System OS: Windows 10, Architecture: AMD64
Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium
.NET Core Info: N/A


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)
  - E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.mzML	DDA
  - E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.mzML	DDA


25 commands to execute:
CheckCentroid
C:\FragPipe\fragpipe\jre\bin\java.exe -Xmx108G -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar;C:\FragPipe\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.mzML 30
WorkspaceCleanInit [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\u0126651\AppData\Local\Temp\08010a78-98f2-433f-85fa-9de5ad39c0d9
MSFragger [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx108G C:\FragPipe\fragpipe\tools\MSFragger-4.1\MSFragger-4.1.jar E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\fragger.params E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.mzML E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.mzML
MSFragger move pepxml
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.pepXML E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.pepXML
MSFragger move pin
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.pin E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.pin
MSFragger move pepxml
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.pepXML E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.pepXML
MSFragger move pin
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.pin E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.pin
MSBooster [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\jre\bin\java.exe -Xmx108G -cp C:\FragPipe\fragpipe\tools\MSBooster-1.2.31.jar;C:\FragPipe\fragpipe\tools\batmass-io-1.33.4.jar Features.MainClass --paramsList E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\msbooster_params.txt
Percolator [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_percolator_target_psms.tsv --decoy-results-psms PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_edited.pin
Percolator [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_percolator_target_psms.tsv --decoy-results-psms PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_edited.pin
Percolator: Convert to pepxml [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.pin PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1 PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_percolator_target_psms.tsv PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_percolator_decoy_psms.tsv interact-PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1 DDA 0.5 E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.mzML
Percolator: Delete temp
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_percolator_target_psms.tsv
Percolator: Delete temp
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.pin PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2 PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_percolator_target_psms.tsv PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_percolator_decoy_psms.tsv interact-PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2 DDA 0.5 E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.mzML
Percolator: Delete temp
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_percolator_target_psms.tsv
Percolator: Delete temp
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_percolator_decoy_psms.tsv
ProteinProphet [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe database --annotate C:\FASTAs\2024-08-06-decoys-contam-20231120_Homo_Sapiens_Uniprot_canonical+isoforms.fasta.fas --prefix rev_
PhilosopherFilter [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --picked --ion 0.05 --psm 0.05 --pep 0.05 --prot 0.05 --tag rev_ --pepxml E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger --protxml E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\combined.prot.xml --razor
PhilosopherReport [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
WorkspaceClean [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
IonQuant [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\jre\bin\java.exe -Xmx108G -Dlibs.bruker.dir=C:\FragPipe\fragpipe\tools\MSFragger-4.1\ext\bruker -Dlibs.thermo.dir=C:\FragPipe\fragpipe\tools\MSFragger-4.1\ext\thermo -cp C:\FragPipe\fragpipe\tools\jfreechart-1.5.3.jar;C:\FragPipe\fragpipe\tools\batmass-io-1.33.4.jar;C:\FragPipe\fragpipe\tools\IonQuant-1.10.27.jar ionquant.IonQuant --threads 30 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 0 --msstats 0 --minexps 1 --mbr 0 --maxlfq 0 --requantify 0 --mztol 10 --imtol 0.05 --rttol 1 --normalization 0 --minisotopes 1 --minscans 1 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0 --uniqueness 0 --filelist E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\filelist_ionquant.txt --modlist E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\modmasses_ionquant.txt
IonQuant [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\jre\bin\java.exe -Xmx108G -Dlibs.bruker.dir=C:\FragPipe\fragpipe\tools\MSFragger-4.1\ext\bruker -Dlibs.thermo.dir=C:\FragPipe\fragpipe\tools\MSFragger-4.1\ext\thermo -cp C:\FragPipe\fragpipe\tools\jfreechart-1.5.3.jar;C:\FragPipe\fragpipe\tools\batmass-io-1.33.4.jar;C:\FragPipe\fragpipe\tools\IonQuant-1.10.27.jar ionquant.IonQuant --threads 30 --perform-ms1quant 0 --perform-isoquant 1 --isotol 20.0 --isolevel 2 --isotype TMT-16 --ionmobility 0 --site-reports 0 --msstats 0 --annotation E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\psm.tsv=E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\20250204_TMT16_annotation.txt --minexps 1 --mbr 0 --maxlfq 0 --requantify 0 --mztol 10 --imtol 0.05 --rttol 1 --normalization 0 --minisotopes 1 --minscans 1 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0 --uniqueness 0 --filelist E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\filelist_ionquant.txt --modlist E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\modmasses_ionquant.txt
TmtIntegrator [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\jre\bin\java.exe -Xmx108G -cp C:\FragPipe\fragpipe\tools\tmt-integrator-5.0.9.jar tmtintegrator.TMTIntegrator E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\tmt-integrator-conf.yml E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\psm.tsv
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
    Cmd: [CheckCentroid], Work dir: [E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
    Cmd: [WorkspaceCleanInit], Work dir: [E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
    Cmd: [MSFragger], Work dir: [E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
    Cmd: [MSBooster], Work dir: [E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
    Cmd: [Percolator], Work dir: [E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
    Cmd: [ProteinProphet], Work dir: [E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
    Cmd: [PhilosopherDbAnnotate], Work dir: [E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
    Cmd: [PhilosopherFilter], Work dir: [E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
    Cmd: [PhilosopherReport], Work dir: [E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
    Cmd: [WorkspaceClean], Work dir: [E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
    Cmd: [IonQuant], Work dir: [E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
    Cmd: [IonQuant], Work dir: [E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
    Cmd: [TmtIntegrator], Work dir: [E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]

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

~~~~~~Sample of C:\FASTAs\2024-08-06-decoys-contam-20231120_Homo_Sapiens_Uniprot_canonical+isoforms.fasta.fas~~~~~~~
>rev_sp|A0A024R1R8|TMA7B_HUMAN Translation machinery-associated protein 7B OS=Homo sapiens OX=9606 GN=TMA7B PE=3 SV=1
>rev_sp|O75251|NDUS7_HUMAN NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial OS=Homo sapiens OX=9606 GN=NDUFS7 PE=1 SV=3
>rev_sp|P17039|ZNF30_HUMAN Zinc finger protein 30 OS=Homo sapiens OX=9606 GN=ZNF30 PE=2 SV=5
>rev_sp|P56945-2|BCAR1_HUMAN Isoform 2 of Breast cancer anti-estrogen resistance protein 1 OS=Homo sapiens OX=9606 GN=BCAR1
>rev_sp|Q15431|SYCP1_HUMAN Synaptonemal complex protein 1 OS=Homo sapiens OX=9606 GN=SYCP1 PE=1 SV=2
>rev_sp|Q6P1K2|PMF1_HUMAN Polyamine-modulated factor 1 OS=Homo sapiens OX=9606 GN=PMF1 PE=1 SV=2
>rev_sp|Q8IYH5-4|ZZZ3_HUMAN Isoform 4 of ZZ-type zinc finger-containing protein 3 OS=Homo sapiens OX=9606 GN=ZZZ3
>rev_sp|Q92478|CLC2B_HUMAN C-type lectin domain family 2 member B OS=Homo sapiens OX=9606 GN=CLEC2B PE=1 SV=2
>rev_sp|Q9BUN8-2|DERL1_HUMAN Isoform 2 of Derlin-1 OS=Homo sapiens OX=9606 GN=DERL1
