/usr/local/bin/easypqp convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml '['"'"'/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank1.pep.xml'"'"', '"'"'/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank2.pep.xml'"'"', '"'"'/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank3.pep.xml'"'"', '"'"'/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank4.pep.xml'"'"', '"'"'/home/projects/proteomics/workingdir01/interact-20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_rank5.pep.xml'"'"']' --spectra /home/projects/proteomics/sample1/20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01_uncalibrated.mzML --exclude-range -1.5,3.5 --psms 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.psmpkl --peaks 20240911_AST0_NEO4_IAH_collab_SAG_U2OS_Frac_Control_Sol_01.peakpkl
/usr/local/bin/easypqp library --psmtsv /home/projects/proteomics/workingdir01/psm.tsv --peptidetsv /home/projects/proteomics/workingdir01/peptide.tsv --out easypqp_lib_openswath.tsv --rt_lowess_fraction 0.0 /home/projects/proteomics/workingdir01/filelist_easypqp_library.txt