useDetect = false
numThreads = 30
DiaNN = C:\FragPipe\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe
renamePin = 1
useRT = true
useSpectra = true
fragger = E:\FW_MS\Charlotte_Philips\PRC-6611\MSFragger\fragger.params
deletePreds = false
rtModel=DIA-NN
spectraModel=AlphaPept_ms2_generic
findBestRtModel = true
findBestSpectraModel = true
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 = E:\FW_MS\Charlotte_Philips\PRC-6611\Raw 
pinPepXMLDirectory = PRC-6611DDA_UPRC_9606_F014137_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_2.pin PRC-6611DDA_UPRC_9606_F014135_1p_IonOpt_trapPM1_Neo_EASYJB_Weiland_OT-OT_3h_DDA_1.pin
useMultipleCorrelatedFeatures = false
