so my question is, what do the 'peptideprophet probability' and 'interprophet probability' in pep.xml, and 'initial probability' and 'nsp_adjusted probability' in prot.xml stand for? Thanks a lot!
Amy On Apr 19, 6:08 pm, grassworm <[email protected]> wrote: > 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 > athttp://groups.google.com/group/spctools-discuss?hl=en. -- 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.
