useDetect = false
numThreads = 16
DiaNN = C:\FragPipe\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe
renamePin = 1
useRT = true
useSpectra = true
fragger = C:\FragPipe\Data\FW\JN\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\FW\JN 
pinPepXMLDirectory = H095805_1p_Ionopticks7_PM7_PRC-6265_Weiland_1_20231204180816.pin H095807_1p_Ionopticks7_PM7_PRC-6265_Weiland_2_20231204221318.pin H095809_1p_Ionopticks7_PM7_PRC-6265_Weiland_3_20231206170431.pin
useMultipleCorrelatedFeatures = false