev_sp|Q14699|RFTN1_HUMAN Raftlin OS=Homo sapiens OX=9606 GN=RFTN1 PE=1 SV=4
>rev_sp|Q9BX70|BTBD2_HUMAN BTB/POZ domain-containing protein 2 OS=Homo sapiens OX=9606 GN=BTBD2 PE=1 SV=1
>rev_tr|A0A0J9YY89|A0A0J9YY89_HUMAN T cell receptor beta variable 6-6 (Fragment) OS=Homo sapiens OX=9606 GN=TRBV6-6 PE=4 SV=3
>rev_tr|A0A7I2V3H1|A0A7I2V3H1_HUMAN BAG cochaperone 6 OS=Homo sapiens OX=9606 GN=BAG6 PE=1 SV=1
>rev_tr|A0A9L9PY84|A0A9L9PY84_HUMAN Rubicon autophagy regulator OS=Homo sapiens OX=9606 GN=RUBCN PE=1 SV=1
>rev_tr|D6RBA5|D6RBA5_HUMAN Complexin-2 (Fragment) OS=Homo sapiens OX=9606 GN=CPLX2 PE=1 SV=1
>rev_tr|F5H5J8|F5H5J8_HUMAN Caprin family member 2 OS=Homo sapiens OX=9606 GN=CAPRIN2 PE=1 SV=2
>rev_tr|H0YIL9|H0YIL9_HUMAN DEAD-box helicase 23 (Fragment) OS=Homo sapiens OX=9606 GN=DDX23 PE=1 SV=1
>rev_tr|J3QLK3|J3QLK3_HUMAN Testis expressed 14, intercellular bridge forming factor OS=Homo sapiens OX=9606 GN=TEX14 PE=1 SV=1
>rev_tr|X6RIU2|X6RIU2_HUMAN Cilia and flagella associated protein 221 (Fragment) OS=Homo sapiens OX=9606 GN=CFAP221 PE=1 SV=1
>sp|Q14954|KI2S1_HUMAN Killer cell immunoglobulin-like receptor 2DS1 OS=Homo sapiens OX=9606 GN=KIR2DS1 PE=1 SV=2
>sp|Q9BXM7|PINK1_HUMAN Serine/threonine-protein kinase PINK1, mitochondrial OS=Homo sapiens OX=9606 GN=PINK1 PE=1 SV=1
>tr|A0A0R4J2E0|A0A0R4J2E0_HUMAN Potassium sodium-activated channel subfamily T member 1 OS=Homo sapiens OX=9606 GN=KCNT1 PE=1 SV=1
>tr|A0A7I2V3N0|A0A7I2V3N0_HUMAN Exportin 1 OS=Homo sapiens OX=9606 GN=XPO1 PE=1 SV=1
>tr|A0A9Y1QPT7|A0A9Y1QPT7_HUMAN Breast cancer type 1 susceptibility protein OS=Homo sapiens OX=9606 GN=BRCA1 PE=1 SV=1
>tr|D6RBG5|D6RBG5_HUMAN non-specific serine/threonine protein kinase OS=Homo sapiens OX=9606 GN=NEK1 PE=1 SV=1
>tr|F5H5X9|F5H5X9_HUMAN Cadherin 7 OS=Homo sapiens OX=9606 GN=CDH7 PE=1 SV=1
>tr|H0YIV5|H0YIV5_HUMAN LETM1 domain containing 1 (Fragment) OS=Homo sapiens OX=9606 GN=LETMD1 PE=1 SV=1
>tr|J3QLR2|J3QLR2_HUMAN Septin-4 (Fragment) OS=Homo sapiens OX=9606 GN=SEPTIN4 PE=1 SV=1
>tr|X6RM24|X6RM24_HUMAN Enolase superfamily member 1 (Fragment) OS=Homo sapiens OX=9606 GN=ENOSF1 PE=1 SV=1
~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v22.0ui state cache


# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=D\:\\20240927_SW-KF\\sequence\\2024-10-03-decoys-contam-UP000005640.fas

