I am trying to search mzML files with Thermo Proteome Discoverer 1.3 and I got the following error in the Spectrum Selector node: "Error: The number of spectrum data doesn't fit the expected value!" My mzML files were created with a very recent version of ProteoWizard and they worked fine in Mascot, which seems to be very picky about the schema. I tried mzML files from a variety of different raw data types and they all give the same problem. I even tried with a sample mzML data file provided by HUPO-PSI (http://dev.thep.lu.se/fp6-prodac/browser/trunk/mzML/dta_example.mzML?format=raw) and it had the same issue so it seems likely that this is a Proteome Discoverer bug. Has anybody else seen this and/or found a workaround?
Oh, the joys of proprietary proteomics software.
I doubt that it's a bug; sounds more like some software/format version incompatibility.
You could try asking a specialist mailing list such as spctools. But since you're paying for the software, I'd get your moneys worth and just contact Thermo technical support.