>rev_sp|Q9NWZ5|UCKL1_HUMAN Uridine-cytidine kinase-like 1 OS=Homo sapiens OX=9606 GN=UCKL1 PE=1 SV=2
>rev_sp|X6R8R1|ST15B_HUMAN Synaptotagmin-15B OS=Homo sapiens OX=9606 GN=SYT15B PE=3 SV=1
>sp|O75251-2|NDUS7_HUMAN Isoform 2 of NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial OS=Homo sapiens OX=9606 GN=NDUFS7
>sp|P17039-3|ZNF30_HUMAN Isoform 3 of Zinc finger protein 30 OS=Homo sapiens OX=9606 GN=ZNF30
>sp|P56937|DHB7_HUMAN 3-keto-steroid reductase/17-beta-hydroxysteroid dehydrogenase 7 OS=Homo sapiens OX=9606 GN=HSD17B7 PE=1 SV=1
>sp|Q15428|SF3A2_HUMAN Splicing factor 3A subunit 2 OS=Homo sapiens OX=9606 GN=SF3A2 PE=1 SV=2
>sp|Q6P1K2-6|PMF1_HUMAN Isoform 6 of Polyamine-modulated factor 1 OS=Homo sapiens OX=9606 GN=PMF1
>sp|Q8IYH5-3|ZZZ3_HUMAN Isoform 3 of ZZ-type zinc finger-containing protein 3 OS=Homo sapiens OX=9606 GN=ZZZ3
>sp|Q92466|DDB2_HUMAN DNA damage-binding protein 2 OS=Homo sapiens OX=9606 GN=DDB2 PE=1 SV=1
>sp|Q9BUN5|CC28B_HUMAN Coiled-coil domain-containing protein 28B OS=Homo sapiens OX=9606 GN=CCDC28B PE=1 SV=2
>sp|Q9NWZ5-4|UCKL1_HUMAN Isoform 4 of Uridine-cytidine kinase-like 1 OS=Homo sapiens OX=9606 GN=UCKL1
>sp|X6R8D5|CMIP3_HUMAN Putative uncharacterized protein CIMIP3 OS=Homo sapiens OX=9606 GN=CIMIP3 PE=5 SV=2
~~~~~~~~~~~~~~~~~~~~~~

~~~~~~annotation files~~~~~~~
E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\20250204_TMT16_annotation.txt:
126 sample-01
127N sample-02
127C sample-03
128N sample-04
128C sample-05
129N sample-06
129C sample-07
130N sample-08
130C sample-09
131N sample-10
131C sample-11
132N sample-12
132C sample-13
133N sample-14
133C sample-15
134N sample-16
~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~ 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=C\:\\FASTAs\\2024-08-06-decoys-contam-20231120_Homo_Sapiens_Uniprot_canonical+isoforms.fasta.fas

crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
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=false
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=true
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\:\\FragPipe\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe
fragpipe-config.bin-python=C\:\\Users\\u0126651\\AppData\\Local\\Programs\\Python\\Python310\\python
fragpipe-config.tools-folder=C\:\\FragPipe\\fragpipe
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=0
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=true
msbooster.find-best-spectra-model=true
msbooster.koina-url=https\://koina.wilhelmlab.org\:443/v2/models/
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.rt-model=DIA-NN
msbooster.run-msbooster=true
msbooster.spectra-model=DIA-NN
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.analyzer_types=all
msfragger.calibrate_mass=2
msfragger.check_spectral_files=true
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=-1/0/1/2/3
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=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=134.5
msfragger.misc.fragger.clear-mz-lo=125.5
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=200
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.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=-18.01056 79.96633
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.require_precursor=true
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
msfragger.run-msfragger=true
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; 304.20715,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,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 304.20715,n^,true,1; 304.20715,S,true,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 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=150
msfragger.write_calibrated_mzml=false
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=--sequential --picked --ion 0.05 --psm 0.05 --pep 0.05 --prot 0.05
phi-report.pep-level-summary=false
phi-report.print-decoys=false
phi-report.prot-level-summary=false
phi-report.remove-contaminants=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=
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.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_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=00.2
ptmshepherd.glyco_fdr=1.00
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.iterloc_maxEpoch=100
ptmshepherd.iterloc_mode=false
ptmshepherd.localization_allowed_res=
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_mass=0.5
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=true
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=3
saintexpress.run-saint-express=true
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=false
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-16
tmtintegrator.extraction_tool=IonQuant
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=2
tmtintegrator.log2transformed=true
tmtintegrator.max_pep_prob_thres=0.9
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=true
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=E\:\\FW_MS\\Charlotte_Philips\\PRC-6611\\MSFragger
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.misc.save-sdrf=true
workflow.ram=0
workflow.threads=30

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
C:\FragPipe\fragpipe\jre\bin\java.exe -Xmx108G -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar;C:\FragPipe\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.mzML 30
Done in 1.2 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="13:56:13" level=info msg="Executing Workspace  v5.1.1"
time="13:56:13" level=info msg="Removing workspace"
time="13:56:13" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\u0126651\AppData\Local\Temp\08010a78-98f2-433f-85fa-9de5ad39c0d9
time="13:56:13" level=info msg="Executing Workspace  v5.1.1"
time="13:56:13" level=info msg="Creating workspace"
time="13:56:13" level=info msg=Done
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFragger [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx108G C:\FragPipe\fragpipe\tools\MSFragger-4.1\MSFragger-4.1.jar E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\fragger.params E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.mzML E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.mzML
MSFragger version MSFragger-4.1
Batmass-IO version 1.33.4
timsdata library version timsdata-2-21-0-4
(c) University of Michigan
RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved.
System OS: Windows 10, Architecture: AMD64
Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium
JVM started with 108 GB memory
Checking database...
Checking spectral files...
E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.mzML: Scans = 49707; ITMS: false; FTMS: true; Isolation sizes = [0.9]
E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.mzML: Scans = 50628; ITMS: false; FTMS: true; Isolation sizes = [0.9]
***********************************FIRST SEARCH************************************
Parameters:
num_threads = 30
database_name = C:\FASTAs\2024-08-06-decoys-contam-20231120_Homo_Sapiens_Uniprot_canonical+isoforms.fasta.fas
decoy_prefix = rev_
precursor_mass_lower = -20.0
precursor_mass_upper = 20.0
precursor_mass_units = 1
data_type = 0
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 20.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = 0
write_calibrated_mzml = 0
write_uncalibrated_mgf = 0
write_mzbin_all = 0
isotope_error = 0/1
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = 0
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = stricttrypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = 1
allow_multiple_variable_mods_on_residue = 0
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = pepxml_pin
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = 0
override_charge = 0
precursor_charge_low = 2
precursor_charge_high = 3
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 200.0
digest_mass_range_high = 5000.0
max_fragment_charge = 1
deisotope = 1
deneutralloss = 1
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
minimum_peaks = 15
use_topN_peaks = 150
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 0
activation_types = all
analyzer_types = all
group_variable = 0
require_precursor = 1
reuse_dia_fragment_peaks = 0
remove_precursor_peak = 1
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 125.5
clear_mz_range_high = 134.5
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = 1
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 [^ 1
variable_mod_06 = 304.20715 n^ 1
variable_mod_07 = 304.20715 S 1
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.02146
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 304.20715
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Selected fragment index width 0.10 Da.
