perl np_parse_ProteinProphet.pl yeast_MSMS_YPD_LCQDecaPlus_5inj-prot.xml 0.05 yeast_LCQ_5inj_YPD perl np_parse_ProteinProphet.pl yeast_MSMS_YMD_LCQDecaPlus_6inj-prot.xml 0.05 yeast_LCQ_6inj_YMD perl np_APEX_from_Oi_and_protlist.pl yeast_LCQ_66attrib_ALLpredictions.oi yeast_LCQ_5inj_YPD_0.05.protlst 4000 perl np_APEX_from_Oi_and_protlist.pl yeast_LCQ_66attrib_ALLpredictions.oi yeast_LCQ_6inj_YMD_0.05.protlst 4000 perl np_two_files_Zscore.pl yeast_LCQ_6inj_YMD_0.05.protlst.apex yeast_LCQ_5inj_YPD_0.05.protlst.apex yeast_YMD_YPD.zscore ##### yeast_LCQ_5inj_YPD_0.05.protlst yeast_LCQ_5inj_YPD_0.05.protlst.apex YPD data yeast_LCQ_66attrib_ALLpredictions.oi Oi values from prior predictions yeast_LCQ_6inj_YMD_0.05.protlst yeast_LCQ_6inj_YMD_0.05.protlst.apex YMD data yeast_MSMS_YMD_LCQDecaPlus_6inj-prot.xml yeast_MSMS_YPD_LCQDecaPlus_6inj-prot.xml original MS/MS files (ProteinProphet output) yeast_YMD_YPD.zscore final Z-score assessment #####