perl np_parse_ProteinProphet.pl yeast_MSMS_LCQDecaPlus_5inj-prot.xml 0.05 yeast_LCQ

perl np_arf_to_arff_TRAINING.pl yeast_PEPTIDE_PROPERTIES_Lengthonly.arf yeast_TRAINING_LCQ_0.05.protlst yeast_LCQ 1 25 0 0 N
perl np_arf_to_arff_TRAINING.pl yeast_PEPTIDE_PROPERTIES_Lengthonly.arf yeast_TRAINING_LCQ_0.05.protlst yeast_LCQ 1 50 0 0 N
perl np_arf_to_arff_TRAINING.pl yeast_PEPTIDE_PROPERTIES_Lengthonly.arf yeast_TRAINING_LCQ_0.05.protlst yeast_LCQ 1 75 0 0 N


#### 

Other_Training_Sets

	other .arff for different parameter settings (see above)

Results_Training

	saved resultbuffers from WEKA training runs

yeast_66attrib_LCQ_p1p50p0p0.model.gz

	final model

yeast_LCQ_66attrib_TRAINING_prprob1_prspec50_peprob0_pespec0_10xCV.result.gz

	resultbuffer for final model

yeast_LCQ_66attrib_TRAINING_prprob1_prspec50_peprob0_pespec0.arff.gz
yeast_LCQ_66attrib_TRAINING_prprob1_prspec50_peprob0_pespec0.log.gz
yeast_LCQ_66attrib_TRAINING_prprob1_prspec50_peprob0_pespec0.names.gz

	data for final model

yeast_MSMS_LCQDecaPlus_5inj-prot.xml.gz
yeast_TRAINING_LCQ_0.05.protlst.gz

	original MS/MS data for training	

yeast_PEPTIDE_PROPERTIES_66attrib.arf.gz

	all yeast proteins (and their peptides' attributes)