The BiblioSpec library builder builds spectral libraries from many peptide search formats. It has long supported pepXML from PeptideProphet. I am now looking at expanding this support to include pepXML from iProphet. One issue I have encountered, however, is that unlike the PeptideProphet pepXML it does not seem possible to know how many <msms_run_summary> elements the file contains without reading the entire file. In the PeptideProphet element:
<analysis_summary analysis="peptideprophet" ...> The number of <inputfile> elements usually corresponds to the number of <msms_run_summary> to follow, which is extremely useful in presenting progress information during pepXML parsing. Unfortunately, in the corresponding iProphet element: <analysis_summary analysis="interprophet" ...> The <inputfile> elements are for pepXML files, which themselves may have contained results for many <msms_run_summary> elements, and many <inputfile> elements. It sure would be nice to have some way of knowing early in the file parsing how many <msms_run_summary> elements there might be. Also, it seems like the current strategy of discarding all <inputfile> elements from included pepXML files and representing them as only a single <inputfile> element for the containing pepXML file loses useful information. Perhaps <inputfile> elements could be nested to preserve the original input files. Any other way to have the pepXML forecast the number of <msms_run_summary> elements would suit my current need as well. Thanks for considering. --Brendan -- 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.