2056390080 fragments to be searched in 1 slices (30.64 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 8.53 s
	001. PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.mzML 1.2 s | deisotoping 1.2 s
		[progress: 49707/49707 (100%) - 35683 spectra/s] 1.4s | postprocessing 0.2 s
	002. PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.mzML 1.0 s | deisotoping 0.1 s
		[progress: 50627/50627 (100%) - 69447 spectra/s] 0.7s | postprocessing 0.1 s
***************************FIRST SEARCH DONE IN 0.317 MIN**************************

*********************MASS CALIBRATION AND PARAMETER OPTIMIZATION*******************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |   0.00   0.86 |  -0.04   0.55 |   0.65   0.90 |  -0.02   0.84  
 002 |   0.28   0.91 |  -0.06   0.46 |   0.67   0.91 |  -0.03   0.83  
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------|-------|-------
  MS2  |    5  |    7  |   10  |   15  |   20  |   25  |   30  |   50  
-------|-------|-------|-------|-------|-------|-------|-------|-------
 Count |  12951|  12882| skip rest
-------|-------|-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------|-------
 Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 
-------|-------|-------|-------|-------|-------|-------
 Count |  12907|  12945|  12950|  12951|  12946| skip rest
-------|-------|-------|-------|-------|-------|-------
-------|-------
 Int.  |    1  
-------|-------
 Count |  12884
-------|-------
-------|-------
 Rm P. |    0  
-------|-------
 Count |  12933
-------|-------
New fragment_mass_tolerance = 5.000000 PPM
New use_topN_peaks = 150
New minimum_ratio = 0.010000
New intensity_transform = 0
New remove_precursor_peak = 1
************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 1.909 MIN*********

************************************MAIN SEARCH************************************
Checking database...
Parameters:
num_threads = 30
database_name = C:\FASTAs\2024-08-06-decoys-contam-20231120_Homo_Sapiens_Uniprot_canonical+isoforms.fasta.fas
decoy_prefix = rev_
precursor_mass_lower = -20.0
precursor_mass_upper = 20.0
precursor_mass_units = 1
data_type = 0
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 5.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = 0
write_calibrated_mzml = 0
write_uncalibrated_mgf = 0
write_mzbin_all = 0
isotope_error = -1/0/1/2/3
mass_offsets = 0.0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = 0
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = stricttrypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = 
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = 1
allow_multiple_variable_mods_on_residue = 0
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = pepxml_pin
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = 1
override_charge = 0
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 200.0
digest_mass_range_high = 5000.0
max_fragment_charge = 1
deisotope = 1
deneutralloss = 1
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
minimum_peaks = 15
use_topN_peaks = 150
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 0
activation_types = all
analyzer_types = all
group_variable = 0
require_precursor = 1
reuse_dia_fragment_peaks = 0
remove_precursor_peak = 1
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 125.5
clear_mz_range_high = 134.5
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = 1
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 [^ 1
variable_mod_06 = 304.20715 n^ 1
variable_mod_07 = 304.20715 S 1
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.02146
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 304.20715
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Selected fragment index width 0.02 Da.
2056390080 fragments to be searched in 1 slices (30.64 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 9.86 s
	001. PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.mzBIN_calibrated 0.2 s
		[progress: 49707/49707 (100%) - 44223 spectra/s] 1.1s | remapping alternative proteins and postprocessing 2.4 s
	002. PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.mzBIN_calibrated 0.3 s
		[progress: 50627/50627 (100%) - 48170 spectra/s] 1.1s | remapping alternative proteins and postprocessing 1.7 s
***************************MAIN SEARCH DONE IN 0.310 MIN***************************

*******************************TOTAL TIME 2.536 MIN********************************
Process 'MSFragger' finished, exit code: 0
MSFragger move pepxml
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.pepXML E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.pin E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.pin
Process 'MSFragger move pin' finished, exit code: 0
MSFragger move pepxml
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.pepXML E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar;/C:/FragPipe/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.pin E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.pin
Process 'MSFragger move pin' finished, exit code: 0
MSBooster [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\jre\bin\java.exe -Xmx108G -cp C:\FragPipe\fragpipe\tools\MSBooster-1.2.31.jar;C:\FragPipe\fragpipe\tools\batmass-io-1.33.4.jar Features.MainClass --paramsList E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\msbooster_params.txt
2025-02-04 13:58:48 [INFO] - MSBooster v1.2.31
2025-02-04 13:58:48 [INFO] - Using 30 threads
2025-02-04 13:58:48 [INFO] - Initializing E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.mzML
2025-02-04 13:58:49 [INFO] - Instrument detected: Lumos
2025-02-04 13:58:49 [INFO] - Initializing E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.mzML
2025-02-04 13:58:50 [INFO] - Fragmentation type detected: HCD
2025-02-04 13:58:50 [INFO] - NCE detected: 37.0
2025-02-04 13:58:50 [INFO] - Searching for best RT model for your data
2025-02-04 13:58:50 [INFO] - Searching the following models: 
2025-02-04 13:58:50 [INFO] - [DIA-NN, Deeplc_hela_hf, AlphaPept_rt_generic, Prosit_2019_irt, Prosit_2020_irt_TMT]
Iteration 1...2...3...4...5...
2025-02-04 13:58:51 [INFO] - DIA-NN has root mean squared error of 7.1317
Iteration 1...2...3...4...5...
2025-02-04 13:58:52 [INFO] - Deeplc_hela_hf has root mean squared error of 8.3586
Iteration 1...2...3...4...5...
2025-02-04 13:58:53 [INFO] - AlphaPept_rt_generic has root mean squared error of 8.8782
Iteration 1...2...3...4...5...
2025-02-04 13:58:54 [INFO] - Prosit_2019_irt has root mean squared error of 10.2758
Iteration 1...2...3...4...5...
