The Tandem2XML program will try to read each scan's retention time from the mzXML and add it to the resulting pep.xml. If not it can't find the mzXML file, it issues the warning and leaves out the retention time.
This warning does imply that the standard TPP convention of expected files and filenames in expected locations isn't being followed. Not a horrible thing in itself but there's a decent chance of experiencing some other problems downstream if this is the case. On Wed, May 5, 2010 at 3:28 PM, Jesse J <[email protected]> wrote: > Oh, whoops, silly me. Since it said that it couldn't open the file, I > assumed it never created the pepXML file. Thank you for those points > though. > > So then what is it upset about? Is it trying to open the mzXML file in > addition to the output xml file? > > -- > 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. > > -- 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.
