Question: Why Am I Getting An Error When Searching Mzml Data With Thermo Proteome Discoverer 1.3?
gravatar for Craig
7.5 years ago by
Craig30 wrote:

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 ( 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?

proteomics • 2.1k views
ADD COMMENTlink written 7.5 years ago by Craig30
gravatar for Neilfws
7.5 years ago by
Sydney, Australia
Neilfws48k wrote:

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.

ADD COMMENTlink written 7.5 years ago by Neilfws48k
gravatar for User 3178
7.5 years ago by
User 317810
User 317810 wrote:

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

ADD COMMENTlink written 7.5 years ago by User 317810

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.

ADD REPLYlink written 7.5 years ago by Craig30
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