Table.editor=43.0422
crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=--var-mod PS,87.03203,DE --var-mod PE,43.0422,DE --peptidoforms
diann.generate-msstats=true
diann.heavy=
diann.library=
diann.light=
diann.medium=
diann.q-value=0.01
diann.quantification-strategy=3
diann.quantification-strategy-2=QuantUMS (high accuracy)
diann.run-dia-nn=true
diann.run-dia-plex=false
diann.run-specific-protein-q-value=false
diann.unrelated-runs=false
diann.use-predicted-spectra=false
diatracer.corr-threshold=0.3
diatracer.delta-apex-im=0.01
diatracer.delta-apex-rt=3
diatracer.mass-defect-filter=false
diatracer.mass-defect-offset=0.1
diatracer.rf-max=500
diatracer.run-diatracer=false
diatracer.write-intermediate-files=false
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=false
fpop.fpop-tmt=false
fpop.label_control=
fpop.label_fpop=
fpop.region_size=1
fpop.run-fpop=false
fpop.subtract-control=false
fragpipe-config.bin-diann=C\:\\Users\\dubia\\OneDrive\\Desktop\\FragPipe-jre-22.0\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe
fragpipe-config.bin-ionquant=C\:\\Users\\dubia\\OneDrive\\Desktop\\FragPipe-jre-21.1\\fragpipe\\tools\\IonQuant-1.10.27.jar
fragpipe-config.bin-msfragger=C\:\\Users\\dubia\\OneDrive\\Desktop\\FragPipe-jre-21.1\\fragpipe\\tools\\MSFragger-4.1\\MSFragger-4.1.jar
fragpipe-config.bin-philosopher=C\:\\Users\\dubia\\OneDrive\\Desktop\\FragPipe-jre-21.1\\fragpipe\\tools\\philosopher_v5.1.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\dubia\\anaconda3\\python
fragpipe-config.tools-folder=C\:\\Users\\dubia\\OneDrive\\Desktop\\FragPipe-jre-22.0\\fragpipe\\lib\\..\\tools
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=1
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.find-best-rt-model=false
msbooster.find-best-spectra-model=false
msbooster.koina-url=
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.rt-model=DIA-NN
msbooster.run-msbooster=false
msbooster.spectra-model=DIA-NN
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.analyzer_types=all
msfragger.calibrate_mass=2
msfragger.check_spectral_files=false
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.group_variable=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.mass_offsets_detailed=
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=10000
msfragger.max_variable_mods_per_peptide=4
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.00
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
msfragger.misc.fragger.enzyme-dropdown-2=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.output_report_topN_dda_plus=5
msfragger.output_report_topN_dia1=5
msfragger.output_report_topN_dia2=3
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.require_precursor=true
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=true
msfragger.run-msfragger=false
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name_1=stricttrypsin
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
msfragger.table.var-mods=15.9949,M,true,2; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 43.0422,]^,true,1; 43.0422,DE,true,2; 87.03203,]^,true,1; 87.03203,DE,true,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_detailed_offsets=false
msfragger.use_topN_peaks=300
msfragger.write_calibrated_mzml=true
msfragger.write_uncalibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
opair.activation1=HCD
opair.activation2=ETD
opair.filterOxonium=true
opair.glyco_db=
opair.max_glycans=4
opair.max_isotope_error=2
opair.min_isotope_error=0
opair.ms1_tol=20
opair.ms2_tol=20
opair.oxonium_filtering_file=
opair.oxonium_minimum_intensity=0.05
opair.reverse_scan_order=false
opair.run-opair=false
opair.single_scan_type=false
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=false
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.5
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--picked --prot 0.01
phi-report.pep-level-summary=true
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.remove-contaminants=true
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106,c\:43.0422,DE\:43.0422,c\:87.03203,DE\:87.03203 MINPROB\=0.5
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagextract_mode=false
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=00.2
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=00.1
ptmshepherd.diagmine_fragMinSpecDiff=00.1
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_mode=false
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=00.2
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=1.00
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_mode=true
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=true
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=true
ptmshepherd.iterloc_maxEpoch=100
ptmshepherd.iterloc_mode=false
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=true
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=false
ptmshepherd.print_full_glyco_params=false
ptmshepherd.prob_dhexOx=
ptmshepherd.prob_dhexY=
ptmshepherd.prob_mass=0.5
ptmshepherd.prob_neuacOx=
ptmshepherd.prob_neugcOx=
ptmshepherd.prob_phosphoOx=
ptmshepherd.prob_regY=
ptmshepherd.prob_sulfoOx=
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=false
ptmshepherd.run_diagextract_mode=false
ptmshepherd.run_diagmine_mode=false
ptmshepherd.run_glyco_mode=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=false
run-psm-validation=true
run-validation-tab=false
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=10
saintexpress.run-saint-express=false
saintexpress.virtual-controls=100
skyline.run-skyline=false
skyline.skyline=true
skyline.skyline-custom=false
skyline.skyline-custom-path=
skyline.skyline-daily=false
skyline.skyline-mode=0
skyline.skyline-mods-mode=Default
speclibgen.convert-pepxml=true
speclibgen.convert-psm=false
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.max_glycan_qval=1
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.fragment.a=false
speclibgen.easypqp.fragment.b=true
speclibgen.easypqp.fragment.c=false
speclibgen.easypqp.fragment.x=false
speclibgen.easypqp.fragment.y=true
speclibgen.easypqp.fragment.z=false
speclibgen.easypqp.ignore_unannotated=false
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.labile_mode=Regular (not glyco)
speclibgen.easypqp.neutral_loss=false
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=false
tab-run.sub_mzml_prob_threshold=0.5
tab-run.write_sub_mzml=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.extraction_tool=IonQuant
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.log2transformed=true
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.philosopher-msstats=false
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=D\:\\20240927_SW-KF\\PLD_method\\output
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.misc.save-sdrf=true
workflow.ram=0
workflow.threads=20

