Hi all, In the ProteinProphet ProtXML viewer, one can see for each identified protein the number of unique peptides. See example here: http://161.116.29.106/tpp-bin/protxml_help.png
In this example, there are 7 unique peptides. But actually one can see these peptides are variations of precursor charge states and post- translational modifications of only 3 peptide sequences. I therefore understand that in this context, "unique peptides" should be understoof as "peptides with a different precursor ion". However the MCP guidelines recommend that "multiple matches to peptides with the same primary sequence should be counted as a single distinct peptide, including multiple matches that represent different precursor charge states or modification states". My question is therefore: is there a way to automatically extract from the TPP results the number of unique peptides per proteins, as defined by the MCP guidelines? Thanks in advance for your comments or tips. Nicolas -- 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.
