msConvert

msConvert is a command-line tool designed for the conversion of mass spectrometry data files. It supports a wide range of proprietary and open-source data formats commonly generated by mass spectrometers, enabling users to transform them into standardized or more accessible formats. This utility is particularly useful for researchers who need to share data across different software platforms or archive it in a universally readable format.

The primary function of msConvert is to act as a data converter, facilitating interoperability within the mass spectrometry community. It can convert files such as mzXML, mzML, and others into different versions of these formats or into formats suitable for specific downstream analyses. The tool is part of the ProteoWizard software suite, a collection of open-source tools and libraries for mass spectrometry data processing.

Key features of msConvert include its ability to handle large datasets efficiently, its support for various mass spectrometry data types including centroided and profile data, and its extensibility through a plugin architecture. Users can specify conversion parameters, such as filtering, data format adjustments, and retention time alignment, to tailor the output to their specific needs. The command-line interface makes it suitable for scripting and batch processing, which is essential for high-throughput proteomics and metabolomics studies. Its open-source nature also allows for community contributions and adaptation for specialized applications.