LipidXplorer msconvert conversion
MSConvert
Only a few mass spectrometers directly produce mzXML/mzML files but there are several tools available that generate mzXML/mzML files from native acquired files.
MSConvert is the currently most featured converter (MSConvert) and further it is under ongoing maintenance. It supports various vendor file formats:
- Agilent Mass Hunter Data Access Component Library
- Waters Raw Data Access Component Library
- Bruker CompassXtract
- Thermo-Scientific MSFileReader Library
- Waters Raw Data Access Component Library
- AB Sciex WIFF Reader Library
Download and installation
Download MSConvert from MSConvert. It is part of Protewizard, a tool for proteomics. Just click on the button "I agree to the license terms, download Proteowizard" and install the downloaded file.
For LipidXplorer set the options in MSConvert like this:
For convenience store your settings by clicking "Use these settings next time I start MSConvert". Then upload your file(s) using "Browse" and "Add", respectively.
Use "Start" to do the conversion.
The format mzML is preferred from LipidXplorer. This will be the main data format to be supported by LipidXplorer in the future. However, you can use *.mzXML as well with these settings.
