Why Am I Getting An Error When Searching Mzml Data With Thermo Proteome Discoverer 1.3?

Question

[Craig]

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?

Answer 1

[Neilfws]

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.

Answer 2

[User 3178]

Proteome Discoverer 1.2 cannot process mzXML files although it was intended to. Check the Release Notes of PD 1.3 and if it is not lisetd as a fixed issue then it is not possible with 1.3

[Craig]

Do you happen to have a link to the Proteome Discoverer 1.3 Release Notes? I can't find them online. It is certainly interesting to hear that mzXML didn't work in 1.2 though.