2025-02-04 13:58:54 [INFO] - Prosit_2020_irt_TMT has root mean squared error of 10.5464
2025-02-04 13:58:54 [INFO] - RT model chosen is DIA-NN
2025-02-04 13:58:54 [INFO] - Searching for best spectra model for your data
2025-02-04 13:58:54 [INFO] - Searching the following models: 
2025-02-04 13:58:54 [INFO] - [DIA-NN, ms2pip_2021_HCD, AlphaPept_ms2_generic, Prosit_2019_intensity, Prosit_2023_intensity_timsTOF, Prosit_2020_intensity_CID, Prosit_2020_intensity_TMT, Prosit_2020_intensity_HCD]
2025-02-04 13:58:55 [INFO] - Median similarity for DIA-NN is 0.8251
2025-02-04 13:58:56 [INFO] - Median similarity for ms2pip_2021_HCD is 0.7715
2025-02-04 13:58:56 [INFO] - Calibrating NCE
2025-02-04 13:59:00 [INFO] - Best NCE for AlphaPept_ms2_generic after calibration is 35
2025-02-04 13:59:00 [INFO] - Median similarity for AlphaPept_ms2_generic is 0.8484
2025-02-04 13:59:00 [INFO] - Calibrating NCE
2025-02-04 13:59:04 [INFO] - Best NCE for Prosit_2019_intensity after calibration is 0
2025-02-04 13:59:04 [INFO] - Median similarity for Prosit_2019_intensity is 0.0000
2025-02-04 13:59:04 [INFO] - Calibrating NCE
2025-02-04 13:59:09 [INFO] - Best NCE for Prosit_2023_intensity_timsTOF after calibration is 0
2025-02-04 13:59:09 [INFO] - Median similarity for Prosit_2023_intensity_timsTOF is 0.0000
2025-02-04 13:59:12 [INFO] - Median similarity for Prosit_2020_intensity_CID is 0.0000
2025-02-04 13:59:12 [INFO] - Calibrating NCE
2025-02-04 13:59:17 [INFO] - Best NCE for Prosit_2020_intensity_TMT after calibration is 0
2025-02-04 13:59:17 [INFO] - Median similarity for Prosit_2020_intensity_TMT is 0.0000
2025-02-04 13:59:17 [INFO] - Calibrating NCE
2025-02-04 13:59:21 [INFO] - Best NCE for Prosit_2020_intensity_HCD after calibration is 0
2025-02-04 13:59:21 [INFO] - Median similarity for Prosit_2020_intensity_HCD is 0.0000
2025-02-04 13:59:21 [INFO] - Spectra model chosen is AlphaPept_ms2_generic
2025-02-04 13:59:21 [INFO] - Creating input file for createFull
2025-02-04 13:59:21 [INFO] - 46238 PSMs for prediction
2025-02-04 13:59:21 [INFO] - createFull input file generation took 160 milliseconds
2025-02-04 13:59:21 [INFO] - Input file at E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\spectraRT_full.tsv
2025-02-04 13:59:21 [INFO] - Generating input file for DIA-NN
2025-02-04 13:59:21 [INFO] - Creating input file for Diann
2025-02-04 13:59:21 [INFO] - 44271 PSMs for prediction
2025-02-04 13:59:21 [INFO] - Writing DIA-NN input file
2025-02-04 13:59:21 [INFO] - Diann input file generation took 120 milliseconds
2025-02-04 13:59:21 [INFO] - Input file at E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\spectraRT.tsv
2025-02-04 13:59:21 [INFO] - Creating input file for AlphaPept_ms2_generic
2025-02-04 13:59:22 [INFO] - 44271 PSMs for prediction
2025-02-04 13:59:22 [INFO] - AlphaPept_ms2_generic input file generation took 245 milliseconds
2025-02-04 13:59:22 [INFO] - Input files in E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\jsonFiles
2025-02-04 13:59:22 [INFO] - Calling AlphaPept_ms2_generic model
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-02-04 13:59:27 [INFO] - cURL and parse time in milliseconds: 5500
2025-02-04 13:59:27 [INFO] - Generating DIA-NN predictions
2025-02-04 13:59:27 [INFO] - C:\FragPipe\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\spectraRT.tsv --predict --threads 30 --strip-unknown-mods --predict-n-frag 100
2025-02-04 13:59:27 [INFO] - DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks)
2025-02-04 13:59:27 [INFO] - Compiled on Sep 15 2022 18:28:57
2025-02-04 13:59:27 [INFO] - Current date and time: Tue Feb  4 13:59:27 2025
2025-02-04 13:59:27 [INFO] - CPU: GenuineIntel 13th Gen Intel(R) Core(TM) i9-13900K
2025-02-04 13:59:27 [INFO] - SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 
2025-02-04 13:59:27 [INFO] - Logical CPU cores: 32
2025-02-04 13:59:27 [INFO] - Predicted spectra will be saved in a binary format
2025-02-04 13:59:27 [INFO] - Thread number set to 30
2025-02-04 13:59:27 [INFO] - DIA-NN will use deep learning to predict spectra/RTs/IMs even for peptides carrying modifications which are not recognised by the deep learning predictor. In this scenario, if also generating a spectral library from the DIA data or using the MBR mode, it might or might not be better (depends on the data) to also use the --out-measured-rt option - it's recommended to test it with and without this option
2025-02-04 13:59:27 [INFO] - Deep learning predictor will predict 100 fragments
2025-02-04 13:59:27 [INFO] - 
2025-02-04 13:59:27 [INFO] - 0 files will be processed
2025-02-04 13:59:27 [INFO] - [0:00] Loading spectral library E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\spectraRT.tsv
2025-02-04 13:59:27 [INFO] - [0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
2025-02-04 13:59:28 [INFO] - [0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 44271 precursors in 39200 elution groups.
2025-02-04 13:59:28 [INFO] - [0:00] Encoding peptides for spectra and RTs prediction
2025-02-04 13:59:28 [INFO] - [0:00] Predicting spectra and IMs
2025-02-04 13:59:33 [INFO] - [0:05] Predicting RTs
2025-02-04 13:59:35 [INFO] - [0:07] Decoding predicted spectra and IMs
2025-02-04 13:59:35 [INFO] - [0:07] Decoding RTs
2025-02-04 13:59:35 [INFO] - [0:07] Saving the list of predictions to E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\spectraRT.predicted.bin
2025-02-04 13:59:35 [INFO] - Finished
2025-02-04 13:59:36 [INFO] - Done generating DIA-NN predictions
2025-02-04 13:59:36 [INFO] - Model running took 8180 milliseconds
2025-02-04 13:59:36 [INFO] - Generating edited pin with following features: [predRTrealUnits, unweightedSpectralEntropy, deltaRTLOESS]
2025-02-04 13:59:36 [INFO] - Loading predicted RT: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\spectraRT.predicted.bin
2025-02-04 13:59:37 [INFO] - Loading predicted spectra: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\spectraRT_koina.mgf
2025-02-04 13:59:37 [INFO] - Merging libraries
2025-02-04 13:59:37 [INFO] - Processing pin E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.pin
2025-02-04 13:59:37 [INFO] - E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.pin has 33055 PSMs
2025-02-04 13:59:37 [INFO] - Processing E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-02-04 13:59:38 [INFO] - RT regression using 5000 PSMs
Iteration 1...2...3...4...5...
2025-02-04 13:59:41 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.082
2025-02-04 13:59:42 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-02-04 13:59:42 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-02-04 13:59:42 [INFO] - Edited pin file at E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_edited.pin
2025-02-04 13:59:43 [INFO] - Processing pin E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.pin
2025-02-04 13:59:43 [INFO] - E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.pin has 31619 PSMs
2025-02-04 13:59:43 [INFO] - Processing E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.mzML
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-02-04 13:59:44 [INFO] - RT regression using 4636 PSMs
Iteration 1...2...3...4...5...
2025-02-04 13:59:46 [INFO] - Best average bandwidth for mass  from grid search of 0.01,0.05,0.1,0.2 after 5 iterations is 0.08
2025-02-04 13:59:47 [INFO] - Calculating features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-02-04 13:59:47 [INFO] - Writing features
...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
2025-02-04 13:59:47 [INFO] - Edited pin file at E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_edited.pin
2025-02-04 13:59:47 [INFO] - Feature calculation, edited pin writing, and QC plot generation done in 11270 ms
Process 'MSBooster' finished, exit code: 0
Percolator [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_percolator_target_psms.tsv --decoy-results-psms PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_edited.pin
Percolator version 3.06.5, Build Date Feb  8 2024 10:07:48
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
C:\FragPipe\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_percolator_target_psms.tsv --decoy-results-psms PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_edited.pin
Started Tue Feb  4 13:59:48 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_edited.pin
Features:
rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 304.20715S 304.20715n^ pred_RT_real_units unweighted_spectral_entropy delta_RT_loess 
Found 33055 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 24582 positives and 8473 negatives, size ratio=2.90122 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 9503 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 8 as initial direction. Could separate 9375 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 8 as initial direction. Could separate 9329 training set positives with q<0.01 in that direction.
