Supported file formats

We currently support the mzXML and Finnigan RAW file formats.

  • mzXML — tested output from ProteoWizard’s MSConvert tool and native mzXML files generated from Agilent.
  • RAW — These files are converted to mzXML using ProteoWizard’s MSConvert tool.

These file formats are currently being tested and should be deployed in the next week or so.

  • Bruker — The mzXML files directly generated are “fixed” to remove nesting and replace with proper references to “parent” scans.  The Bruker “.d” folders are properly converted to mzXML on our servers, but since we do not allow folders to be uploaded, you should compress them into “.zip”, “.rar”, or “.7z” files and upload the resulting archive file.  The file is automatically decompressed and converted once the analysis is submitted.

Generally, archive files (.ZIP, .RAR, or .7Z) can also be uploaded and contain one or multiple data files to be analyzed.  The files (or folders in the “.d” format for Bruker) should be at the top level in the archive, or they will be missed.

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