Converting vendor formats (.RAW, .hdf5, .d, .txt) to .mzML - MateuszFido/LCMSpector GitHub Wiki

🚫 The problem with proprietary formats (.RAW, .d, etc.)

LC-Inspector uses mzML files for mass spectrometry analysis.

mzML is an XML-based, vendor-agnostic file format that can be translated from any major manufacturer’s propriety mass spectrometry raw data file via tools such as MS Convert (ProteoWizard package).

Loading proprietary file formats (Thermo .RAW, Waters .RAW, Agilent .d, Bruker .d, Sciex .wiff, and so on) is only possible using the vendors' own licensed libraries, which depend on .NET and are only available on Windows. This makes creating cross-platform software for reading those files effectively impossible.

The most popular solution for open-source applications has been to use MSConvert, a part of the ProteoWizard package, which bundles readers from most manufacturers and is able to convert the file formats from proprietary to mzML, mzXML, txt, etc.

This short tutorial shows how to convert proprietary formats into mzML that can be then uploaded into LC-Inspector.

↔ Converting using MSConvert (ProteoWizard)

You can download ProteoWizard's executable (of which MSConvert is a part) here. There are binaries available for Windows and a Dockerized version for Linux.

On Windows you need the .NET Framework 4.7.2 (or newer), for newer Windows versions it should be already installed.

The usage is straightforward:

  1. Launch MSConvert

  1. Browse to the files that you want to convert, select them, click Add.

  2. Choose the Output directory (defaults to the same directory as input).

  3. Choose your Output format: mzML and in the Extension field type: .mzml

  • (optional) if you know the exact content of the files you're converting and want to include SIM (single ion monitoring, MS1) and/or SRM (single reaction monitoring, MS2) scans, select those options now, apply peak picking filters, sum scans, etc. -- none of this is necessary for LC-Inspector, though

  1. Click Start to start the conversion

  2. ✨ You can now use the converted mzML files as input to LC-Inspector and other open-source mass spectrometry tools!

In the future, support for other open file formats (.txt, .hdf5, mzXML, etc.) is also planned.

Also check out this tutorial from FragPipe for a DIA proteomics pipeline: https://fragpipe.nesvilab.org/docs/tutorial_convert.html