So in these cases, all the proteins in the protein group share at least one peptide. The different sub groups occur because certain "clusters" of proteins share peptides that are specific to the cluster.
As an example, imagine a group that consists of 3 sibling groups: a,b, and c. All of the protein identifiers in the group correspond to Histones. Sibling group 'a' contains peptides that are unique to Histone2A. While sibling group 'b' contains Histone3 and sibling group 'c' has Histone4A. All 3 sibling groups share at least some peptides in common, but each sibling group also has some peptides, unique to itself. Because peptide probabilities in ProteinProphet are adjusted based upon the number of sibling peptides (nsp) and how the peptides are shared among various proteins (wt) the probability for a sibling group can be different from the probability of the group as a whole. I don't know how clear that is, but that's my attempt at explaining it. On Aug 12, 7:40 pm, LW <[email protected]> wrote: > Hi, > > I have a question on the prot.xml. It seems like each protein group is > a probability and each > subgroup (those with group_sibling_id="a", "b", etc) has a > probability. > > <protein_group group_number="1" probability="1.0000"> > <protein protein_name="DECOY_40330" n_indistinguishable_proteins="1" > probability="1.0000" percent_coverage="2.9" > unique_stripped_peptides="LMVSNQFK+NMMTIETNSSTSVVSPRASTAR" > group_sibling_id="a" total_number_peptides="8" > pct_spectrum_ids="0.019" confidence="0.004"> > > How is the probability for the protein_group determined? I came across > cases where all the > subgroup probabilities are 0 but the protein_group probability is > 1.0. > How do I explain this? > > Thanks, > LW -- 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.