Found 14139 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.3230 cpu seconds or 0 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 15599 PSMs with q<0.01
Iteration 2:	Estimated 15746 PSMs with q<0.01
Iteration 3:	Estimated 15752 PSMs with q<0.01
Iteration 4:	Estimated 15756 PSMs with q<0.01
Iteration 5:	Estimated 15754 PSMs with q<0.01
Iteration 6:	Estimated 15756 PSMs with q<0.01
Iteration 7:	Estimated 15748 PSMs with q<0.01
Iteration 8:	Estimated 15748 PSMs with q<0.01
Iteration 9:	Estimated 15757 PSMs with q<0.01
Iteration 10:	Estimated 15755 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0000	 0.0000	 0.0000	rank
-0.9059	-0.9269	-1.0723	abs_ppm
-0.1107	-0.0789	-0.0022	isotope_error_negative
 0.2456	 0.2486	 0.2028	isotope_error_0
 0.0646	 0.0814	 0.0752	isotope_error_1
-0.1322	-0.0999	-0.0803	isotope_error_2
-0.2340	-0.3323	-0.3560	isotope_error_3_more
-1.3813	-0.7901	-1.1774	log10_evalue
 0.9132	 1.4772	 1.7052	hyperscore
 0.9049	 0.8555	 0.7457	delta_hyperscore
 1.1380	 1.1146	 0.9487	matched_ion_num
-0.7355	-0.8959	-0.9415	complementary_ions
 0.1932	 0.1083	 0.2448	ion_series
 0.0178	 0.0042	 0.0147	weighted_average_abs_fragment_ppm
-0.1352	-0.0603	-0.0545	length_7
-0.0442	-0.0192	-0.0494	length_8
 0.0838	 0.0817	 0.0733	length_9_30
 0.0403	-0.0460	-0.0138	length_31
 0.0000	 0.0000	 0.0000	ntt
 0.1507	 0.1464	 0.2128	nmc
 0.0000	 0.0000	 0.0000	charge_1
 0.0076	 0.0401	 0.0263	charge_2
 0.1029	 0.1025	 0.1087	charge_3
 0.0189	 0.0239	 0.1022	charge_4
-0.1045	-0.0713	-0.1401	charge_5
-0.0723	-0.0255	-0.1551	charge_6
-0.1042	-0.3710	-0.2255	charge_7_or_more
 0.0000	 0.0000	 0.0000	group_1
 0.0000	 0.0000	 0.0000	group_2
 0.0000	 0.0000	 0.0000	group_3
 0.0000	 0.0000	 0.0000	group_other
 0.0870	 0.0299	-0.0183	15.9949M
-0.0956	-0.1353	-0.1207	304.20715S
 0.1917	 0.2110	 0.1438	304.20715n^
-0.1489	-0.0857	-0.0909	pred_RT_real_units
 0.5781	 0.5164	 0.4998	unweighted_spectral_entropy
-0.7446	-0.9540	-0.9594	delta_RT_loess
 0.6928	 0.7777	 0.9231	m0
Found 15709 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 24582 target PSMs and 8473 decoy PSMs.
Calculating q values.
Final list yields 15715 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 3.5360 cpu seconds or 4 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_percolator_target_psms.tsv --decoy-results-psms PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_edited.pin
Percolator version 3.06.5, Build Date Feb  8 2024 10:07:48
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
C:\FragPipe\fragpipe\tools\percolator_3_6_5\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_percolator_target_psms.tsv --decoy-results-psms PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_edited.pin
Started Tue Feb  4 13:59:52 2025
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_edited.pin
Features:
rank abs_ppm isotope_error_negative isotope_error_0 isotope_error_1 isotope_error_2 isotope_error_3_more log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 15.9949M 304.20715S 304.20715n^ pred_RT_real_units unweighted_spectral_entropy delta_RT_loess 
Found 31619 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 21976 positives and 9643 negatives, size ratio=2.27896 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1:	Selected feature 8 as initial direction. Could separate 6814 training set positives with q<0.01 in that direction.
Split 2:	Selected feature 9 as initial direction. Could separate 6680 training set positives with q<0.01 in that direction.
Split 3:	Selected feature 9 as initial direction. Could separate 6823 training set positives with q<0.01 in that direction.
Found 10076 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.2830 cpu seconds or 0 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 11536 PSMs with q<0.01
Iteration 2:	Estimated 11780 PSMs with q<0.01
Iteration 3:	Estimated 11833 PSMs with q<0.01
Iteration 4:	Estimated 11836 PSMs with q<0.01
Iteration 5:	Estimated 11826 PSMs with q<0.01
Iteration 6:	Estimated 11820 PSMs with q<0.01
Iteration 7:	Estimated 11816 PSMs with q<0.01
Iteration 8:	Estimated 11825 PSMs with q<0.01
Iteration 9:	Estimated 11820 PSMs with q<0.01
Iteration 10:	Estimated 11828 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
 0.0000	 0.0000	 0.0000	rank
-0.8236	-0.9189	-1.1813	abs_ppm
 0.0113	-0.0332	 0.0182	isotope_error_negative
 0.2275	 0.2037	 0.2197	isotope_error_0
 0.0487	 0.0733	 0.1269	isotope_error_1
-0.1544	-0.0892	-0.1507	isotope_error_2
-0.2737	-0.2830	-0.3680	isotope_error_3_more
-0.5989	-0.4701	-0.8564	log10_evalue
 0.7460	 1.2140	 1.7688	hyperscore
 0.7348	 0.7247	 0.8558	delta_hyperscore
 1.4936	 1.1786	 1.1385	matched_ion_num
-0.8038	-0.7198	-0.8509	complementary_ions
 0.1448	-0.0526	 0.1079	ion_series
 0.0830	 0.1303	 0.2179	weighted_average_abs_fragment_ppm
-0.1241	-0.0738	-0.1994	length_7
-0.0602	 0.0075	-0.0395	length_8
 0.0470	 0.0338	 0.0370	length_9_30
 0.1129	 0.0168	 0.1869	length_31
 0.0000	 0.0000	 0.0000	ntt
 0.0981	 0.1223	 0.0778	nmc
 0.0000	 0.0000	 0.0000	charge_1
 0.0439	-0.0571	-0.0515	charge_2
 0.0270	 0.0927	 0.0538	charge_3
 0.0750	 0.0725	 0.1005	charge_4
-0.1035	-0.0981	-0.1384	charge_5
-0.1706	-0.1010	-0.0087	charge_6
 0.0143	 0.0122	-0.0037	charge_7_or_more
 0.0000	 0.0000	 0.0000	group_1
 0.0000	 0.0000	 0.0000	group_2
 0.0000	 0.0000	 0.0000	group_3
 0.0000	 0.0000	 0.0000	group_other
-0.1150	-0.0761	-0.0669	15.9949M
-0.2666	-0.2110	-0.2143	304.20715S
 0.3320	 0.2336	 0.1871	304.20715n^
-0.0789	-0.0459	-0.1451	pred_RT_real_units
 0.6174	 0.5586	 0.6612	unweighted_spectral_entropy
-0.8904	-0.7101	-1.1065	delta_RT_loess
-0.2625	-0.3095	-0.2886	m0
Found 11712 test set PSMs with q<0.01.
Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 21976 target PSMs and 9643 decoy PSMs.
Calculating q values.
Final list yields 11721 target PSMs with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 3.1440 cpu seconds or 4 seconds wall clock time.
Process 'Percolator' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.pin PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1 PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_percolator_target_psms.tsv PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_percolator_decoy_psms.tsv interact-PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1 DDA 0.5 E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Convert to pepxml [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.pin PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2 PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_percolator_target_psms.tsv PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_percolator_decoy_psms.tsv interact-PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2 DDA 0.5 E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.mzML
Process 'Percolator: Convert to pepxml' finished, exit code: 0
Percolator: Delete temp
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_percolator_target_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
Percolator: Delete temp
C:\FragPipe\fragpipe\jre\bin\java.exe -cp C:\FragPipe\fragpipe\lib\fragpipe-22.0.jar com.github.chhh.utils.FileDelete E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2_percolator_decoy_psms.tsv
Process 'Percolator: Delete temp' finished, exit code: 0
ProteinProphet [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\filelist_proteinprophet.txt
time="13:59:58" level=info msg="Executing ProteinProphet  v5.1.1"
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64))
 (no FPKM) (no groups) (using degen pep info)
Reading in E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\interact-PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.pep.xml...
...read in 0 1+, 3220 2+, 6659 3+, 4141 4+, 1571 5+, 454 6+, 158 7+ spectra with min prob 0.5

Reading in E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\interact-PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.pep.xml...
...read in 0 1+, 2703 2+, 5237 3+, 3093 4+, 1043 5+, 320 6+, 127 7+ spectra with min prob 0.5

Initializing 15702 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database C:\FASTAs\2024-08-06-decoys-contam-20231120_Homo_Sapiens_Uniprot_canonical+isoforms.fasta.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........39000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........40000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........41000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........42000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........43000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........44000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........45000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........46000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........47000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........48000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........49000
.......WARNING: Found the following zero-mass residues in protein entry sp|P07203|GPX1_HUMAN : U
MCAARLAAAAAAAQSVYAFSARPLAGGEPVSLGSLRGKVLLIENVASLUGTTVRDYTQMNELQRRLGPRGLVVLGFPCNQFGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVNGAGAHPLFAFLREALPAPSDDATALMTDPKLITWSPVCRNDVAWNFEKFLVGPDGVPLRRYSRRFQTIDIEPDIEALLSQGPSCA
..:.........:.........:.........:.........:.........:.........:.........:.........:.........50000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........51000
.........:.........:.........:.........:.........:........WARNING: Found the following zero-mass residues in protein entry sp|P22352|GPX3_HUMAN : U
MARLLQASCLLSLLLAGFVSQSRGQEKSKMDCHGGISGTIYEYGALTIDGEEYIPFKQYAGKYVLFVNVASYUGLTGQYIELNALQEELAPFGLVILGFPCNQFGKQEPGENSEILPTLKYVRPGGGFVPNFQLFEKGDVNGEKEQKFYTFLKNSCPPTSELLGTSDRLFWEPMKVHDIRWNFEKFLVGPDGIPIMRWHHRTTVSNVKMDILSYMRRQAALGVKRK
.:.........:.........:.........:.........52000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........53000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........54000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........55000
.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry sp|P59797|SELV_HUMAN : U
MNNQARTPAPSSARTSTSVRASTPTRTPTPLRTPTPVRTRTPIRTLTPVLTPSPAGTSPLVLTPAPAQIPTLVPTPALARIPRLVPPPAPAWIPTPVPTPVPVRNPTPVPTPARTLTPPVRVPAPAPAQLLAGIRAALPVLDSYLAPALPLDPPPEPAPELPLLPEEDPEPAPSLKLIPSVSSEAGPAPGPLPTRTPLAANSPGPTLDFTFRADPSAIGLADPPIPSPVPSPILGTIPSAISLQNCTETFPSSSENFALDKRVLIRVTYCGLUSYSLRYILLKKSLEQQFPNHLLFEEDRAAQATGEFEVFVNGRLVHSKKRGDGFVNESRLQKIVSVIDEEIKKR
........:.........:.........:.........:.........:.........56000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........57000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........58000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........59000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........60000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........61000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........62000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........63000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........64000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........65000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........66000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........67000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........68000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........69000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........70000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........71000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........72000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........73000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........74000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........75000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........76000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........77000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........78000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........79000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........80000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........81000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........82000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........83000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........84000
.........:.........:.........:.........:.........:.........:.........:.........:.........:  Total: 84902
Computing degenerate peptides for 4142 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 5066 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 5066 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 5066 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 5066 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Calculating sensitivity...and error tables...
INFO: mu=5.49206e-06, db_size=97669806
Computing MU for 5066 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
time="14:00:23" level=info msg=Done
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe database --annotate C:\FASTAs\2024-08-06-decoys-contam-20231120_Homo_Sapiens_Uniprot_canonical+isoforms.fasta.fas --prefix rev_
time="14:00:23" level=info msg="Executing Database  v5.1.1"
time="14:00:23" level=info msg="Annotating the database"
