useDetect = false
numThreads = 32
DiaNN = C:\DIA-NN\2.2.0\diann.exe
renamePin = 1
useRT = true
useSpectra = true
fragger = Z:\FragPipe\251030_Asto232_234_ML_2ME_2MEIAA_3vs3\fragger.params
deletePreds = false
rtModel=DIA-NN
spectraModel=DIA-NN
findBestRtModel = false
findBestSpectraModel = false
KoinaURL = 
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 = Z:\Exploris240_Data\2025\m04\Asto232to234_ForFragpipe 
pinPepXMLDirectory = 2_ME\Asto233_m009_s009_tML_2ME_300mM_2uL_T30.pin IAA\Asto232_m002_s002_tML_IAA_2uL_T30.pin IAA\Asto224_m002_s002_ML_IAA_2uL_T30.pin 2_ME\Asto232_m009_s009_tML_2ME_300mM_2uL_T30.pin 2_ME\Asto224_m009_s009_ML_2ME_300mM_2uL_T30.pin IAA\Asto233_m002_s002_tML_IAA_2uL_T30.pin
useMultipleCorrelatedFeatures = false