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -Xmx47G -cp C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid D:\20240927_SW-KF\PLD_method\raw\20240927_SW-KF_S1_PLD_Slot2-38_1_8058.d 20
Done in 0.0 s.
Process 'CheckCentroid' finished, exit code: 0
DIA-NN [Work dir: D:\20240927_SW-KF\PLD_method\output]
C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib library.tsv --threads 20 --verbose 1 --out diann-output\report.tsv --qvalue 0.01 --matrices --no-prot-inf --smart-profiling --no-quant-files --peak-center --no-ifs-removal --report-lib-info --var-mod PS,87.03203,DE --var-mod PE,43.0422,DE --peptidoforms --cfg D:\20240927_SW-KF\PLD_method\output\filelist_diann.txt
DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks)
Compiled on Sep 15 2022 18:28:57
Current date and time: Mon Oct 14 10:14:55 2024
CPU: GenuineIntel 12th Gen Intel(R) Core(TM) i7-12700H
SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 
Logical CPU cores: 20
Thread number set to 20
Output will be filtered at 0.01 FDR
Precursor/protein x samples expression level matrices will be saved along with the main report
Protein inference will not be performed
When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones
.quant files will not be saved to the disk
Fixed-width center of each elution peak will be used for quantification
Interference removal from fragment elution curves disabled
Modification PS with mass delta 87.032 at DE will be considered as variable
Modification PE with mass delta 43.0422 at DE will be considered as variable
WARNING: unrecognised option [--peptidoforms]
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.
Cannot find a UniMod modification match for PE: 0.0363846 minimal mass discrepancy; using the original modificaiton name
Cannot find a UniMod modification match for PS: 7.0657 minimal mass discrepancy; using the original modificaiton name

6 files will be processed
[0:00] Loading spectral library library.tsv
[0:06] Spectral library loaded: 6907 protein isoforms, 6907 protein groups and 80925 precursors in 68338 elution groups.
[0:06] Initialising library
[0:06] Saving the library to library.tsv.speclib