time="14:00:23" level=info msg=Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --picked --ion 0.05 --psm 0.05 --pep 0.05 --prot 0.05 --tag rev_ --pepxml E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger --protxml E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\combined.prot.xml --razor
time="14:00:23" level=info msg="Executing Filter  v5.1.1"
time="14:00:23" level=info msg="Processing peptide identification files"
time="14:00:23" level=info msg="Parsing E:\\FW_MS\\Charlotte_Philips\\PRC-6611\\MSFragger\\interact-PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.pep.xml"
time="14:00:23" level=info msg="Parsing E:\\FW_MS\\Charlotte_Philips\\PRC-6611\\MSFragger\\interact-PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.pep.xml"
time="14:00:24" level=info msg="1+ Charge profile" decoy=0 target=0
time="14:00:24" level=info msg="2+ Charge profile" decoy=178 target=5745
time="14:00:24" level=info msg="3+ Charge profile" decoy=220 target=11676
time="14:00:24" level=info msg="4+ Charge profile" decoy=113 target=7121
time="14:00:24" level=info msg="5+ Charge profile" decoy=25 target=2589
time="14:00:24" level=info msg="6+ Charge profile" decoy=14 target=760
time="14:00:24" level=info msg="Database search results" ions=15477 peptides=9807 psms=28726
time="14:00:24" level=info msg="Converged to 1.97 % FDR with 28172 PSMs" decoy=554 threshold=0.500203 total=28726
time="14:00:24" level=info msg="Converged to 5.00 % FDR with 9321 Peptides" decoy=466 threshold=0.508522 total=9787
time="14:00:24" level=info msg="Converged to 3.24 % FDR with 14991 Ions" decoy=486 threshold=0.500351 total=15477
time="14:00:24" level=info msg="Protein inference results" decoy=473 target=1836
time="14:00:24" level=info msg="Converged to 4.99 % FDR with 982 Proteins" decoy=49 threshold=0.9404 total=1031
time="14:00:24" level=info msg="Applying sequential FDR estimation" ions=14600 peptides=8947 psms=27752
time="14:00:24" level=info msg="Converged to 0.30 % FDR with 27670 PSMs" decoy=82 threshold=0.500203 total=27752
time="14:00:24" level=info msg="Converged to 0.61 % FDR with 8893 Peptides" decoy=54 threshold=0.500489 total=8947
time="14:00:24" level=info msg="Converged to 0.41 % FDR with 14540 Ions" decoy=60 threshold=0.500471 total=14600
time="14:00:24" level=info msg="Post processing identifications"
time="14:00:24" level=info msg="Assigning protein identifications to layers"
time="14:00:33" level=info msg="Processing protein inference"
time="14:00:34" level=info msg="Synchronizing PSMs and proteins"
time="14:00:34" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=14539 peptides=8892 proteins=981 psms=27668
time="14:00:34" level=info msg=Saving
time="14:00:34" level=info msg=Done
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report
time="14:00:34" level=info msg="Executing Report  v5.1.1"
time="14:00:34" level=info msg="Creating reports"
time="14:00:34" level=info msg=Done
Process 'PhilosopherReport' finished, exit code: 0
WorkspaceClean [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck
time="14:00:34" level=info msg="Executing Workspace  v5.1.1"
time="14:00:34" level=info msg="Removing workspace"
time="14:00:34" level=info msg=Done
Process 'WorkspaceClean' finished, exit code: 0
IonQuant [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\jre\bin\java.exe -Xmx108G -Dlibs.bruker.dir=C:\FragPipe\fragpipe\tools\MSFragger-4.1\ext\bruker -Dlibs.thermo.dir=C:\FragPipe\fragpipe\tools\MSFragger-4.1\ext\thermo -cp C:\FragPipe\fragpipe\tools\jfreechart-1.5.3.jar;C:\FragPipe\fragpipe\tools\batmass-io-1.33.4.jar;C:\FragPipe\fragpipe\tools\IonQuant-1.10.27.jar ionquant.IonQuant --threads 30 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 0 --msstats 0 --minexps 1 --mbr 0 --maxlfq 0 --requantify 0 --mztol 10 --imtol 0.05 --rttol 1 --normalization 0 --minisotopes 1 --minscans 1 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0 --uniqueness 0 --filelist E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\filelist_ionquant.txt --modlist E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\modmasses_ionquant.txt
IonQuant version IonQuant-1.10.27
Batmass-IO version 1.33.4
timsdata library version timsdata-2-21-0-4
(c) University of Michigan
System OS: Windows 10, Architecture: AMD64
Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium
JVM started with 108 GB memory
2025-02-04 14:00:35 [INFO] - Collecting variable modifications from all psm.tsv files...
2025-02-04 14:00:35 [INFO] - Loading and indexing all psm.tsv files...
2025-02-04 14:00:35 [INFO] - Collecting all compensation voltages if applicable...
2025-02-04 14:00:36 [INFO] - PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1 does not have FAIMS. If there are any other runs having FAIMS, IonQuant will crash.
2025-02-04 14:00:36 [INFO] - There is no FAIMS in the dataset.
2025-02-04 14:00:37 [INFO] - Parameters:
2025-02-04 14:00:37 [INFO] - perform-ms1quant = 1
2025-02-04 14:00:37 [INFO] - perform-isoquant = 0
2025-02-04 14:00:37 [INFO] - isotol = 20.0
2025-02-04 14:00:37 [INFO] - isolevel = 2
2025-02-04 14:00:37 [INFO] - isotype = tmt10
2025-02-04 14:00:37 [INFO] - site-reports = 0
2025-02-04 14:00:37 [INFO] - msstats = 0
2025-02-04 14:00:37 [INFO] - threads = 30
2025-02-04 14:00:37 [INFO] - mztol = 10.0
2025-02-04 14:00:37 [INFO] - rttol = 1.0
2025-02-04 14:00:37 [INFO] - imtol = 0.05
2025-02-04 14:00:37 [INFO] - minisotopes = 1
2025-02-04 14:00:37 [INFO] - minscans = 1
2025-02-04 14:00:37 [INFO] - psm = E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\psm.tsv
2025-02-04 14:00:37 [INFO] - multidir = null
2025-02-04 14:00:37 [INFO] - excludemods = 
2025-02-04 14:00:37 [INFO] - minions = 1
2025-02-04 14:00:37 [INFO] - maxlfq = 0
2025-02-04 14:00:37 [INFO] - ibaq = 0
2025-02-04 14:00:37 [INFO] - normalization = 0
2025-02-04 14:00:37 [INFO] - minexps = 1
2025-02-04 14:00:37 [INFO] - minfreq = 0.0
2025-02-04 14:00:37 [INFO] - tp = 0
2025-02-04 14:00:37 [INFO] - mbr = 0
2025-02-04 14:00:37 [INFO] - mbrrttol = 1.0
2025-02-04 14:00:37 [INFO] - mbrimtol = 0.05
2025-02-04 14:00:37 [INFO] - mbrtoprun = 10
2025-02-04 14:00:37 [INFO] - mbrmincorr = 0.0
2025-02-04 14:00:37 [INFO] - ionmobility = 0
2025-02-04 14:00:37 [INFO] - ionfdr = 0.01
2025-02-04 14:00:37 [INFO] - peptidefdr = 1.0
2025-02-04 14:00:37 [INFO] - proteinfdr = 1.0
2025-02-04 14:00:37 [INFO] - light = 
2025-02-04 14:00:37 [INFO] - medium = 
2025-02-04 14:00:37 [INFO] - heavy = 
2025-02-04 14:00:37 [INFO] - requantify = 0
2025-02-04 14:00:37 [INFO] - writeindex = 0
2025-02-04 14:00:37 [INFO] - locprob = 0.0
2025-02-04 14:00:37 [INFO] - uniqueness = 0
2025-02-04 14:00:37 [INFO] - filelist = E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\filelist_ionquant.txt
2025-02-04 14:00:37 [INFO] - specdir = E:\FW_MS\Charlotte_Philips\PRC-6611\Raw
2025-02-04 14:00:37 [INFO] - modlist = E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\modmasses_ionquant.txt
2025-02-04 14:00:37 [INFO] - mod masses:
2025-02-04 14:00:37 [INFO] - 15.9949
2025-02-04 14:00:37 [INFO] - 42.0106
2025-02-04 14:00:37 [INFO] - 57.02146
2025-02-04 14:00:37 [INFO] - 304.20715
2025-02-04 14:00:37 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-02-04 14:00:37 [INFO] - Loading E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.mzML...
2025-02-04 14:00:39 [INFO] - Building index...
2025-02-04 14:00:39 [INFO] - Quantifying...
2025-02-04 14:00:40 [INFO] - Loading E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.mzML...
2025-02-04 14:00:41 [INFO] - Building index...
2025-02-04 14:00:41 [INFO] - Quantifying...
2025-02-04 14:00:42 [INFO] - Updating Philosopher's tables...
2025-02-04 14:00:42 [INFO] - Done!
