useDetect = false
numThreads = 31
DiaNN = C:\FragPipe\FragPipe-24.0\tools\diann\1.8.2_beta_8\windows\DiaNN.exe
renamePin = 1
useRT = true
useSpectra = true
useIM = false
fragger = E:\Students\KU_Leuven_PhD\Katharina_Seibel\Experiments\PRC-7194_Data_Analysis\Fragpipe_Output\fragger.params
deletePreds = false
rtModel=DIA-NN
spectraModel=DIA-NN
imModel=
findBestRtModel = false
findBestSpectraModel = false
findBestImModel = false
KoinaURL = https://koina.wilhelmlab.org:443/v2/models/
rtSearchModelsString = DIA-NN,Deeplc_hela_hf,AlphaPept_rt_generic,Prosit_2019_irt,Prosit_2020_irt_TMT,Prosit_2024_irt_cit
ms2SearchModelsString = DIA-NN,ms2pip_2021_hcd,ms2pip_timsTOF2024,ms2pip_ttof5600,ms2pip_immuno_hcd,ms2pip_CID_TMT,ms2pip_iTRAQphospho,AlphaPept_ms2_generic,Prosit_2019_intensity,Prosit_2023_intensity_timsTOF,Prosit_2020_intensity_CID,Prosit_2020_intensity_TMT,Prosit_2020_intensity_HCD,UniSpec,Prosit_2024_intensity_cit,Prosit_2025_intensity_MultiFrag
imSearchModelsString = DIA-NN,AlphaPept_ccs_generic,IM2Deep
FragmentationType = auto
unimodObo = C:\FragPipe\FragPipe-24.0\tools\unimod.obo
mzmlDirectory = E:\Backup_MS\PRC-7194\PRC-7194 
pinPepXMLDirectory = PRC-7194TMT_UPRC_559292A007490_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR26.pin PRC-7194TMT_UPRC_559292A007440_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR2.pin PRC-7194TMT_UPRC_559292A007478_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR20.pin PRC-7194TMT_UPRC_559292A008078_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR20.pin PRC-7194TMT_UPRC_559292A007460_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR12.pin PRC-7194TMT_UPRC_559292A008104_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR33.pin PRC-7194TMT_UPRC_559292A007510_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR36.pin PRC-7194TMT_UPRC_559292A008040_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR2.pin PRC-7194TMT_UPRC_559292A007494_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR28.pin PRC-7194TMT_UPRC_559292A008072_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR17.pin PRC-7194TMT_UPRC_559292A007492_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR27.pin PRC-7194TMT_UPRC_559292A008054_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR9.pin PRC-7194TMT_UPRC_559292A008110_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR36.pin PRC-7194TMT_UPRC_559292A007462_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR13.pin PRC-7194TMT_UPRC_559292A008084_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR23.pin PRC-7194TMT_UPRC_559292A008058_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR11.pin PRC-7194TMT_UPRC_559292A008102_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR32.pin PRC-7194TMT_UPRC_559292A007466_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR15.pin PRC-7194TMT_UPRC_559292A007474_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR18.pin PRC-7194TMT_UPRC_559292A007496_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR29.pin PRC-7194TMT_UPRC_559292A007476_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR19.pin PRC-7194TMT_UPRC_559292A008096_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR29.pin PRC-7194TMT_UPRC_559292A008074_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR18.pin PRC-7194TMT_UPRC_559292A007464_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR14.pin PRC-7194TMT_UPRC_559292A008038_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR1.pin PRC-7194TMT_UPRC_559292A007458_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR11.pin PRC-7194TMT_UPRC_559292A008042_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR3.pin PRC-7194TMT_UPRC_559292A007468_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR16.pin PRC-7194TMT_UPRC_559292A008052_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR8.pin PRC-7194TMT_UPRC_559292A007488_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR25.pin PRC-7194TMT_UPRC_559292A008114_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR38.pin PRC-7194TMT_UPRC_559292A008088_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR25.pin PRC-7194TMT_UPRC_559292A008108_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR35.pin PRC-7194TMT_UPRC_559292A008044_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR4.pin PRC-7194TMT_UPRC_559292A008060_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR12.pin PRC-7194TMT_UPRC_559292A008050_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR7.pin PRC-7194TMT_UPRC_559292A008066_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR15.pin PRC-7194TMT_UPRC_559292A008098_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR30.pin PRC-7194TMT_UPRC_559292A008068_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR16.pin PRC-7194TMT_UPRC_559292A007500_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR31.pin PRC-7194TMT_UPRC_559292A008082_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR22.pin PRC-7194TMT_UPRC_559292A007438_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR1.pin PRC-7194TMT_UPRC_559292A008106_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR34.pin PRC-7194TMT_UPRC_559292A007498_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR30.pin PRC-7194TMT_UPRC_559292A007448_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR6.pin PRC-7194TMT_UPRC_559292A007484_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR23.pin PRC-7194TMT_UPRC_559292A008100_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR31.pin PRC-7194TMT_UPRC_559292A007456_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR10.pin PRC-7194TMT_UPRC_559292A008046_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR5.pin PRC-7194TMT_UPRC_559292A008090_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR26.pin PRC-7194TMT_UPRC_559292A008094_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR28.pin PRC-7194TMT_UPRC_559292A007472_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR17.pin PRC-7194TMT_UPRC_559292A008062_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR13.pin PRC-7194TMT_UPRC_559292A007502_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR32.pin PRC-7194TMT_UPRC_559292A008048_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR6.pin PRC-7194TMT_UPRC_559292A007446_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR5.pin PRC-7194TMT_UPRC_559292A007454_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR9.pin PRC-7194TMT_UPRC_559292A007486_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR24.pin PRC-7194TMT_UPRC_559292A007444_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR4.pin PRC-7194TMT_UPRC_559292A008112_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR37.pin PRC-7194TMT_UPRC_559292A008064_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR14.pin PRC-7194TMT_UPRC_559292A008086_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR24.pin PRC-7194TMT_UPRC_559292A007508_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR35.pin PRC-7194TMT_UPRC_559292A007514_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR38.pin PRC-7194TMT_UPRC_559292A007504_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR33.pin PRC-7194TMT_UPRC_559292A007480_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR21.pin PRC-7194TMT_UPRC_559292A007452_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR8.pin PRC-7194TMT_UPRC_559292A008056_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR10.pin PRC-7194TMT_UPRC_559292A008080_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR21.pin PRC-7194TMT_UPRC_559292A007442_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR3.pin PRC-7194TMT_UPRC_559292A007512_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR37.pin PRC-7194TMT_UPRC_559292A007506_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR34.pin PRC-7194TMT_UPRC_559292A008076_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR19.pin PRC-7194TMT_UPRC_559292A007450_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR7.pin PRC-7194TMT_UPRC_559292A007482_1p_ih10cm_1-5um_PM5_NeoLumos_noFAIMS_30min_TMT_custom_spR22.pin PRC-7194TMT_UPRC_559292A008092_1p_ih10cm_1-5um_PM5_Neo_noFAIMS_30min_TMT_custom_800ng_spR27.pin
spectraPredFilePDV=E:\Students\KU_Leuven_PhD\Katharina_Seibel\Experiments\PRC-7194_Data_Analysis\Fragpipe_Output\MSBooster\spectraRT.predicted.bin