mzML Conversion

Convert vendor raw files (.wiff, .raw, .d) to open mzML with ProteoWizard MSConvert — the input INTEGRATOR expects

INTEGRATOR reads MS data in the open mzML format. MSConvert, part of the ProteoWizard suite, converts vendor raw files — SCIEX .wiff, Waters .raw folders, Thermo Fisher .raw files, Agilent .d folders — to mzML. Conversion runs on Windows only.

  1. Install or upgrade to a recent version of ProteoWizard on a Windows computer. A recent version ensures support for current vendor formats.

  2. Launch MSConvertGUI from the Start menu, or by right-clicking the raw files and selecting MSConvertGUI.

  3. Click Browse to select the raw files to convert. For SCIEX data, keep the .wiff and .wiff.scan files together in the same folder.

  4. Set the options: Output format → mzML, Binary encoding precision → 32-bit, and enable Write index. To speed up large batches, raise Files to convert in parallel to the number of available CPU cores.

  5. Click Start, then copy the resulting mzML files into the mzML subfolder of your MRMhub project.

Screenshot of the MSConvertGUI window configured to output mzML. In the Options panel, Output format is set to mzML with 32-bit binary encoding, and Write index and Use zlib compression are enabled; the Start button at the bottom right runs the conversion.

See also