Data access library: MSFTBX - Mass-Spec File Toolbox

The data access library is at the core of BatMass, but is a separate standalone project. It can be used in regular Java programs (read as a jar library) and NetBeans platform applications via the included NetBeans Module wrapper.

Features

• Single API to mzML and mzXML files
• mzML and mzXML parsing
  • Very fast multi-threaded parser
  • Can separately parse LC/MS run information, the index and data
  • Separation of parsing of scan meta-information and spectral data
  • Automatic indexing of the data
    • maps from scan numbers to scans
    • maps from retention time to scans
    • same maps separately at each MS level
    • automatic DIA (data Independent Acquisition) detection and automated grouping of DIA MS2 scans according to the corresponding isolation windows
  • Memory management
    • can parse the whole structure of the run (all scans with all meta-info) and dynamically parse spectral data from the disk only when it's accessed
    • an object can be used as the ‘owner’ of loaded data, if the ‘owner’ is garbage collected, and no other ‘owners’ claimed the scans, the corresponding resources can be automatically released
  • Tolerance to broken index
    • automatically detects errors in the index, such as all scan offsets are the same (which happens with some versions of ProteoWizard's msconvert when converting large files)
    • if the index is not present, will reindex the file
  • Tolerance to MS2 scan tags being enclosed in the corresponding MS1 scan tag (old data converted with ReAdW)
• PepXML parsing/writing
• ProtXML parsing/writing
• MzIdentML parsing/writing

Usage

Take a look at this tutorial for a short introduction and check the sources at github.