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Vendor files

Chromascope opens mzML and mzML.gz directly. Files from instrument vendors are converted first, by a separate program, ProteoWizard (msconvert), which you install yourself.

Set it up

  1. Install ProteoWizard with the vendor readers you need. Most native readers work on Windows only. Which formats work depends on your ProteoWizard build and on the vendor libraries.
  2. Chromascope looks for msconvert in this order: the environment variable CHROMASCOPE_MSCONVERT, the path saved earlier, your PATH, and the standard Windows ProteoWizard folders.
  3. If it is not found, choose File, then Vendor import settings, then Locate msconvert… and select msconvert.exe (not msConvertGUI.exe). Detect msconvert again searches once more.

Open the data

  • Single files (Thermo .raw, SCIEX .wiff and .wiff2, Shimadzu .lcd): File then Open data…. Keep companion files next to them.
  • Folders (Agilent and Bruker .d, Waters .raw): File then Open dataset folder….

Conversion runs on your computer, never changes the original and never uploads anything. A spinner shows the progress, and Cancel stops an import. Every run of a multi-sample dataset is added to the file list. Converted files live in a temporary folder while the runs are open, so leave enough disk space; opening the data again converts again.