[0:06] File #1/6
[0:06] Loading run D:\20240927_SW-KF\PLD_method\raw\20240927_SW-KF_S1_PLD_Slot2-38_1_8058.d
For most diaPASEF datasets it is better to manually fix both the MS1 and MS2 mass accuracies to values in the range 10-15 ppm.
[0:58] 80925 library precursors are potentially detectable
[0:58] Processing...
[1:06] RT window set to 0.984184
[1:06] Ion mobility window set to 0.014896
[1:06] Peak width: 4.96
[1:06] Scan window radius set to 10
[1:06] Recommended MS1 mass accuracy setting: 13.5847 ppm
[1:12] Optimised mass accuracy: 18.1174 ppm
[1:29] Removing low confidence identifications
[1:29] Removing interfering precursors
[1:31] Training neural networks: 76434 targets, 78277 decoys
[1:36] Number of IDs at 0.01 FDR: 52376
[1:37] Calculating protein q-values
[1:37] Number of protein isoforms identified at 1% FDR: 5802 (precursor-level), 5666 (protein-level) (inference performed using proteotypic peptides only)
[1:37] Quantification

[1:41] File #2/6
[1:41] Loading run D:\20240927_SW-KF\PLD_method\raw\20240927_SW-KF_S2_sup_Slot2-40_1_8061.d
[2:29] 80925 library precursors are potentially detectable
[2:29] Processing...
[2:31] RT window set to 0.965125
[2:31] Ion mobility window set to 0.0129349
[2:31] Recommended MS1 mass accuracy setting: 13.761 ppm
[2:46] Removing low confidence identifications
[2:46] Removing interfering precursors
[2:49] Training neural networks: 77345 targets, 76956 decoys
[2:54] Number of IDs at 0.01 FDR: 73170
[2:55] Calculating protein q-values
[2:55] Number of protein isoforms identified at 1% FDR: 6641 (precursor-level), 6620 (protein-level) (inference performed using proteotypic peptides only)
[2:55] Quantification

[2:59] File #3/6
[2:59] Loading run D:\20240927_SW-KF\PLD_method\raw\20240927_SW-KF_S2_total_Slot2-39_1_8060.d
[3:47] 80925 library precursors are potentially detectable
[3:47] Processing...
[3:49] RT window set to 0.966793
[3:49] Ion mobility window set to 0.0136224
[3:49] Recommended MS1 mass accuracy setting: 13.6196 ppm
[4:04] Removing low confidence identifications
[4:04] Removing interfering precursors
[4:07] Training neural networks: 77339 targets, 77203 decoys
[4:12] Number of IDs at 0.01 FDR: 74132
[4:13] Calculating protein q-values
[4:13] Number of protein isoforms identified at 1% FDR: 6657 (precursor-level), 6650 (protein-level) (inference performed using proteotypic peptides only)
[4:13] Quantification

[4:17] File #4/6
[4:17] Loading run D:\20240927_SW-KF\PLD_method\raw\20240927_SW-KF_S1_sup_Slot2-37_1_8056.d
[5:03] 80925 library precursors are potentially detectable
[5:03] Processing...
[5:05] RT window set to 0.970659
[5:05] Ion mobility window set to 0.0133568
[5:05] Recommended MS1 mass accuracy setting: 13.3056 ppm
[5:20] Removing low confidence identifications
[5:20] Removing interfering precursors
[5:23] Training neural networks: 76991 targets, 76569 decoys
[5:28] Number of IDs at 0.01 FDR: 73194
[5:29] Calculating protein q-values
[5:29] Number of protein isoforms identified at 1% FDR: 6635 (precursor-level), 6618 (protein-level) (inference performed using proteotypic peptides only)
[5:29] Quantification

[5:34] File #5/6
[5:34] Loading run D:\20240927_SW-KF\PLD_method\raw\20240927_SW-KF_S1_total_Slot2-36_1_8055.d
[6:19] 80925 library precursors are potentially detectable
[6:19] Processing...
[6:22] RT window set to 0.965863
[6:22] Ion mobility window set to 0.0131645
[6:22] Recommended MS1 mass accuracy setting: 13.3421 ppm
[6:36] Removing low confidence identifications
[6:36] Removing interfering precursors
[6:40] Training neural networks: 77206 targets, 76502 decoys
[6:45] Number of IDs at 0.01 FDR: 74059
[6:46] Calculating protein q-values
[6:46] Number of protein isoforms identified at 1% FDR: 6643 (precursor-level), 6623 (protein-level) (inference performed using proteotypic peptides only)
[6:46] Quantification

