v1.8.0

v1.8.0 introduces some incompatible changes.
PepXml, ProtXml and MzId (MzIdentMl) parsers/writers now use Double everywhere instead of Float even if the schema dictates for a float value. Text representations of digits in files often exceed storage capabilities of float.

v1.6.0-RC2

• Added @XmlRootElement annotation to MzIdentMlType JAXB class to enable proper marshalling.
• Changed how precursor ions are reported. PrecursorInfo now provides mzTarget as the actual targeted m/z, and also mzTargetMono, which is the assumed monoisotopic m/z of that ion.
• Fixed regression bug in mzXML header parsing. Original files without parent location were causing NPEs.
• PepXML parser updated to pepxml schema v120. Includes PTM Prophet and related changes.
• Multiple improvements to mzML parsing.
• Support for ReferenceableParamGroups in mzML.
• Significant non-indexed files parsing speed up.

Now built with maven and published to Central repository

Maven Central: http://search.maven.org/#artifactdetails%7Ccom.github.chhh%7Cmsftbx%7C1.2.1%7Cjar

v1.2.0

• Added fragmentation energy and reaction time.
• A single String for precursor fragmentation method name has been replaced by ActivationInfo getActivationInfo(), which has the method name, energy and time.
• More detailed information in LCMSRunInfo

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