MSFTBX

The acronym stands for Mass Spectrometry File Toolbox. This is a library for access to some common mass-spectrometry/proteomics data formats from Java:

• mzML
• mzXML
• pepXML/pep.xml
• protXML/prot.xml
• mzIdentML
• cef (Agilent)
• GPMdb XML

This library is what drives BatMass.

Maven dependency

<dependency>
    <groupId>com.github.chhh</groupId>
    <artifactId>msftbx</artifactId>
    <version>1.3.1</version>
</dependency>

How to use

To get started quickly, follow the tutorial: http://www.batmass.org/tutorial/data-access-layer/#parsing-lc-ms-data-mzml-mzxml-files

Features

• Parsers for mzML/mzXML with unified API
  • Very fast, multi-threaded
  • Rich standardized API for contents of those files (scan and run meta-info, not just spectra).
  • msNumpress compression support for mzML
  • Automated LC/MS run structure determination:
    • Data structures for parent-child relationship between spectra
    • Indexes for scans based on scan numbers, retention times both globally and for each MS level separately
    • Convenient methods to get next-previous scans at the same MS level
  • Tolerant to malformed data
    • Can handle MS2 scan tags nested inside MS1 scans
    • Tolerant to missing or broken file index
    • Reindexing on the fly
  • Memory management
    • Automated spectra parsing on demand
      • You can parse just the structure of an LC/MS run without the spectral data, the memory footprint in this case will be very small. Only when spectra are requested will they be parsed.
      • Soft referencing of spectral data for GC
    • Tracking of which loaded data is not being used by any components with automated unloading.
• Upcoming support for Thermo RAW files on Windows
• pepXML parser and writer
• protXML parser and writer
• mzIdentML parser
• GPMdb XML files parser
• Agilent .cef files parser

Binary distribution

Get jars from Maven Central.
Some older pre-compiled binaries can be found here.

Building with Maven (preferred)

cd ./MSFileToolbox && mvn clean package
Will produce the jar files with just the library msftbx-X.X.X.jar as well as one large jar msftbx-X.X.X-jar-with-dependencies.jar. The latter can be used as is, it includes all the needed dependencies.

Building a NetBeans Platform module

NetBeans Module: Open the root directory in NetBeans as a project. You will see MSFTBX module suite which consists of 3 modules: MSFileToolbox Module - (this is the main thing), MSFileToolbox Libx - these are the depencies, and Auto Update (MSFTBX) - this is the update center for NetBeans Platform projects (you definitely don't need this) .

Dependencies

• SLF4J
• Google Guava
• Apache Commons Pool 2
• OboParser from Biojava's submodule Ontology
• Javolution Core (slightly modified, sources are here, this modified dependency is published on Maven Central)