hello everyone, i'm starting to use TPP and would like to thanks the authors for this great program! i yet have some questions about the meanings of several probabilities in the pep.xml and prot.xml files.
first there's this 'peptideprophet_result probability' in the in the pep.xml file, in lines that look like this: <peptideprophet_result probability="0.6908" all_ntt_prob="(0.0000,0.6967,0.6908)">. at first i thought it was the same as the 'initial probability' in the corresponding prot.xml (e.g. <peptide peptide_sequence="HGVQELEIELQSQLSK" initial_probability="0.9990" nsp_adjusted_probability="0.9999" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="8.20" n_sibling_peptides_bin="6" n_instances="23" exp_tot_instances="22.05" is_contributing_evidence="Y">), and that the interprophet_result probability in lines like <interprophet_result probability="0.518555" all_ntt_prob="(0,0.525484,0.518555)"> are the same as the nsp_adjusted_probability in the prot.xml. however i checked the values of several peptides and found that they don't always match. the peptide values are often smaller than the ones in the prot.xml. i'm not sure if this has been discussed before. appologies if i've brought up a toooold question, and please direct me to the relevent discussions or documentations. thanks for your help! Amy -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
