Hi, I am encountering some strange output from the peptide prophet: the column with the ions is always 0/xx (where xx is any number). Is that normal behaviour for peptideprophet analysis of ETD data?
here is my set-up: * TPP 4.4 on Mac OS 10.6.4 - convert raw files to mzXML with CompassXport - analyse the mzXML files with X!tandem using a parameter file with scoring, x ions: no scoring, y ions: no scoring, z ions: yes scoring, a ions: no scoring, b ions: no scoring, c ions: yes - run peptideprophet on the resulting pep.xml files enabling the gamma distribution and decoy's. Is there anything I need to add/delete in the parameter file before analysing them or has anyone seen the same behaviour for ETD? Thanks! bjorn -- 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.
