Java parsers for common mass-spectrometry and proteomics data formats

• mzML/mzXML
• pepXML
• protXML
• mzIdentML
• GPdb XML
• Agilent CEF

Thermo RAW on Windows in the next release.

Check out a small tutorial on how to use the library: http://www.batmass.org/tutorial/data-access-layer/

• msftbx-with-deps.jar - includes ass the dependencies in the jar file, can be used as is
• msftbx-bin.jar - this is the compiled library without the dependencies
• msftbx-deps.jar - these are only the dependencies, to be used with msftbx-bin.jar
• msftbx-src.jar - sources for easy integration with IDE's code-completion