[6:50] File #6/6
[6:50] Loading run D:\20240927_SW-KF\PLD_method\raw\20240927_SW-KF_S2_PLD_Slot2-41_1_8063.d
[7:35] 80925 library precursors are potentially detectable
[7:35] Processing...
[7:44] RT window set to 0.960382
[7:44] Ion mobility window set to 0.0138776
[7:44] Recommended MS1 mass accuracy setting: 13.6557 ppm
[7:59] Removing low confidence identifications
[7:59] Removing interfering precursors
[8:01] Training neural networks: 75019 targets, 74801 decoys
[8:06] Number of IDs at 0.01 FDR: 40755
[8:07] Calculating protein q-values
[8:07] Number of protein isoforms identified at 1% FDR: 5274 (precursor-level), 5101 (protein-level) (inference performed using proteotypic peptides only)
[8:07] Quantification

[8:11] Cross-run analysis
[8:11] Reading quantification information: 6 files
[8:11] Quantifying peptides
[8:14] Quantifying proteins
[8:14] Calculating q-values for protein and gene groups
[8:14] Calculating global q-values for protein and gene groups
[8:14] Writing report
[8:43] Report saved to diann-output\report.tsv.
[8:43] Saving precursor levels matrix
[8:43] Precursor levels matrix (1% precursor and protein group FDR) saved to diann-output\report.pr_matrix.tsv.
[8:43] Saving protein group levels matrix
[8:43] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to diann-output\report.pg_matrix.tsv.
[8:43] Saving gene group levels matrix
[8:44] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to diann-output\report.gg_matrix.tsv.
[8:44] Saving unique genes levels matrix
[8:44] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to diann-output\report.unique_genes_matrix.tsv.
[8:44] Stats report saved to diann-output\report.stats.tsv
[8:44] Log saved to diann-output\report.log.txt
Finished

Process 'DIA-NN' finished, exit code: 0
DIA-NN [Work dir: D:\20240927_SW-KF\PLD_method\output]
C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\tools\diann\1.8.2_beta_8\win\dia-nn-plotter.exe diann-output\report.stats.tsv diann-output\report.tsv diann-output\report.pdf
Generating report. Stats, main report, output file: diann-output\report.stats.tsv, diann-output\report.tsv, diann-output\report.pdf
Process 'DIA-NN' finished, exit code: 0
DIA-NN: Propagate information [Work dir: D:\20240927_SW-KF\PLD_method\output\diann-output]
C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\tools\batmass-io-1.33.4.jar;C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.Propagation D:\20240927_SW-KF\PLD_method\output
Done in 7.41 seconds.
Process 'DIA-NN: Propagate information' finished, exit code: 0
DIA-NN: Convert DIA-NN output to MSstats.csv [Work dir: D:\20240927_SW-KF\PLD_method\output\diann-output]
C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\lib\commons-io-2.15.1.jar;C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;C:\Users\dubia\OneDrive\Desktop\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar com.dmtavt.fragpipe.tools.diann.DiannToMsstats report.tsv ./ D:\20240927_SW-KF\PLD_method\output\psm.tsv 0.01 1 0.01 0.01 D:\20240927_SW-KF\PLD_method\output\fragpipe-files.fp-manifest
Done in 12.26 seconds.
Process 'DIA-NN: Convert DIA-NN output to MSstats.csv' finished, exit code: 0

Please cite:
(Spectral library generation and DIA analysis) Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform. Nat Commun. 14:4154 (2023)
(DIA quantification with DIA-NN) dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts. Nat Commun. 13:3944 (2022)
(Visualization with FragPipe-PDV) PDV: an integrative proteomics data viewer. Bioinformatics. 35(7):1249 (2019)
(Visualization with Skyline) Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics. 26(7):966 (2010)

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