useDetect = false
numThreads = 31
DiaNN = /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/diann/1.8.2_beta_8/linux/diann-1.8.1.8
renamePin = 1
useRT = true
useSpectra = true
useIM = false
fragger = /home/projects/proteomics/workingdir01/fragger_dia.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,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
FragmentationType = auto
unimodObo = /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/tools/unimod.obo
mzmlDirectory = /home/projects/proteomics/sample1 
pinPepXMLDirectory = 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.pin
spectraPredFilePDV=/home/projects/proteomics/workingdir01/MSBooster/spectraRT.predicted.bin