Process 'IonQuant' finished, exit code: 0
IonQuant [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\jre\bin\java.exe -Xmx108G -Dlibs.bruker.dir=C:\FragPipe\fragpipe\tools\MSFragger-4.1\ext\bruker -Dlibs.thermo.dir=C:\FragPipe\fragpipe\tools\MSFragger-4.1\ext\thermo -cp C:\FragPipe\fragpipe\tools\jfreechart-1.5.3.jar;C:\FragPipe\fragpipe\tools\batmass-io-1.33.4.jar;C:\FragPipe\fragpipe\tools\IonQuant-1.10.27.jar ionquant.IonQuant --threads 30 --perform-ms1quant 0 --perform-isoquant 1 --isotol 20.0 --isolevel 2 --isotype TMT-16 --ionmobility 0 --site-reports 0 --msstats 0 --annotation E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\psm.tsv=E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\20250204_TMT16_annotation.txt --minexps 1 --mbr 0 --maxlfq 0 --requantify 0 --mztol 10 --imtol 0.05 --rttol 1 --normalization 0 --minisotopes 1 --minscans 1 --writeindex 0 --tp 0 --minfreq 0 --minions 1 --locprob 0 --uniqueness 0 --filelist E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\filelist_ionquant.txt --modlist E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\modmasses_ionquant.txt
IonQuant version IonQuant-1.10.27
Batmass-IO version 1.33.4
timsdata library version timsdata-2-21-0-4
(c) University of Michigan
System OS: Windows 10, Architecture: AMD64
Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium
JVM started with 108 GB memory
2025-02-04 14:00:43 [INFO] - Collecting variable modifications from all psm.tsv files...
2025-02-04 14:00:43 [INFO] - Loading and indexing all psm.tsv files...
2025-02-04 14:00:43 [INFO] - Collecting all compensation voltages if applicable...
2025-02-04 14:00:44 [INFO] - PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1 does not have FAIMS. If there are any other runs having FAIMS, IonQuant will crash.
2025-02-04 14:00:44 [INFO] - There is no FAIMS in the dataset.
2025-02-04 14:00:45 [INFO] - Parameters:
2025-02-04 14:00:45 [INFO] - perform-ms1quant = 0
2025-02-04 14:00:45 [INFO] - perform-isoquant = 1
2025-02-04 14:00:45 [INFO] - isotol = 20.0
2025-02-04 14:00:45 [INFO] - isolevel = 2
2025-02-04 14:00:45 [INFO] - isotype = tmt-16
2025-02-04 14:00:45 [INFO] - annotation = MSFragger/psm.tsv=E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\20250204_TMT16_annotation.txt
2025-02-04 14:00:45 [INFO] - site-reports = 0
2025-02-04 14:00:45 [INFO] - msstats = 0
2025-02-04 14:00:45 [INFO] - threads = 30
2025-02-04 14:00:45 [INFO] - mztol = 10.0
2025-02-04 14:00:45 [INFO] - rttol = 1.0
2025-02-04 14:00:45 [INFO] - imtol = 0.05
2025-02-04 14:00:45 [INFO] - minisotopes = 1
2025-02-04 14:00:45 [INFO] - minscans = 1
2025-02-04 14:00:45 [INFO] - psm = E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\psm.tsv
2025-02-04 14:00:45 [INFO] - multidir = null
2025-02-04 14:00:45 [INFO] - excludemods = 
2025-02-04 14:00:45 [INFO] - minions = 1
2025-02-04 14:00:45 [INFO] - maxlfq = 0
2025-02-04 14:00:45 [INFO] - ibaq = 0
2025-02-04 14:00:45 [INFO] - normalization = 0
2025-02-04 14:00:45 [INFO] - minexps = 1
2025-02-04 14:00:45 [INFO] - minfreq = 0.0
2025-02-04 14:00:45 [INFO] - tp = 0
2025-02-04 14:00:45 [INFO] - mbr = 0
2025-02-04 14:00:45 [INFO] - mbrrttol = 1.0
2025-02-04 14:00:45 [INFO] - mbrimtol = 0.05
2025-02-04 14:00:45 [INFO] - mbrtoprun = 10
2025-02-04 14:00:45 [INFO] - mbrmincorr = 0.0
2025-02-04 14:00:45 [INFO] - ionmobility = 0
2025-02-04 14:00:45 [INFO] - ionfdr = 0.01
2025-02-04 14:00:45 [INFO] - peptidefdr = 1.0
2025-02-04 14:00:45 [INFO] - proteinfdr = 1.0
2025-02-04 14:00:45 [INFO] - light = 
2025-02-04 14:00:45 [INFO] - medium = 
2025-02-04 14:00:45 [INFO] - heavy = 
2025-02-04 14:00:45 [INFO] - requantify = 0
2025-02-04 14:00:45 [INFO] - writeindex = 0
2025-02-04 14:00:45 [INFO] - locprob = 0.0
2025-02-04 14:00:45 [INFO] - uniqueness = 0
2025-02-04 14:00:45 [INFO] - filelist = E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\filelist_ionquant.txt
2025-02-04 14:00:45 [INFO] - specdir = E:\FW_MS\Charlotte_Philips\PRC-6611\Raw
2025-02-04 14:00:45 [INFO] - modlist = E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\modmasses_ionquant.txt
2025-02-04 14:00:45 [INFO] - mod masses:
2025-02-04 14:00:45 [INFO] - 15.9949
2025-02-04 14:00:45 [INFO] - 42.0106
2025-02-04 14:00:45 [INFO] - 57.02146
2025-02-04 14:00:45 [INFO] - 304.20715
2025-02-04 14:00:45 [INFO] - Use each MS2 scan's calculated MZ in peak tracing.
2025-02-04 14:00:45 [INFO] - Loading and quantifying E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.mzML...
2025-02-04 14:00:47 [INFO] - Loading and quantifying E:\FW_MS\Charlotte_Philips\PRC-6611\Raw\PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.mzML...
2025-02-04 14:00:48 [INFO] - Updating Philosopher's tables...
2025-02-04 14:00:48 [INFO] - Done!
Process 'IonQuant' finished, exit code: 0
TmtIntegrator [Work dir: E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger]
C:\FragPipe\fragpipe\jre\bin\java.exe -Xmx108G -cp C:\FragPipe\fragpipe\tools\tmt-integrator-5.0.9.jar tmtintegrator.TMTIntegrator E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\tmt-integrator-conf.yml E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\psm.tsv
TMT-Integrator v5.0.9
Load parameters and check PSMs--- 0.00220 min.
UpdateColumns--- 0.01562 min.
LoadPsms--- 0.00167 min.
Take log and normalize--- 0.00272 min.
PSM normalization--- 0.00000 min.
outlierRemoval--- 0.00283 min.
Collapse--- 0.00167 min.
protNorm--- 0.00000 min.
Report--- 0.00142 min.
Total run time--- 0.02812 min.
Finish!!!
Process 'TmtIntegrator' finished, exit code: 0

Please cite:
(Any searches) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Methods 14:513 (2017)
(Any searches) Fast deisotoping algorithm and its implementation in the MSFragger search engine. J. Proteome Res. 20:498 (2021)
(timsTOF ddaPASEF) Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics 19:1575 (2020)
(Open search) Identification of modified peptides using localization-aware open search. Nat Commun. 11:4065 (2020)
(Glyco search) Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 17:1125 (2020)
(Labile search) MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics. Mol Cell Proteomics 22:100538 (2023)
(MSBooster) MSBooster: improving peptide identification rates using deep learning-based features. Nat Commun. 14:4539 (2023)
(PSM validation with Percolator) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4:923 (2007)
(Protein inference with ProteinProphet)A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75:4646 (2003)
(FDR filtering and reporting) Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods 17:869 (2020)
(Isobaric-labeling quantification) Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors. Nat Commun. 11:1723 (2020)
(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)

=============================================================ALL JOBS DONE IN 4.6 MINUTES=============================================================
