[proteowizard-developer] Scaffold .mzid files

[B. F. <frewen@u.washington.edu>]

Hello,

I am trying to build an application that parses mzIdentML files using a 
pwiz MzIdentMLFile object.  The mzIdentML files are produced by Scaffold. 
Both examples I have give me an error and I was wondering if anyone had 
worked with these files.  Perhaps there is a known issue?

I get the same error using the command line tool mzidtxt, as follows

$ ./mzidtxt orbi3protexport.mzid orbi3protexport.txt
[References::resolve()] Failed to resolve reference.
   object type: N4pwiz8mziddata11SpectraDataE
   reference id: Scaffold_Spectrum_DATA_o100720_3prot_02.RAW (F001608)
   referent list: 1
     Scaffold_Spectrum_DATA_o100720_3prot_01.RAW (F001607)

Suggestions?  I can provide the files on request.

Thanks,

Barbara Frewen