useDetect = false
numThreads = 9
DiaNN = C:\FragPipe\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe
renamePin = 1
useRT = true
useSpectra = true
fragger = C:\FragPipe\Data\AM\PRC-6481\Output\fragger.params
deletePreds = false
rtModel=DIA-NN
spectraModel=Prosit_2020_intensity_TMT
findBestRtModel = false
findBestSpectraModel = 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
ms2SearchModelsString = 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
mzmlDirectory = C:\FragPipe\Data\AM\PRC-6481 
pinPepXMLDirectory = H0648_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-1.pin H0654_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-4.pin H0652_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-3.pin H0658_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-6.pin H0656_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-5.pin H0664_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-9_less.pin H0662_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-8.pin H0660_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-7.pin H0650_2p_IonOpt11_PRC-6481_Weiland_TMT-DDA-2.pin
useMultipleCorrelatedFeatures = false