useDetect = false
numThreads = 23
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 = F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\fragger.params
deletePreds = false
rtModel=DIA-NN
spectraModel=DIA-NN
imModel=
findBestRtModel = false
findBestSpectraModel = false
findBestImModel = false
KoinaURL = 
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 = F:\Research\PXD069532-Broccoli-Agilent-QqTOF\mzML-ProteoWizard 
pinPepXMLDirectory = NPS_5\202505617.pin OCBS_12\202505624.pin NPS_4\202505616.pin OCBS_11\202505623.pin OCBS_10\202505622.pin NPS_6\202505618.pin
spectraPredFilePDV=F:\Research\PXD069532-Broccoli-Agilent-QqTOF\20260720-FragPipe-LFQ-MBR3\MSBooster\spectraRT.predicted.bin
